Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2023-11-05 11:51:40 and 2023-11-05 16:23:11; pypath version: 0.15.13 (from git, installed by poetry; 8bbc1e4 )
| Modules collected: | 182 |
|---|---|
| Modules failed to import: | 1 |
| Functions collected: | 620 |
| Functions run without error: | 248 |
| Functions returned empty value: | 22 |
| Functions skipped due to lack of arguments: | 176 |
| Functions run with error: | 196 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2023-11-05 11:51:41 | 2023-11-05 11:51:41 | 0.40 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2023-11-05 11:51:41 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2023-11-05 11:51:41 | 2023-11-05 11:51:42 | 0.56 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2023-11-05 11:51:41 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2023-11-05 11:51:42 | 2023-11-05 11:51:43 | 0.51 | list | [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) | 9,570 | {} | 2023-11-05 11:51:42 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2023-11-05 11:51:43 | 2023-11-05 11:51:44 | 1.03 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/adhesome.py", line 82, in adhesome_annotations
for _uniprot in mapping.map_name(uniprot, 'uniprot', 'uniprot'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:05:53 | |||
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2023-11-05 11:51:44 | 2023-11-05 11:51:45 | 1.26 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2023-11-05 11:51:44 | |
| ¶ | pypath.inputs.adrecs._adrecs_base |
Not calling `pypath.inputs.adrecs._adrecs_base`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.adrecs._adrecs_drug_adr | 2023-11-05 11:51:45 | 2023-11-05 11:52:21 | 35.98 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2023-11-05 11:51:45 | |
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2023-11-05 11:52:21 | 2023-11-05 11:52:27 | 6.57 | list | [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) | 13,855 | {} | 2023-11-05 11:52:21 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2023-11-05 11:52:27 | 2023-11-05 11:52:28 | 0.81 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2023-11-05 11:52:27 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2023-11-05 11:52:28 | 2023-11-05 11:52:31 | 2.95 | list | [AdrecsDrug(badd='BADD_D00001', drug='1,2-hexanediol', synonyms=('1,2-hexanediol',), drugbank='DB14108', pubchem_cid='94335', mesh='C119102', kegg=None, tdd=None), AdrecsDrug(badd='BADD_D00002', drug='2-hydroxy-3-phenylpropanoic acid', synonyms=('3-phenyllactate', '3-phenyllactic acid', '3-phenyllac...(truncated) | 2,526 | {} | 2023-11-05 11:52:28 | |
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2023-11-05 11:52:31 | 2023-11-05 11:52:32 | 1.21 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='21.12.02.006', badd='BADD_A07682'), parent=AdrecsAdr(adr_class='21.12.02', badd='BADD_A03943')), AdrecsChildParent(child=AdrecsAdr(adr_class='24.04.01.005', badd='BADD_A08350'), parent=AdrecsAdr(adr_class='24.04.01', badd='BADD_A00283')), AdrecsChildPare...(truncated) | 13,828 | {} | 2023-11-05 11:52:31 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2023-11-05 11:52:32 | 2023-11-05 11:52:33 | 0.76 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/almen2009.py", line 63, in almen2009_annotations
uniprots = mapping.map_name(row[0], 'ipi', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/ipi.py", line 68, in _ipi_uniprot_pairs
for ipi, uniprots in iteritems(ipi_uniprot()):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/ipi.py", line 40, in ipi_uniprot
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 15:06:35 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2023-11-05 11:52:33 | 2023-11-05 11:52:34 | 0.53 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/baccin2019.py", line 190, in baccin2019_annotations
ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/baccin2019.py", line 121, in baccin2019_interactions
data = inputs_common.read_xls(c.fileobj.name, sheet = 'SuppTable3')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-10-20 15:06:36 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2023-11-05 11:52:34 | 2023-11-05 11:52:34 | 0.37 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/baccin2019.py", line 121, in baccin2019_interactions
data = inputs_common.read_xls(c.fileobj.name, sheet = 'SuppTable3')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-10-20 15:06:36 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2023-11-05 11:52:34 | 2023-11-05 11:52:34 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2023-11-05 11:52:34 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2023-11-05 11:52:34 | 2023-11-05 11:53:10 | 35.49 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2023-11-05 11:52:34 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2023-11-05 11:53:10 | 2023-11-05 11:53:47 | 36.69 | list | [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855', experimental_system='Two-hybrid', experimental_system_type='physical', ltp=True, htp_score=None, multi_validated=True, tax_a='9606', tax_b='9606'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272', experimen...(truncated) | 8,336 | {} | 2023-11-05 11:53:10 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2023-11-05 11:53:47 | 2023-11-05 11:53:48 | 1.11 | list | [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) | 7,088 | {} | 2023-11-05 11:53:47 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2023-11-05 11:53:48 | 2023-11-05 11:54:37 | 49.02 | list | [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) | 177,409 | {} | 2023-11-05 11:53:48 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2023-11-05 11:54:38 | 2023-11-05 11:54:38 | 0.25 | list | [{'format': 'EXPRESSION', 'array': 'OneArray', 'vendor': 'PHALANX', 'type': 'OLIGO', 'description': None, 'label': 'PHALANX OneArray'}, {'array': 'CODELINK', 'vendor': 'CODELINK', 'type': 'OLIGO', 'description': None, 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'type': 'OLIGO', 'descript...(truncated) | 35 | {} | 2023-11-05 11:54:38 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomodels._get_biomodels | 2023-11-05 11:54:38 | 2023-11-05 11:54:38 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/biomodels.py", line 101, in _get_biomodels
loginurl = urls.urls['biomodels']['login'] % t
KeyError: 'login'
|
{} | 2023-10-20 15:08:22 | |||
| ¶ | pypath.inputs.biomodels.download_single_model |
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomodels.get_biomodels | 2023-11-05 11:54:38 | 2023-11-05 11:54:38 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/biomodels.py", line 160, in get_biomodels
c0.perform()
pycurl.error: (3, '')
|
{} | 2023-10-20 15:08:22 | |||
| ¶ | pypath.inputs.biomodels.get_biomodels_req | 2023-11-05 11:54:38 | 2023-11-05 11:54:39 | 0.70 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/biomodels.py", line 193, in get_biomodels_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-10-20 15:08:22 | |||
| ¶ | pypath.inputs.biomodels.get_single_model |
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2023-11-05 11:54:39 | 2023-11-05 11:54:39 | 0.20 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/ca1.py", line 53, in ca1_interactions
path = science_input.science_download(url = url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 15:08:23 | |||
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2023-11-05 11:54:39 | 2023-11-05 11:54:40 | 0.89 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2023-11-05 11:54:39 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2023-11-05 11:54:40 | 2023-11-05 11:57:12 | 152.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cancerdrugsdb.py", line 203, in cancerdrugsdb_annotations
data = cancerdrugsdb_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cancerdrugsdb.py", line 135, in cancerdrugsdb_interactions
target_uniprots = mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:08:24 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2023-11-05 11:57:12 | 2023-11-05 11:57:12 | 0.00 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 304 | {} | 2023-11-05 11:57:12 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2023-11-05 11:57:12 | 2023-11-05 11:57:12 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cancerdrugsdb.py", line 135, in cancerdrugsdb_interactions
target_uniprots = mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:08:48 | |||
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2023-11-05 11:57:12 | 2023-11-05 11:57:12 | 0.28 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cancersea.py", line 63, in cancersea_annotations
uniprots = mapping.map_name(line[1], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:08:48 | |||
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2023-11-05 11:57:12 | 2023-11-05 11:57:30 | 17.83 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellcall.py", line 219, in cellcall_annotations
interactions = cellcall_interactions(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellcall.py", line 155, in cellcall_interactions
ligands = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:08:48 | |||
| ¶ | pypath.inputs.cellcall.cellcall_download | 2023-11-05 11:57:30 | 2023-11-05 11:57:30 | 0.05 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2023-11-05 11:57:30 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2023-11-05 11:57:30 | 2023-11-05 11:57:31 | 0.88 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2023-11-05 11:57:30 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2023-11-05 11:57:31 | 2023-11-05 11:57:31 | 0.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellcall.py", line 155, in cellcall_interactions
ligands = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:07 | |||
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2023-11-05 11:57:31 | 2023-11-05 11:57:32 | 0.69 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellcellinteractions.py", line 50, in cellcellinteractions_annotations
uniprots = mapping.map_name(row[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:07 | |||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2023-11-05 11:57:32 | 2023-11-05 11:57:32 | 0.00 | int | 9606 | 0 | {} | 2023-11-05 11:57:32 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_cofactors |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_complexes |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2023-11-05 11:57:32 | 2023-11-05 11:57:38 | 5.87 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 322, in cellchatdb_annotations
interactions = cellchatdb_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 226, in cellchatdb_interactions
_complexes = _cellchatdb_process_complexes(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 112, in _cellchatdb_process_complexes
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 113, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:09 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2023-11-05 11:57:38 | 2023-11-05 11:57:43 | 5.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 141, in cellchatdb_cofactors
return _cellchatdb_process_cofactors(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 158, in _cellchatdb_process_cofactors
uniprots = mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:15 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2023-11-05 11:57:43 | 2023-11-05 11:57:48 | 5.46 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 95, in cellchatdb_complexes
return _cellchatdb_process_complexes(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 112, in _cellchatdb_process_complexes
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 113, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:20 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2023-11-05 11:57:48 | 2023-11-05 11:57:54 | 5.53 | dict | {'interaction': interaction_name ... rownames TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 TGFB1_ACVR1B_TGF...(truncated) | 4 | {} | 2023-11-05 11:57:48 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2023-11-05 11:57:54 | 2023-11-05 11:57:59 | 4.92 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 226, in cellchatdb_interactions
_complexes = _cellchatdb_process_complexes(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 112, in _cellchatdb_process_complexes
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellchatdb.py", line 113, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:31 | |||
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.35 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2023-11-05 11:57:59 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 456, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 316, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 163, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 164, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:37 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.03 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 513, in cellinker_complex_annotations
return cellinker_annotations(organism = organism, entity_type = 'complex')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 456, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 316, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 163, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 164, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:37 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 197, in cellinker_complexes
for cplex in components_to_complex(c.components, organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 163, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 164, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:37 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2023-11-05 11:57:59 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 316, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 163, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 164, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:37 | |||
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2023-11-05 11:57:59 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 495, in cellinker_protein_annotations
return cellinker_annotations(organism = organism, entity_type = 'protein')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 456, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 316, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 163, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 164, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 384, in cellinker_smol_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 387, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 163, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 164, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.01 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {} | 2023-11-05 11:57:59 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_annotations |
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_get_entity |
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_hla |
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.22 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 219, in cellphonedb_complex_annotations
return _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 127, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 208, in name_method
comp = get_stoichiometry(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 202, in get_stoichiometry
return tuple(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 203, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2023-11-05 11:57:59 | 2023-11-05 11:57:59 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 347, in cellphonedb_complexes
annot = cellphonedb_complex_annotations()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 219, in cellphonedb_complex_annotations
return _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 127, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 208, in name_method
comp = get_stoichiometry(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 202, in get_stoichiometry
return tuple(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 203, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2023-11-05 11:57:59 | 2023-11-05 11:58:00 | 0.22 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 283, in cellphonedb_interactions
ligands, receptors = cellphonedb_ligands_receptors()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 62, in cellphonedb_ligands_receptors
proteins = cellphonedb_protein_annotations()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 162, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 127, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 158, in name_method
uniprot = mapping.map_names(uniprot, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2023-11-05 11:58:00 | 2023-11-05 11:58:00 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 62, in cellphonedb_ligands_receptors
proteins = cellphonedb_protein_annotations()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 162, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 127, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 158, in name_method
uniprot = mapping.map_names(uniprot, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2023-11-05 11:58:00 | 2023-11-05 11:58:00 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 162, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 127, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cellphonedb.py", line 158, in name_method
uniprot = mapping.map_names(uniprot, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2023-11-05 11:58:00 | 2023-11-05 11:58:15 | 15.42 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/celltalkdb.py", line 181, in celltalkdb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:38 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2023-11-05 11:58:15 | 2023-11-05 11:58:15 | 0.00 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2023-11-05 11:58:15 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2023-11-05 11:58:15 | 2023-11-05 11:58:15 | 0.01 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2023-11-05 11:58:15 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2023-11-05 11:58:15 | 2023-11-05 11:58:15 | 0.27 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/celltypist.py", line 71, in celltypist_annotations
uniprots = mapping.map_names(genesymbols, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:09:40 | |||
| ¶ | pypath.inputs.chembl.chembl_activities |
Not calling `pypath.inputs.chembl.chembl_activities`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.chembl.chembl_documents | 2023-11-05 11:58:15 | 2023-11-05 12:00:11 | 115.65 | dict | {'CHEMBL1139451': 14695813, 'CHEMBL1148466': 14695814, 'CHEMBL1139452': 14695824, 'CHEMBL1139453': 14695825, 'CHEMBL1139454': 14695826, 'CHEMBL1139455': 14695827, 'CHEMBL1139456': 14695815, 'CHEMBL1139457': 14695828, 'CHEMBL1139458': 14695816, 'CHEMBL1148467': 14695833, 'CHEMBL1139459': 14695834, 'C...(truncated) | 80,293 | {} | 2023-11-05 11:58:15 | |
| ¶ | pypath.inputs.chembl.chembl_drug_indications | 2023-11-05 12:00:11 | 2023-11-05 12:01:14 | 63.12 | list | [ChemblIndication(efo_id='EFO:0000404', efo_term='diffuse scleroderma', max_phase=2.0, mesh_heading='Scleroderma, Diffuse', mesh_id='D045743', molecule_chembl='CHEMBL1201823'), ChemblIndication(efo_id='EFO:0000685', efo_term='rheumatoid arthritis', max_phase=4.0, mesh_heading='Arthritis, Rheumatoid'...(truncated) | 51,582 | {} | 2023-11-05 12:00:11 | |
| ¶ | pypath.inputs.chembl.chembl_mechanisms | 2023-11-05 12:01:14 | 2023-11-05 12:01:26 | 11.64 | list | [ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_action='Carbonic anhydrase VII inhibitor', chembl='CHEMBL19', target_chembl='CHEMBL2326'), ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_acti...(truncated) | 7,098 | {} | 2023-11-05 12:01:14 | |
| ¶ | pypath.inputs.chembl.chembl_targets | 2023-11-05 12:01:26 | 2023-11-05 12:03:32 | 125.96 | list | [ChemblTarget(accession='O43451', target_chembl_id='CHEMBL2074'), ChemblTarget(accession='O60706', target_chembl_id='CHEMBL1971'), ChemblTarget(accession='O76074', target_chembl_id='CHEMBL1827'), ChemblTarget(accession='O95180', target_chembl_id='CHEMBL1859'), ChemblTarget(accession='O96760', target...(truncated) | 15,398 | {} | 2023-11-05 12:01:26 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2023-11-05 12:03:32 | 2023-11-05 12:04:03 | 31.17 | list | [Citation(allele='1291788', variation_id='1301502', nsv='', citation_source='PubMedCentral', citation_id='4544753'), Citation(allele='526429', variation_id='535799', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='1398716', variation_id='1501848', nsv='', citation_source=...(truncated) | 2,746,378 | {} | 2023-11-05 12:03:32 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2023-11-05 12:04:07 | 2023-11-05 12:06:30 | 143.23 | list | [Variant(allele='1666010', type='single nucleotide variant', variant='NM_030930.4(UNC93B1):c.829C>A (p.Arg277=)', entrez='81622', genesymbol='UNC93B1', clinical_significance='Likely benign', review_status='criteria provided, single submitter', rs='-1', phenotype_ids=('MONDO:MONDO:0024563', 'MedGen:C...(truncated) | 4,706,038 | {} | 2023-11-05 12:04:07 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2023-11-05 12:18:14 | 2023-11-05 12:18:15 | 0.72 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/collectri.py", line 218, in collectri_interactions
mapping.map_name(rec.tf, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:33:14 | |||
| ¶ | pypath.inputs.collectri.collectri_raw | 2023-11-05 12:18:15 | 2023-11-05 12:18:15 | 0.08 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2023-11-05 12:18:15 | |
| ¶ | pypath.inputs.compath._compath_mappings | 2023-11-05 12:18:15 | 2023-11-05 12:18:15 | 0.13 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {} | 2023-11-05 12:18:15 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2023-11-05 12:18:15 | 2023-11-05 12:18:15 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/compath.py", line 55, in compath_mappings
return pd.DataFrame(result) if return_df else result
NameError: name 'return_df' is not defined
|
{} | 2023-10-20 15:33:15 | |||
| ¶ | pypath.inputs.compleat.compleat_complexes | 2023-11-05 12:18:15 | 2023-11-05 12:18:16 | 0.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/compleat.py", line 84, in compleat_complexes
uniprot = mapping.map_name0(entrez.strip(), 'entrez', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:33:15 | |||
| ¶ | pypath.inputs.compleat.compleat_raw | 2023-11-05 12:18:16 | 2023-11-05 12:18:16 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2023-11-05 12:18:16 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2023-11-05 12:18:16 | 2023-11-05 12:19:32 | 76.19 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:Q86XT2_Q99816_Q9NZ09_Q9UK41': Complex ESCRT-I complex, VPS37D-UBAP1 variant: COMPLEX:Q86XT2_Q99816_Q9NZ09_Q9UK41, 'COMPLEX:Q86XE3_Q8NE86_Q9BPX6_Q9H4I9': Comple...(truncated) | 1,780 | {} | 2023-11-05 12:18:16 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2023-11-05 12:19:32 | 2023-11-05 12:19:33 | 0.93 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/comppi.py", line 128, in comppi_interaction_locations
mapping.map_name(l[0], 'uniprot', 'uniprot'),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:34:39 | |||
| ¶ | pypath.inputs.comppi.comppi_locations | 2023-11-05 12:19:33 | 2023-11-05 12:19:33 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/comppi.py", line 144, in comppi_locations
for iloc in comppi_interaction_locations(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/comppi.py", line 128, in comppi_interaction_locations
mapping.map_name(l[0], 'uniprot', 'uniprot'),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:34:40 | |||
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2023-11-05 12:19:33 | 2023-11-05 12:19:34 | 0.29 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/connectomedb.py", line 93, in connectomedb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:34:40 | |||
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2023-11-05 12:19:34 | 2023-11-05 12:19:34 | 0.01 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2023-11-05 12:19:34 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2023-11-05 12:19:34 | 2023-11-05 12:19:35 | 0.98 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2023-11-05 12:19:34 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2023-11-05 12:19:35 | 2023-11-05 12:19:36 | 1.54 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cosmic.py", line 132, in cancer_gene_census_annotations
data = csv.DictReader(c.fileobj, delimiter = ',')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 15:34:42 | |||
| ¶ | pypath.inputs.cpad.cpad_annotations | 2023-11-05 12:19:36 | 2023-11-05 12:19:58 | 22.29 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cpad.py", line 69, in cpad_annotations
mirbase = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 76, in mirbase_mature
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 15:34:44 | |||
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2023-11-05 12:19:58 | 2023-11-05 12:19:59 | 0.08 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='Mitochondrial apoptosis pathway', cancer='Glioma', pathway_category='Apoptosis', effect_on_cancer='Activating', effect_on_cancer_outcome='promote cisplatin-induced apoptosis'), CpadPathwayCancer(pathway='MAPK signaling pathway', cancer='Glioma', pathway_catego...(truncated) | 2 | {} | 2023-11-05 12:19:58 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2023-11-05 12:19:59 | 2023-11-05 12:19:59 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2023-11-05 12:19:59 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2023-11-05 12:19:59 | 2023-11-05 12:20:05 | 6.43 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | {} | 2023-11-05 12:19:59 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2023-11-05 12:20:05 | 2023-11-05 12:20:08 | 2.90 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {} | 2023-11-05 12:20:05 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2023-11-05 12:20:09 | 2023-11-05 12:20:09 | 0.68 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cspa.py", line 58, in cspa_annotations
raw = inputs_common.read_xls(xlsname, sheets[str_organism])[1:]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-10-20 15:34:58 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2023-11-05 12:20:09 | 2023-11-05 12:20:10 | 0.50 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cspa.py", line 127, in cspa_cell_type_annotations
cell_type_data = cspa_cell_types(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cspa.py", line 92, in cspa_cell_types
raw = inputs_common.read_xls(xlsname, sheets[str_organism])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'float' object has no attribute 'value'
|
{} | 2023-10-20 15:34:58 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2023-11-05 12:20:10 | 2023-11-05 12:20:10 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cspa.py", line 92, in cspa_cell_types
raw = inputs_common.read_xls(xlsname, sheets[str_organism])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'float' object has no attribute 'value'
|
{} | 2023-10-20 15:34:59 | |||
| ¶ | pypath.inputs.ctdbase._ctdbase_download |
Not calling `pypath.inputs.ctdbase._ctdbase_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase._map_keys |
Not calling `pypath.inputs.ctdbase._map_keys`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase._modify_dict |
Not calling `pypath.inputs.ctdbase._modify_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2023-11-05 12:20:10 | 2023-11-05 12:20:11 | 0.65 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cytosig.py", line 105, in cytosig_annotations
u_target = map_to_uniprot(target)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cytosig.py", line 85, in map_to_uniprot
uniprots = mapping.map_name(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 15:34:59 | |||
| ¶ | pypath.inputs.cytosig.cytosig_df | 2023-11-05 12:20:11 | 2023-11-05 12:20:11 | 0.04 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {} | 2023-11-05 12:20:11 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2023-11-05 12:20:11 | 2023-11-05 12:20:13 | 2.26 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2023-11-05 12:20:11 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2023-11-05 12:20:13 | 2023-11-05 12:20:16 | 2.38 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/dbptm.py", line 97, in dbptm_enzyme_substrate_old
for k, data in iteritems(extra):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-tWRce4VM-py3.10/lib/python3.10/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2023-10-20 15:35:02 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2023-11-05 12:20:16 | 2023-11-05 12:20:17 | 1.18 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2023-11-05 12:20:16 | |
| ¶ | pypath.inputs.ddinter._ensure_hashable |
Not calling `pypath.inputs.ddinter._ensure_hashable`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2023-11-05 12:20:17 | 2023-11-05 12:53:28 | 1,990.49 | list | [{DdinterInteraction(drug1_id='DDInter1', drug1_name='Abacavir', drug2_id='DDInter1357', drug2_name='Oxandrolone', level=('Unknown',), actions=('unknown',)), DdinterInteraction(drug1_id='DDInter1', drug1_name='Abacavir', drug2_id='DDInter1166', drug2_name='Methadone', level=('Moderate',), actions=('...(truncated) | 1,972 | {} | 2023-11-05 12:20:17 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2023-11-05 12:53:28 | 2023-11-05 13:42:03 | 2,915.12 | list | [DdinterIdentifiers(ddinter='DDInter1', drugbank='DB01048', chembl='CHEMBL1380', pubchem='441300'), DdinterIdentifiers(ddinter='DDInter2', drugbank='DB05084', chembl=None, pubchem=None), DdinterIdentifiers(ddinter='DDInter3', drugbank='DB11932', chembl='CHEMBL2205807', pubchem='15664'), DdinterIdent...(truncated) | 1,972 | {} | 2023-11-05 12:53:28 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2023-11-05 13:42:03 | 2023-11-05 13:42:04 | 0.51 | int | 1972 | 0 | {} | 2023-11-05 13:42:03 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2023-11-05 13:42:04 | 2023-11-05 13:42:04 | 0.03 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/deathdomain.py", line 43, in deathdomain_interactions
soup = bs4.BeautifulSoup(html, 'lxml')
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-tWRce4VM-py3.10/lib/python3.10/site-packages/bs4/__init__.py", line 315, in __init__
elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
|
{} | 2023-10-20 17:04:22 | |||
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2023-11-05 13:42:04 | 2023-11-05 13:42:04 | 0.21 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2023-11-05 13:42:04 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2023-11-05 13:42:04 | 2023-11-05 13:42:04 | 0.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/depod.py", line 112, in depod_enzyme_substrate
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:04:22 | |||
| ¶ | pypath.inputs.depod.depod_interactions | 2023-11-05 13:42:04 | 2023-11-05 13:42:04 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {} | 2023-11-05 13:42:04 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2023-11-05 13:42:04 | 2023-11-05 13:42:07 | 2.06 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/dgidb.py", line 99, in dgidb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:04:22 | |||
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2023-11-05 13:42:07 | 2023-11-05 13:42:12 | 5.42 | list | [DgidbInteraction(genesymbol='PIK3CG', entrez='5294', resource='NCI', type=None, drug_name='SULFORAPHANE', drug_chembl='chembl:CHEMBL48802', score='0.18', pmid='15896333'), DgidbInteraction(genesymbol='AKT1', entrez='207', resource='ClearityFoundationBiomarkers', type=None, drug_name='TRICIRIBINE', ...(truncated) | 85,022 | {} | 2023-11-05 13:42:07 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2023-11-05 13:42:12 | 2023-11-05 13:43:16 | 63.91 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/dgidb.py", line 142, in get_dgidb_old
return mapping.map_names(genesymbols, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:04:30 | |||
| ¶ | pypath.inputs.dip.dip_interactions | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.29 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2023-11-05 13:43:16 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases._diseases_general |
Not calling `pypath.inputs.diseases._diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.diseases.experiments_full | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.diseases.knowledge_full | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.diseases.textmining_filtered | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.diseases.textmining_full | 2023-11-05 13:43:16 | 2023-11-05 13:43:16 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.domino.domino_ddi | 2023-11-05 13:43:16 | 2023-11-05 13:44:04 | 47.75 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/domino.py", line 239, in domino_ddi
domi = domino_enzsub()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/domino.py", line 413, in domino_enzsub
intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/internals/intera.py", line 651, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 128, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 464, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3703, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2663, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2041, in map_name
uniprots = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:05:32 | |||
| ¶ | pypath.inputs.domino.domino_enzsub | 2023-11-05 13:44:04 | 2023-11-05 13:44:05 | 0.46 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/domino.py", line 413, in domino_enzsub
intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/internals/intera.py", line 651, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 128, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 464, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3703, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2663, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2041, in map_name
uniprots = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:06:20 | |||
| ¶ | pypath.inputs.domino.domino_interactions | 2023-11-05 13:44:05 | 2023-11-05 13:44:05 | 0.38 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2023-11-05 13:44:05 | |
| ¶ | pypath.inputs.domino.get_domino | 2023-11-05 13:44:05 | 2023-11-05 13:44:05 | 0.35 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2023-11-05 13:44:05 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2023-11-05 13:44:05 | 2023-11-05 13:44:14 | 8.52 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2023-11-05 13:44:05 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2023-11-05 13:44:14 | 2023-11-05 13:44:28 | 13.63 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2023-11-05 13:44:14 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-11-05 13:44:28 | 2023-11-05 13:44:28 | 0.28 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 17:07:04 | |||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-11-05 13:44:28 | 2023-11-05 13:44:28 | 0.52 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 17:07:04 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2023-11-05 13:44:28 | 2023-11-05 13:44:30 | 1.79 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2023-11-05 13:44:28 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2023-11-05 13:44:30 | 2023-11-05 13:44:31 | 0.66 | list | [['AHR', 'CYP1A1', '0', 'A', True, False, True, False, 'HTRIdb,trrust_signed', '', 'hocomoco_v11', '', 'HTRIdb,trrust_signed,hocomoco_v11'], ['AHR', 'CYP1A2', '0', 'A', True, False, False, False, 'HTRIdb,trrust_signed', '', '', '', 'HTRIdb,trrust_signed'], ['AHR', 'CYP1B1', '0', 'A', True, False, Tr...(truncated) | 14,260 | {} | 2023-11-05 13:44:30 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2023-11-05 13:44:31 | 2023-11-05 13:44:32 | 1.15 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2023-11-05 13:44:31 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2023-11-05 13:44:32 | 2023-11-05 13:44:46 | 13.60 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2023-11-05 13:44:32 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-11-05 13:44:46 | 2023-11-05 13:44:46 | 0.56 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 17:07:04 | |||
| ¶ | pypath.inputs.drugbank._drugbank_credentials | 2023-11-05 13:44:46 | 2023-11-05 13:44:46 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/drugbank.py", line 49, in _drugbank_credentials
return credentials.credentials(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/credentials.py", line 115, in credentials
raise RuntimeError(msg)
RuntimeError: Failed to obtain credentials for resource `DrugBank`
|
{} | 2023-10-20 17:07:05 | |||
| ¶ | pypath.inputs.drugbank._drugbank_download |
Not calling `pypath.inputs.drugbank._drugbank_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_annotations | 2023-11-05 13:44:46 | 2023-11-05 13:44:46 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/drugbank.py", line 352, in drugbank_annotations
drugs = drugbank_drugs(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-10-20 17:07:05 | |||
| ¶ | pypath.inputs.drugbank.drugbank_drugs | 2023-11-05 13:44:46 | 2023-11-05 13:44:46 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-10-20 17:07:05 | |||
| ¶ | pypath.inputs.drugbank.drugbank_interactions | 2023-11-05 13:44:46 | 2023-11-05 13:44:46 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/drugbank.py", line 198, in drugbank_interactions
for d in drugbank_drugs(user = user, passwd = passwd)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-10-20 17:07:05 | |||
| ¶ | pypath.inputs.drugbank.drugbank_mapping |
Not calling `pypath.inputs.drugbank.drugbank_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_raw_interactions | 2023-11-05 13:44:46 | 2023-11-05 13:44:46 | 0.00 | list | [] | 0 | {} | 2023-11-05 13:44:46 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2023-11-05 13:44:46 | 2023-11-05 13:44:47 | 1.20 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2023-11-05 13:44:46 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2023-11-05 13:44:47 | 2023-11-05 13:44:49 | 1.30 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2023-11-05 13:44:47 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2023-11-05 13:44:49 | 2023-11-05 13:44:50 | 0.88 | dict | {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) | 349 | {} | 2023-11-05 13:44:49 | |
| ¶ | pypath.inputs.elm.elm_domains | 2023-11-05 13:44:50 | 2023-11-05 13:44:51 | 0.87 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2023-11-05 13:44:50 | |
| ¶ | pypath.inputs.elm.elm_instances | 2023-11-05 13:44:51 | 2023-11-05 13:46:53 | 122.16 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 4,251 | {'fixed': True} | 2023-11-05 13:44:51 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2023-11-05 13:46:53 | 2023-11-05 13:46:53 | 0.17 | list | [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) | 2,696 | {'fixed': True} | 2023-11-05 13:46:53 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2023-11-05 13:46:53 | 2023-11-05 13:46:53 | 0.09 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 158, in embrace_annotations
for rec in embrace_translated(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:10:30 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2023-11-05 13:46:53 | 2023-11-05 13:46:53 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 124, in embrace_interactions
for rec in embrace_translated(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:10:31 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2023-11-05 13:46:53 | 2023-11-05 13:46:53 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:10:31 | |||
| ¶ | pypath.inputs.embrace.embrace_translated | 2023-11-05 13:46:53 | 2023-11-05 13:46:53 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:10:31 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2023-11-05 13:46:53 | 2023-11-05 13:46:54 | 0.75 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {} | 2023-11-05 13:46:53 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2023-11-05 13:46:54 | 2023-11-05 13:46:55 | 0.64 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 317 | {} | 2023-11-05 13:46:54 | |
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2023-11-05 13:46:55 | 2023-11-05 13:47:11 | 16.22 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {} | 2023-11-05 13:46:55 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2023-11-05 13:47:11 | 2023-11-05 13:47:11 | 0.03 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {} | 2023-11-05 13:47:11 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2023-11-05 13:47:11 | 2023-11-05 13:48:25 | 73.99 | list | [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) | 290,197 | {} | 2023-11-05 13:47:11 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2023-11-05 13:48:25 | 2023-11-05 13:48:25 | 0.25 | list | [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) | 353 | {} | 2023-11-05 13:48:25 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2023-11-05 13:48:25 | 2023-11-05 13:48:26 | 0.86 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,226 | {} | 2023-11-05 13:48:25 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2023-11-05 13:48:26 | 2023-11-05 13:50:08 | 102.28 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0070469', 'GO:0045275', 'GO:0016020', 'GO:0005743', 'GO:0005739'}, 'A0A023I7H2': {'GO:0005739', 'GO:0070469', 'GO:0016020', 'GO:0005743'}, 'A0A023I7H5': {'GO:0005739', 'GO:0045263', 'GO:0016020', 'GO:0005743'}, 'A0A023I7J4': {'GO:0005739...(truncated) | 2 | {} | 2023-11-05 13:48:26 | |
| ¶ | pypath.inputs.go.get_goslim | 2023-11-05 13:50:08 | 2023-11-05 13:50:10 | 1.10 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 141 | {} | 2023-11-05 13:50:08 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2023-11-05 13:50:10 | 2023-11-05 14:02:39 | 749.63 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'...(truncated) | 3 | {} | 2023-11-05 13:50:10 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2023-11-05 14:02:39 | 2023-11-05 14:02:39 | 0.06 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 205, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:28:15 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2023-11-05 14:02:39 | 2023-11-05 14:02:43 | 3.69 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'...(truncated) | 3 | {} | 2023-11-05 14:02:39 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2023-11-05 14:02:43 | 2023-11-05 14:02:48 | 4.87 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005829', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6I0': {'GO:0019814', 'G...(truncated) | 3 | {} | 2023-11-05 14:02:43 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2023-11-05 14:02:48 | 2023-11-05 14:02:53 | 4.82 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0046872', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0479', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) | 19,630 | {} | 2023-11-05 14:02:48 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2023-11-05 14:02:55 | 2023-11-05 14:02:56 | 1.02 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005829', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6I0': {'GO:0019814', 'G...(truncated) | 3 | {} | 2023-11-05 14:02:55 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2023-11-05 14:02:56 | 2023-11-05 14:02:56 | 0.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 852, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:28:35 | |||
| ¶ | pypath.inputs.go.go_annotations_solr | 2023-11-05 14:02:56 | 2023-11-05 14:02:57 | 1.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 738, in go_annotations_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:28:35 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2023-11-05 14:02:57 | 2023-11-05 14:02:57 | 0.20 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 61, in go_annotations_uniprot
for x in [x.split('\t') for x in data.split('\n')]
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-10-20 17:28:36 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2023-11-05 14:02:57 | 2023-11-05 14:03:01 | 3.60 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016006', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2023-11-05 14:02:57 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2023-11-05 14:03:01 | 2023-11-05 14:03:01 | 0.04 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 283, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 205, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:28:41 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2023-11-05 14:03:01 | 2023-11-05 14:03:04 | 3.57 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016006', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2023-11-05 14:03:01 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2023-11-05 14:03:05 | 2023-11-05 14:03:07 | 2.93 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2023-11-05 14:03:05 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2023-11-05 14:03:08 | 2023-11-05 14:03:08 | 0.04 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 578, in go_terms_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:28:50 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2023-11-05 14:03:08 | 2023-11-05 14:03:11 | 2.97 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2023-11-05 14:03:08 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2023-11-05 14:03:11 | 2023-11-05 14:03:11 | 0.62 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/go.py", line 436, in go_terms_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:28:54 | |||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2023-11-05 14:03:11 | 2023-11-05 14:03:11 | 0.21 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 424 | {} | 2023-11-05 14:03:11 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2023-11-05 14:03:11 | 2023-11-05 14:03:13 | 1.39 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2023-11-05 14:03:11 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2023-11-05 14:03:13 | 2023-11-05 14:03:16 | 2.90 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/guide2pharma.py", line 232, in guide2pharma_download
ligand_uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/guide2pharma.py", line 233, in <listcomp>
mapping.map_name0(ligand, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:28:56 | |||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2023-11-05 14:03:16 | 2023-11-05 14:03:17 | 1.17 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/gutmgene.py", line 117, in gutmgene_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:29:00 | |||
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2023-11-05 14:03:17 | 2023-11-05 14:03:17 | 0.00 | list | [GutmgeneRaw(microbe_taxon='Bacteroides fragilis', microbe_ncbi_tax_id='817', gut_microbiota_id='gm0082', classification='species', genesymbol='FOXP3', entrez='50943', effect='activation', throughput='low-throughput'), GutmgeneRaw(microbe_taxon='Escherichia coli EcN', microbe_ncbi_tax_id=None, gut_m...(truncated) | 278 | {} | 2023-11-05 14:03:17 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2023-11-05 14:03:17 | 2023-11-05 14:03:17 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/havugimana.py", line 39, in get_havugimana
path = cell_input.cell_supplementary(supp_url, article_url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:29:02 | |||
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2023-11-05 14:03:17 | 2023-11-05 14:03:17 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/havugimana.py", line 54, in havugimana_complexes
for rec in get_havugimana():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/havugimana.py", line 39, in get_havugimana
path = cell_input.cell_supplementary(supp_url, article_url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:29:02 | |||
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2023-11-05 14:03:17 | 2023-11-05 14:03:19 | 1.71 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/hgnc.py", line 50, in hgnc_genegroups
uniprots = mapping.map_names(uniprots, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:29:02 | |||
| ¶ | pypath.inputs.hippie.hippie_interactions | 2023-11-05 14:03:19 | 2023-11-05 14:03:37 | 18.71 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/hippie.py", line 74, in hippie_interactions
ids_a_1 = mapping.map_name(l[0], 'uniprot-entry', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:29:05 | |||
| ¶ | pypath.inputs.homologene.get_homologene | 2023-11-05 14:03:38 | 2023-11-05 14:03:47 | 9.52 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2023-11-05 14:03:38 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2023-11-05 14:03:47 | 2023-11-05 14:03:47 | 0.00 | dict | {'interactions': [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462...(truncated) | 3 | {} | 2023-11-05 14:03:47 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2023-11-05 14:03:47 | 2023-11-05 14:03:47 | 0.00 | dict | {'P26992': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='CICYTR (Cytokine Type 1 receptors)', subsubclass=None)}, 'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P42...(truncated) | 1,141 | {} | 2023-11-05 14:03:47 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2023-11-05 14:03:47 | 2023-11-05 14:03:47 | 0.00 | dict | {} | 0 | {} | 2023-11-05 14:03:47 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2023-11-05 14:03:47 | 2023-11-05 14:03:47 | 0.00 | list | [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462', 'Ligand', 'P26...(truncated) | 619 | {} | 2023-11-05 14:03:47 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2023-11-05 14:03:47 | 2023-11-05 14:03:48 | 1.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/hpo.py", line 56, in hpo_annotations
uniprots = mapping.map_name(r[0], 'entrez', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:29:35 | |||
| ¶ | pypath.inputs.hpo.hpo_diseases | 2023-11-05 14:03:48 | 2023-11-05 14:03:50 | 2.35 | dict | {'hpo_id': {HpoDisease(omim='database_id', name='disease_name', pmid=None, qualifier='qualifier', evidence='evidence', onset='onset', frequency='frequency', sex='sex', modifier='modifier', aspect='aspect')}, 'HP:0011097': {HpoDisease(omim='OMIM:614558', name='Epileptic encephalopathy, early infantil...(truncated) | 10,708 | {} | 2023-11-05 14:03:48 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2023-11-05 14:03:51 | 2023-11-05 14:03:52 | 1.42 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {} | 2023-11-05 14:03:51 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2023-11-05 14:03:52 | 2023-11-05 14:03:53 | 0.55 | dict | {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) | 17,664 | {} | 2023-11-05 14:03:52 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2023-11-05 14:03:53 | 2023-11-05 14:03:58 | 5.03 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2023-11-05 14:03:53 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2023-11-05 14:03:58 | 2023-11-05 14:04:00 | 1.50 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {} | 2023-11-05 14:03:58 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2023-11-05 14:04:00 | 2023-11-05 14:04:01 | 1.46 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {} | 2023-11-05 14:04:00 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2023-11-05 14:04:01 | 2023-11-05 14:04:02 | 1.35 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2023-11-05 14:04:01 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2023-11-05 14:04:03 | 2023-11-05 14:04:05 | 2.94 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2023-11-05 14:04:03 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2023-11-05 14:04:05 | 2023-11-05 14:04:07 | 1.17 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/humancellmap.py", line 63, in humancellmap_annotations
for uniprot in mapping.map_name(l[9], 'uniprot', 'uniprot'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:21 | |||
| ¶ | pypath.inputs.humap.humap2_complexes | 2023-11-05 14:04:07 | 2023-11-05 14:04:08 | 1.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/humap.py", line 73, in humap2_complexes
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/humap.py", line 74, in <genexpr>
mapping.map_name(uniprot, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:22 | |||
| ¶ | pypath.inputs.humap.humap_complexes | 2023-11-05 14:04:08 | 2023-11-05 14:04:09 | 0.80 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/humap.py", line 39, in humap_complexes
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/humap.py", line 40, in <genexpr>
mapping.map_name(entrez, 'entrez', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:23 | |||
| ¶ | pypath.inputs.humsavar._parse_desc |
Not calling `pypath.inputs.humsavar._parse_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2023-11-05 14:04:09 | 2023-11-05 14:04:13 | 4.54 | dict | {'P04217': {UniprotVariant(genesymbol='A1BG', ftid='VAR_018370', aa_change='p.His395Arg', variant_category='LB/B', dbsnp='rs2241788', disease=None, disease_symbol=None, disease_omim=None), UniprotVariant(genesymbol='A1BG', ftid='VAR_018369', aa_change='p.His52Arg', variant_category='LB/B', dbsnp='rs...(truncated) | 13,055 | {} | 2023-11-05 14:04:09 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2023-11-05 14:04:13 | 2023-11-05 14:04:15 | 1.32 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 324, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 290, in _map_ids
return mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:29 | |||
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2023-11-05 14:04:15 | 2023-11-05 14:04:18 | 3.80 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 324, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 290, in _map_ids
return mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:30 | |||
| ¶ | pypath.inputs.huri.hi_iii_old | 2023-11-05 14:04:18 | 2023-11-05 14:04:18 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 90, in hi_iii_old
url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
|
{} | 2023-10-20 17:30:34 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2023-11-05 14:04:18 | 2023-11-05 14:04:35 | 16.93 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 324, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 290, in _map_ids
return mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:34 | |||
| ¶ | pypath.inputs.huri.huri_interactions | 2023-11-05 14:04:35 | 2023-11-05 14:04:47 | 11.36 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 324, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 290, in _map_ids
return mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:30:51 | |||
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2023-11-05 14:04:47 | 2023-11-05 14:04:48 | 0.99 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2023-11-05 14:04:47 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2023-11-05 14:04:48 | 2023-11-05 14:04:49 | 1.55 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2023-11-05 14:04:48 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2023-11-05 14:04:49 | 2023-11-05 14:05:06 | 17.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 260, in lit_bm_interactions
uniprots_a = mapping.map_name(row[0], 'ensembl', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:31:05 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2023-11-05 14:05:06 | 2023-11-05 14:05:06 | 0.12 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 38, in rolland_hi_ii_14
xlsname = cell.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:31:24 | |||
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2023-11-05 14:05:06 | 2023-11-05 14:05:08 | 2.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 324, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 290, in _map_ids
return mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:31:24 | |||
| ¶ | pypath.inputs.huri.yu2011_interactions | 2023-11-05 14:05:08 | 2023-11-05 14:05:10 | 1.37 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 324, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/huri.py", line 290, in _map_ids
return mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:31:25 | |||
| ¶ | pypath.inputs.i3d.get_i3d | 2023-11-05 14:05:10 | 2023-11-05 14:05:18 | 7.92 | list | [{'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P02647': {'pfam': None, 'chain': 'A', 'seq': [[68, 265]]}, 'uniprots': ['A0A024RAV5', 'P02647'], 'source': 'I3D', 'pdb': ['2mse'], 'references': []}, {'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P10398': {'pfam': N...(truncated) | 15,984 | {} | 2023-11-05 14:05:10 | |
| ¶ | pypath.inputs.icellnet._icellnet_get_components |
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_entity |
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_references |
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_resources |
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2023-11-05 14:05:18 | 2023-11-05 14:05:18 | 0.19 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 166, in icellnet_annotations
for ia in icellnet_interactions():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 72, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 196, in _icellnet_get_components
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 196, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 200, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:31:36 | |||
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2023-11-05 14:05:18 | 2023-11-05 14:05:18 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 103, in icellnet_complexes
for ia in icellnet_interactions():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 72, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 196, in _icellnet_get_components
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 196, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 200, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:31:36 | |||
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2023-11-05 14:05:18 | 2023-11-05 14:05:18 | 0.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 72, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 196, in _icellnet_get_components
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 196, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/icellnet.py", line 200, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:31:36 | |||
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2023-11-05 14:05:18 | 2023-11-05 14:05:19 | 0.87 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/imweb.py", line 72, in _get_imweb
hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-10-20 17:31:36 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2023-11-05 14:05:19 | 2023-11-05 14:05:19 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/imweb.py", line 105, in get_imweb
c0.perform()
pycurl.error: (3, '')
|
{} | 2023-10-20 17:31:37 | |||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2023-11-05 14:05:19 | 2023-11-05 14:05:19 | 0.24 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/imweb.py", line 138, in get_imweb_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-10-20 17:31:37 | |||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2023-11-05 14:05:19 | 2023-11-05 14:05:23 | 3.87 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2023-11-05 14:05:19 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2023-11-05 14:05:23 | 2023-11-05 14:05:24 | 0.63 | NoneType | None | 0 | {} | 2023-11-05 14:05:23 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2023-11-05 14:05:24 | 2023-11-05 14:05:24 | 0.41 | NoneType | None | 0 | {} | 2023-11-05 14:05:24 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2023-11-05 14:05:24 | 2023-11-05 14:09:31 | 246.60 | list | [IntactInteraction(id_a='Q05193', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, interaction_types={'direct interaction'}, mi_score=0.77, isoform_a=None, isoform_b=None), IntactInteraction(id_a='Q05193', id_b='P49418', id_type_a='uniprot', i...(truncated) | 72,106 | {} | 2023-11-05 14:05:24 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2023-11-05 14:09:31 | 2023-11-05 14:09:32 | 0.75 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/integrins.py", line 61, in get_integrins
return mapping.map_names(integrins, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:36:48 | |||
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2023-11-05 14:09:32 | 2023-11-05 14:09:33 | 1.45 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0008270', go_term_name='zinc ion binding'), Interpro2GOAnnotation(go_term_id='GO:0005634', go_term_name='nucleus'), Interpro2GOAnnotation(go_term_id='GO:0006355', go_term_name='regulation of DNA-templated transcription'),...(truncated) | 14,721 | {} | 2023-11-05 14:09:32 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2023-11-05 14:09:33 | 2023-11-05 14:10:07 | 34.22 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR027284', organism='9606', start=1, end=726), InterproAnnotation(interpro_id='IPR000001', organism='9606', start=388, end=471), InterproAnnotation(interpro_id='IPR018056', organism='9606', start=176, end=189), InterproAnnotatio...(truncated) | 16,756 | {} | 2023-11-05 14:09:33 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2023-11-05 14:10:07 | 2023-11-05 14:10:27 | 19.58 | list | [InterproEntry(interpro_id='IPR000001', protein_count='19039', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 40,338 | {} | 2023-11-05 14:10:07 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2023-11-05 14:10:27 | 2023-11-05 14:10:28 | 0.55 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/intogen.py", line 73, in intogen_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:38:00 | |||
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2023-11-05 14:10:28 | 2023-11-05 14:10:28 | 0.45 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/ipi.py", line 40, in ipi_uniprot
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:38:04 | |||
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2023-11-05 14:10:28 | 2023-11-05 14:12:27 | 119.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/iptmnet.py", line 118, in iptmnet_interactions
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2023, in map_name
reflists.get_reflist(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/reflists.py", line 279, in get_reflist
return manager.which_list(id_type = id_type, ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/reflists.py", line 95, in which_list
self.load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/reflists.py", line 118, in load
self.lists[key] = self._load(key)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/reflists.py", line 153, in _load
data = set(input_func(organism = ncbi_tax_id))
UnboundLocalError: local variable 'input_func' referenced before assignment
|
{} | 2023-10-20 17:38:04 | |||
| ¶ | pypath.inputs.italk.italk_annotations | 2023-11-05 14:12:27 | 2023-11-05 14:12:28 | 0.63 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/italk.py", line 105, in italk_annotations
mapping.map_name(row[2], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:40:51 | |||
| ¶ | pypath.inputs.italk.italk_interactions | 2023-11-05 14:12:28 | 2023-11-05 14:12:28 | 0.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/italk.py", line 70, in italk_interactions
ligands = mapping.map_name(row[2], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:40:52 | |||
| ¶ | pypath.inputs.italk.italk_raw | 2023-11-05 14:12:28 | 2023-11-05 14:12:28 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2023-11-05 14:12:28 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2023-11-05 14:12:28 | 2023-11-05 14:12:30 | 2.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kea.py", line 107, in kea_enzyme_substrate
for rec in kea_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kea.py", line 74, in kea_interactions
e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:40:52 | |||
| ¶ | pypath.inputs.kea.kea_interactions | 2023-11-05 14:12:30 | 2023-11-05 14:12:30 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kea.py", line 74, in kea_interactions
e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:09 | |||
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2023-11-05 14:12:30 | 2023-11-05 14:12:34 | 4.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 125, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 126, in <listcomp>
common.flat_list([
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 127, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:09 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus | 2023-11-05 14:12:34 | 2023-11-05 14:12:50 | 16.26 | set | {KeggMedicusRawInteraction(id_a='5604', id_b='5594', name_a='MAP2K1', name_b='MAPK1', effect='stimulation', itype='post_translational', pw_type='reference', type_a='gene', type_b='gene', network_id='N00001'), KeggMedicusRawInteraction(id_a='C01245', id_b='C00076', name_a='D-myo-Inositol 1,4,5-trisph...(truncated) | 12,946 | {'fixed': True} | 2023-11-05 14:12:34 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2023-11-05 14:12:50 | 2023-11-05 14:12:51 | 0.32 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 685, in kegg_medicus_complexes
cplexes = kegg_medicus_interactions(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 652, in kegg_medicus_interactions
process_partner(rec.id_a, rec.name_a, rec.type_a),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 643, in process_partner
process_protein(ids, symbols)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 635, in process_protein
mapping.map_name(id_, 'entrez', 'uniprot') or
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:30 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2023-11-05 14:12:51 | 2023-11-05 14:12:51 | 0.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 652, in kegg_medicus_interactions
process_partner(rec.id_a, rec.name_a, rec.type_a),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 643, in process_partner
process_protein(ids, symbols)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 635, in process_protein
mapping.map_name(id_, 'entrez', 'uniprot') or
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:30 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2023-11-05 14:12:51 | 2023-11-05 14:12:51 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 194, in kegg_pathway_annotations
proteins, interactions = kegg_pathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 175, in kegg_pathways
data = kegg_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 125, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 126, in <listcomp>
common.flat_list([
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 127, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:31 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2023-11-05 14:12:51 | 2023-11-05 14:12:52 | 0.48 | dict | {'A8K7J7': {KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Amino sugar ...(truncated) | 813 | {} | 2023-11-05 14:12:51 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2023-11-05 14:12:52 | 2023-11-05 14:12:52 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 175, in kegg_pathways
data = kegg_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 125, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 126, in <listcomp>
common.flat_list([
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg.py", line 127, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:33 | |||
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._generate_conv_functions | 2023-11-05 14:12:52 | 2023-11-05 14:12:52 | 0.00 | NoneType | None | 0 | {} | 2023-11-05 14:12:52 | |
| ¶ | pypath.inputs.kegg_api._generate_relation_functions | 2023-11-05 14:12:52 | 2023-11-05 14:12:52 | 0.00 | NoneType | None | 0 | {} | 2023-11-05 14:12:52 | |
| ¶ | pypath.inputs.kegg_api._kegg_conv |
Not calling `pypath.inputs.kegg_api._kegg_conv`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi |
Not calling `pypath.inputs.kegg_api._kegg_ddi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_async |
Not calling `pypath.inputs.kegg_api._kegg_ddi_async`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_sync |
Not calling `pypath.inputs.kegg_api._kegg_ddi_sync`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general |
Not calling `pypath.inputs.kegg_api._kegg_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general_async |
Not calling `pypath.inputs.kegg_api._kegg_general_async`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_link |
Not calling `pypath.inputs.kegg_api._kegg_link`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_list |
Not calling `pypath.inputs.kegg_api._kegg_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_relations |
Not calling `pypath.inputs.kegg_api._kegg_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2023-11-05 14:12:52 | 2023-11-05 14:12:55 | 3.30 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg_api.py", line 127, in drug_to_drug
entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg_api.py", line 465, in <dictcomp>
self.proc_key(entry[0]): self.proc_value(entry[1])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
return entry[0].split(':')[1]
IndexError: list index out of range
|
{} | 2023-10-20 17:41:33 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2023-11-05 14:12:55 | 2023-11-05 14:12:55 | 0.46 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/kinasedotcom.py", line 63, in kinasedotcom_annotations
uniprots = mapping.map_name(rec[23].strip(), 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:41:36 | |||
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2023-11-05 14:12:55 | 2023-11-05 14:13:01 | 5.32 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {} | 2023-11-05 14:12:55 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2023-11-05 14:13:01 | 2023-11-05 14:13:01 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/lambert2018.py", line 99, in lambert2018_annotations
for r in lambert2018_s1_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/lambert2018.py", line 39, in lambert2018_s1_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:41:40 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2023-11-05 14:13:01 | 2023-11-05 14:13:01 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/lambert2018.py", line 39, in lambert2018_s1_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 17:41:40 | |||
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2023-11-05 14:13:01 | 2023-11-05 14:13:02 | 0.52 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2023-11-05 14:13:01 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2023-11-05 14:13:02 | 2023-11-05 14:13:02 | 0.34 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2023-11-05 14:13:02 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2023-11-05 14:13:02 | 2023-11-05 14:13:10 | 7.95 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2023-11-05 14:13:02 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2023-11-05 14:13:10 | 2023-11-05 14:15:26 | 136.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/li2012.py", line 128, in li2012_dmi
se = seq.swissprot_seq(isoforms = True)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/seq.py", line 66, in swissprot_seq
data = uniprot_input.uniprot_data(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in uniprot_data
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in <genexpr>
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/curl.py", line 764, in iterfile
for line in fileobj:
File "/usr/lib/python3.10/gzip.py", line 314, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.10/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.10/gzip.py", line 496, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid block type
|
{} | 2023-10-20 17:41:50 | |||
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2023-11-05 14:15:26 | 2023-11-05 14:15:26 | 0.03 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2023-11-05 14:15:26 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2023-11-05 14:15:26 | 2023-11-05 14:15:26 | 0.03 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2023-11-05 14:15:26 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2023-11-05 14:15:26 | 2023-11-05 14:15:29 | 3.15 | dict | {'10001': LincsCompound(lincs='LSM-1001', chembl='CHEMBL14762', chebi='CHEBI:354.22', inchi='InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1', inchi_key='BTIHMVBBUGXLCJ-OAHLLOKOSA-N', smil...(truncated) | 1,320 | {} | 2023-11-05 14:15:26 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2023-11-05 14:15:29 | 2023-11-05 14:16:27 | 57.70 | list | [] | 0 | {} | 2023-11-05 14:15:29 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2023-11-05 14:16:27 | 2023-11-05 14:16:27 | 0.37 | list | [] | 0 | {} | 2023-11-05 14:16:27 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2023-11-05 14:16:27 | 2023-11-05 14:16:28 | 0.54 | list | [] | 0 | {} | 2023-11-05 14:16:27 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2023-11-05 14:16:28 | 2023-11-05 14:16:28 | 0.38 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) | 478 | {} | 2023-11-05 14:16:28 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2023-11-05 14:16:28 | 2023-11-05 14:16:29 | 0.52 | list | [] | 0 | {} | 2023-11-05 14:16:28 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2023-11-05 14:16:29 | 2023-11-05 14:16:35 | 5.67 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/locate.py", line 111, in locate_localizations
this_uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:14 | |||
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2023-11-05 14:16:35 | 2023-11-05 14:16:35 | 0.94 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/lrdb.py", line 111, in lrdb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:21 | |||
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2023-11-05 14:16:35 | 2023-11-05 14:16:35 | 0.03 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {} | 2023-11-05 14:16:35 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2023-11-05 14:16:35 | 2023-11-05 14:16:36 | 0.20 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2023-11-05 14:16:35 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2023-11-05 14:16:36 | 2023-11-05 14:16:38 | 2.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrisome.py", line 86, in __matrisome_annotations_2
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-10-20 17:43:21 | |||
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2023-11-05 14:16:38 | 2023-11-05 14:16:38 | 0.25 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrisome.py", line 62, in matrisome_annotations
uniprots = mapping.map_names(uniprots, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:23 | |||
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2023-11-05 14:16:38 | 2023-11-05 14:16:38 | 0.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 160, in matrixdb_annotations
for uniprot in method(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 127, in matrixdb_membrane_proteins
return _matrixdb_protein_list('membrane', organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 109, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:23 | |||
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2023-11-05 14:16:38 | 2023-11-05 14:16:38 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 144, in matrixdb_ecm_proteins
return _matrixdb_protein_list('ecm', organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 109, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:23 | |||
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2023-11-05 14:16:38 | 2023-11-05 14:16:39 | 0.14 | list | [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) | 425 | {} | 2023-11-05 14:16:38 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2023-11-05 14:16:39 | 2023-11-05 14:16:39 | 0.03 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 127, in matrixdb_membrane_proteins
return _matrixdb_protein_list('membrane', organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 109, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:23 | |||
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2023-11-05 14:16:39 | 2023-11-05 14:16:39 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 135, in matrixdb_secreted_proteins
return _matrixdb_protein_list('secreted', organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/matrixdb.py", line 109, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:23 | |||
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2023-11-05 14:16:39 | 2023-11-05 14:16:40 | 1.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mcam.py", line 33, in mcam_cell_adhesion_molecules
return {
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mcam.py", line 37, in <setcomp>
for uniprot in mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:23 | |||
| ¶ | pypath.inputs.membranome.membranome_annotations | 2023-11-05 14:16:40 | 2023-11-05 14:17:01 | 21.12 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/membranome.py", line 65, in membranome_annotations
uniprots = mapping.map_name(p['uniprotcode'], 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:43:25 | |||
| ¶ | pypath.inputs.mimp.get_kinase_class | 2023-11-05 14:17:01 | 2023-11-05 14:17:01 | 0.14 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2023-11-05 14:17:01 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2023-11-05 14:17:01 | 2023-11-05 14:17:04 | 3.15 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2023-11-05 14:17:01 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2023-11-05 14:17:04 | 2023-11-05 14:17:05 | 0.50 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2023-11-05 14:17:04 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2023-11-05 14:17:05 | 2023-11-05 14:17:05 | 0.21 | list | [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) | 805 | {} | 2023-11-05 14:17:05 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2023-11-05 14:17:05 | 2023-11-05 14:17:05 | 0.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:51 | |||
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2023-11-05 14:17:05 | 2023-11-05 14:17:05 | 0.17 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:51 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2023-11-05 14:17:05 | 2023-11-05 14:17:05 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 76, in mirbase_mature
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2023-11-05 14:17:05 | 2023-11-05 14:17:06 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 167, in mirbase_mature_all
return [i[0] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 167, in <listcomp>
return [i[0] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2023-11-05 14:17:06 | 2023-11-05 14:17:06 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 89, in mirbase_precursor
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2023-11-05 14:17:06 | 2023-11-05 14:17:06 | 0.17 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 172, in mirbase_precursor_all
return [i[1] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 172, in <listcomp>
return [i[1] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2023-11-05 14:17:06 | 2023-11-05 14:17:06 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 108, in mirbase_precursor_to_mature
for mmat, mpre in ids:
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:43:53 | |||
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2023-11-05 14:17:06 | 2023-11-05 14:17:06 | 0.22 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2023-11-05 14:17:06 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2023-11-05 14:17:06 | 2023-11-05 14:17:07 | 0.46 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism=9606, target_organism=9606, pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organism=10090, target_or...(truncated) | 3,106 | {} | 2023-11-05 14:17:06 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2023-11-05 14:17:07 | 2023-11-05 14:17:11 | 4.64 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirtarbase.py", line 40, in mirtarbase_interactions
result.extend(_mirtarbase_interactions('curated'))
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/mirtarbase.py", line 75, in _mirtarbase_interactions
tbl = inputs_common.read_xls(c.fileobj.name)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-10-20 17:43:53 | |||
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2023-11-05 14:17:12 | 2023-11-05 14:17:12 | 0.41 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2023-11-05 14:17:12 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2023-11-05 14:17:12 | 2023-11-05 14:18:00 | 48.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/msigdb.py", line 364, in msigdb_annotations
for uniprot in mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 17:44:01 | |||
| ¶ | pypath.inputs.msigdb.msigdb_download | 2023-11-05 14:18:00 | 2023-11-05 14:18:09 | 9.04 | dict | {'chr1p11': {'SRGAP2-AS1', 'LINC01691', 'PDE4DIPP2', 'LINC02798', 'RPL22P6', 'H3P4', 'SRGAP2C', 'RNVU1-19', 'H2BP1', 'LINC00623', 'PPIAL4A', 'NBPF8', 'RNVU1-4', 'FCGR1BP', 'PFN1P2', 'NOTCH2NLR', 'FAM72B', 'EMBP1', 'MTIF2P1', 'NBPF26', 'PDE4DIPP4'}, 'chr1p12': {'PSMC1P12', 'GAPDHP32', 'WDR3', 'NOTCH2...(truncated) | 33,591 | {} | 2023-11-05 14:18:00 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2023-11-05 14:18:10 | 2023-11-05 14:18:10 | 0.39 | dict | {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'PTPRE', 'HBEGF', 'KLF9', 'KLF2', 'CCNL1', 'CCL20', 'PTGER4', 'CXCL2', 'JUN', 'JAG1', 'IFNGR2', 'KYNU', 'AREG', 'GFPT2', 'SERPINB8', 'ETS2', 'PHLDA2', 'CXCL10', 'DRAM1', 'RNF19B', 'DENND5A', 'CSF1', 'DNAJB4', 'GPR183', 'HES1', 'TIPARP', '...(truncated) | 18 | {} | 2023-11-05 14:18:10 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2023-11-05 14:18:11 | 2023-11-05 14:18:11 | 0.35 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2023-11-05 14:18:11 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2023-11-05 14:18:11 | 2023-11-05 14:18:41 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/negatome.py", line 49, in negatome_interactions
for l in f:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-10-20 17:45:00 | |||
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2023-11-05 14:18:41 | 2023-11-05 14:18:41 | 0.14 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2023-11-05 14:18:41 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2023-11-05 14:18:41 | 2023-11-05 14:18:41 | 0.14 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {} | 2023-11-05 14:18:41 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2023-11-05 14:18:41 | 2023-11-05 14:21:43 | 181.27 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/netpath.py", line 43, in netpath_interactions
pwnames = netpath_names()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/netpath.py", line 151, in netpath_names
soup = bs4.BeautifulSoup(html, 'html.parser')
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-tWRce4VM-py3.10/lib/python3.10/site-packages/bs4/__init__.py", line 315, in __init__
elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
|
{} | 2023-10-20 17:45:31 | |||
| ¶ | pypath.inputs.netpath.netpath_names | 2023-11-05 14:21:43 | 2023-11-05 14:24:43 | 180.82 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/netpath.py", line 151, in netpath_names
soup = bs4.BeautifulSoup(html, 'html.parser')
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-tWRce4VM-py3.10/lib/python3.10/site-packages/bs4/__init__.py", line 315, in __init__
elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
|
{} | 2023-10-20 17:48:32 | |||
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2023-11-05 14:24:43 | 2023-11-05 14:30:45 | 361.78 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/netpath.py", line 184, in netpath_pathway_annotations
pathway_ids = netpath_names()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/netpath.py", line 151, in netpath_names
soup = bs4.BeautifulSoup(html, 'html.parser')
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-tWRce4VM-py3.10/lib/python3.10/site-packages/bs4/__init__.py", line 315, in __init__
elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
|
{} | 2023-10-20 17:51:32 | |||
| ¶ | pypath.inputs.offsides._sides_base |
Not calling `pypath.inputs.offsides._sides_base`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2023-11-05 14:30:45 | 2023-11-05 14:31:01 | 15.87 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {} | 2023-11-05 14:30:45 | |
| ¶ | pypath.inputs.oma._id_translate |
Not calling `pypath.inputs.oma._id_translate`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.oma.oma_orthologs | 2023-11-05 14:31:01 | 2023-11-05 14:32:21 | 80.11 | list | [OmaOrthology(a=OmaGene(id='LYPD3_HUMAN', oma_group=970406, hog='HOG:D0616795', taxon=9606, chr='19', start=43461351, end=43465571, strand=-1, main_isoform=True), b=OmaGene(id='LYPD3_MOUSE', oma_group=970406, hog='HOG:D0616795', taxon=10090, chr='7', start=24336015, end=24340026, strand=1, main_isof...(truncated) | 22,379 | {} | 2023-11-05 14:31:01 | |
| ¶ | pypath.inputs.oma.oma_table | 2023-11-05 14:32:21 | 2023-11-05 14:32:26 | 4.32 | defaultdict | defaultdict(<class 'set'>, {'LYPD3_HUMAN': {'LYPD3_MOUSE'}, 'DHB12_HUMAN': {'DHB12_MOUSE'}, 'SAP30_HUMAN': {'SAP30_MOUSE'}, 'HV103_HUMAN': {'A0A075B5Y5', 'A0A0G2JGK2', 'A0A0A6YXN4', 'A0A075B5T7', 'A0A075B5V5', 'A0A0A6YWX0', 'A0A075B5W5', 'A0A075B5X5', 'A0A075B5R7', 'A0A075B5Y6', 'A0A0A6YXJ9', 'A0A0A...(truncated) | 17,896 | {} | 2023-11-05 14:32:21 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2023-11-05 14:32:26 | 2023-11-05 14:32:26 | 0.69 | dict | {'aism': None, 'amphx': None, 'ado': None, 'apo': None, 'agro': None, 'apollo_sv': None, 'aro': None, 'bco': None, 'bfo': None, 'bspo': None, 'bto': None, 'caro': None, 'chebi': None, 'cdno': None, 'cdao': None, 'cheminf': None, 'chiro': None, 'chmo': None, 'cido': None, 'cio': None, 'cl': None, 'cl...(truncated) | 244 | {} | 2023-11-05 14:32:26 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets._opentargets_general |
Not calling `pypath.inputs.opentargets._opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2023-11-05 14:32:26 | 2023-11-05 14:32:51 | 24.44 | list | [{'chembl_id': 'CHEMBL1200632', 'event': 'acute generalised exanthematous pustulosis', 'count': 17, 'llr': 34.164839700408265, 'critval': 13.880781728509543, 'meddraCode': '10048799'}, {'chembl_id': 'CHEMBL1200632', 'event': 'anal ulcer', 'count': 5, 'llr': 16.745304158079307, 'critval': 13.88078172...(truncated) | 112,928 | {} | 2023-11-05 14:32:26 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2023-11-05 14:32:51 | 2023-11-05 14:41:54 | 543.65 | list | [{'id': 'ENSG00000020219', 'tissues': [{'efo_code': 'UBERON_0012249', 'label': 'ectocervix', 'organs': ['reproductive organ', 'reproductive structure'], 'anatomical_systems': ['reproductive system'], 'rna': {'value': 2.0, 'zscore': -1, 'level': -1, 'unit': 'TPM'}, 'protein': {'reliability': False, '...(truncated) | 43,791 | {} | 2023-11-05 14:32:51 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2023-11-05 14:41:54 | 2023-11-05 14:43:45 | 110.82 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) | 2,146,271 | {} | 2023-11-05 14:41:54 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2023-11-05 14:43:45 | 2023-11-05 14:49:04 | 318.64 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001617', 'score': 0.05099149718673741, 'evidenceCount': 4}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001626', 'score': 0.00792543466157194, 'evidenceCount': 3}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000002330', 'score': 0.003...(truncated) | 6,960,486 | {} | 2023-11-05 14:43:45 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2023-11-05 14:49:04 | 2023-11-05 14:51:24 | 140.30 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/opm.py", line 93, in opm_annotations
uniprot = mapping.map_name0(this_name, 'protein-name', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:20:04 | |||
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2023-11-05 14:51:24 | 2023-11-05 14:51:54 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/oreganno.py", line 72, in oreganno_interactions
for l in oreganno_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-10-20 18:20:24 | |||
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2023-11-05 14:51:54 | 2023-11-05 14:52:24 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-10-20 18:20:54 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2023-11-05 14:52:24 | 2023-11-05 14:52:25 | 0.32 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/panglaodb.py", line 80, in panglaodb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:21:24 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2023-11-05 14:52:25 | 2023-11-05 14:52:25 | 0.04 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2023-11-05 14:52:25 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2023-11-05 14:52:25 | 2023-11-05 14:52:25 | 0.00 | list | [] | 0 | {} | 2023-11-05 14:52:25 | |
| ¶ | pypath.inputs.pathwaycommons._create_single_resource_method |
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2023-11-05 14:52:25 | 2023-11-05 14:52:39 | 14.02 | list | [PathwayCommonsInteraction(id_a='ABAT', interaction_type='catalysis-precedes', id_b='ALDH5A1', resource='PANTHER'), PathwayCommonsInteraction(id_a='ABAT', interaction_type='catalysis-precedes', id_b='ALDH6A1', resource='PANTHER'), PathwayCommonsInteraction(id_a='ABAT', interaction_type='catalysis-pr...(truncated) | 1,261,865 | {} | 2023-11-05 14:52:25 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2023-11-05 14:52:40 | 2023-11-05 14:52:40 | 0.31 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2023-11-05 14:52:40 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2023-11-05 14:52:40 | 2023-11-05 14:52:46 | 6.54 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2023-11-05 14:52:40 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2023-11-05 14:52:49 | 2023-11-05 14:52:57 | 7.88 | dict | {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963, 'COMPLEX:P00669': Complex: COMPLEX:P00669, 'COMPLEX:P07378': Complex: COMPLEX:P07378, 'COMPLEX:P01837_P01869': Complex: COMPLEX...(truncated) | 43,987 | {} | 2023-11-05 14:52:49 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2023-11-05 14:52:57 | 2023-11-05 14:53:07 | 9.74 | tuple | ({'P02185': {('5ut8', 'X-ray', 1.78), ('1vxa', 'X-ray', 2.0), ('2g11', 'X-ray', 1.9), ('2zss', 'X-ray', 1.21), ('2zt2', 'X-ray', 1.21), ('5hlu', 'X-ray', 1.5), ('3e5i', 'X-ray', 1.22), ('3h57', 'X-ray', 1.7), ('1mlg', 'X-ray', 2.0), ('7l3y', 'X-ray', 1.18), ('1ufj', 'X-ray', 1.6), ('4tyx', 'X-ray', ...(truncated) | 2 | {} | 2023-11-05 14:52:57 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2023-11-05 14:53:07 | 2023-11-05 14:53:08 | 0.73 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {} | 2023-11-05 14:53:07 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2023-11-05 14:53:08 | 2023-11-05 15:05:17 | 728.71 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2023-11-05 14:53:08 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2023-11-05 15:05:17 | 2023-11-05 15:05:18 | 1.12 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2023-11-05 15:05:17 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2023-11-05 15:05:18 | 2023-11-05 15:05:21 | 3.48 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': PfamDomain(chain='A', star...(truncated) | 2 | {} | 2023-11-05 15:05:18 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2023-11-05 15:05:22 | 2023-11-05 15:11:05 | 342.68 | tuple | ({}, {}) | 2 | {} | 2023-11-05 15:05:22 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2023-11-05 15:11:05 | 2023-11-05 15:11:05 | 0.63 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pfam.py", line 94, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-10-20 18:42:14 | |||
| ¶ | pypath.inputs.pharos._create_query_functions | 2023-11-05 15:11:05 | 2023-11-05 15:11:05 | 0.00 | NoneType | None | 0 | {} | 2023-11-05 15:11:05 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2023-11-05 15:11:05 | 2023-11-05 15:11:24 | 19.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 279, in query_func
return pharos_targets(chunk_size = chunk_size, **args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 244, in pharos_targets
response = response['targets']['targets']
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 18:42:15 | |||
| ¶ | pypath.inputs.pharos.pharos_expression | 2023-11-05 15:11:24 | 2023-11-05 15:11:25 | 0.46 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 279, in query_func
return pharos_targets(chunk_size = chunk_size, **args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 244, in pharos_targets
response = response['targets']['targets']
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 18:43:31 | |||
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2023-11-05 15:11:25 | 2023-11-05 15:11:25 | 0.51 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 279, in query_func
return pharos_targets(chunk_size = chunk_size, **args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 244, in pharos_targets
response = response['targets']['targets']
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 18:43:36 | |||
| ¶ | pypath.inputs.pharos.pharos_ligands | 2023-11-05 15:11:25 | 2023-11-05 15:11:26 | 0.54 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 279, in query_func
return pharos_targets(chunk_size = chunk_size, **args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 244, in pharos_targets
response = response['targets']['targets']
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 18:43:40 | |||
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2023-11-05 15:11:26 | 2023-11-05 15:11:26 | 0.47 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 279, in query_func
return pharos_targets(chunk_size = chunk_size, **args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 244, in pharos_targets
response = response['targets']['targets']
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 18:43:44 | |||
| ¶ | pypath.inputs.pharos.pharos_targets | 2023-11-05 15:11:26 | 2023-11-05 15:12:04 | 37.98 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2023-11-05 15:11:26 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2023-11-05 15:12:04 | 2023-11-05 15:12:05 | 0.51 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 279, in query_func
return pharos_targets(chunk_size = chunk_size, **args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pharos.py", line 244, in pharos_targets
response = response['targets']['targets']
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-10-20 18:44:25 | |||
| ¶ | pypath.inputs.phobius.phobius_annotations | 2023-11-05 15:12:05 | 2023-11-05 15:12:05 | 0.43 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2023-11-05 15:12:05 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2023-11-05 15:12:05 | 2023-11-05 15:12:06 | 0.19 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/phosphatome.py", line 48, in phosphatome_annotations
path = science_input.science_download(url = url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 18:44:30 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2023-11-05 15:12:06 | 2023-11-05 15:12:07 | 1.59 | list | [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) | 2,426 | {} | 2023-11-05 15:12:06 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2023-11-05 15:12:07 | 2023-11-05 15:12:08 | 0.50 | list | [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) | 2,426 | {} | 2023-11-05 15:12:07 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2023-11-05 15:12:08 | 2023-11-05 15:12:08 | 0.16 | dict | {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) | 247 | {} | 2023-11-05 15:12:08 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2023-11-05 15:12:08 | 2023-11-05 15:12:09 | 1.52 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2023-11-05 15:12:08 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2023-11-05 15:12:09 | 2023-11-05 15:12:09 | 0.02 | list | [['CDK5', 'CTTN'], ['FGFR1', 'RPS6KA3'], ['CLK1', 'SFRS1'], ['STK40', 'IRF3'], ['LCK', 'IL2RB'], ['PRKAA2', 'CAMKK1'], ['PRKACA', 'TRIM28'], ['STK38', 'RAD23B'], ['MAPK3', 'GAB2'], ['CLK1', 'PPP2R5D'], ['MAPK3', 'MKNK1'], ['CSNK1E', 'PPP1R13L'], ['PTK6', 'RUVBL2'], ['PRKCA', 'SNAP23'], ['TGFBR2', 'R...(truncated) | 1,821 | {} | 2023-11-05 15:12:09 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2023-11-05 15:12:09 | 2023-11-05 15:12:10 | 0.26 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2023-11-05 15:12:09 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.05 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P45984', 'P46937'], ['P06493', 'Q9GZV5'], ['P11309', 'P52907'], ['O14757', 'Q...(truncated) | 8,971 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.39 | list | [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) | 13,459 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) | 2 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.07 | list | [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) | 9,041 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) | 4,309 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) | 2 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2023-11-05 15:12:10 | 2023-11-05 15:12:10 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'AB;WB;MA'...(truncated) | 4,732 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2023-11-05 15:12:10 | 2023-11-05 15:12:15 | 4.97 | dict | {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) | 198,635 | {} | 2023-11-05 15:12:10 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2023-11-05 15:12:16 | 2023-11-05 15:12:16 | 0.38 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/phosphosite.py", line 331, in phosphosite_ptms
res = intera.Residue(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/internals/intera.py", line 86, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 128, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 464, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3703, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2663, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2041, in map_name
uniprots = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:44:40 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2023-11-05 15:12:16 | 2023-11-05 15:12:17 | 0.61 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'protein degradation', 'intracellular localization', 'phosphorylation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {} | 2023-11-05 15:12:16 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2023-11-05 15:12:17 | 2023-11-05 15:14:36 | 138.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/phosphosite.py", line 511, in phosphosite_regsites_one_organism
dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/phosphosite.py", line 516, in <lambda>
homologene.homologene_uniprot_dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/homologene.py", line 176, in homologene_uniprot_dict
mapping.map_name(e, 'entrez', 'uniprot', target)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:44:41 | |||
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2023-11-05 15:14:36 | 2023-11-05 15:20:36 | 360.02 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2023-11-05 15:14:36 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2023-11-05 15:20:36 | 2023-11-05 15:20:36 | 0.41 | list | [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) | 320,143 | {} | 2023-11-05 15:20:36 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2023-11-05 15:20:36 | 2023-11-05 15:20:39 | 2.79 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/progeny.py", line 104, in progeny_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:51:15 | |||
| ¶ | pypath.inputs.progeny.progeny_raw | 2023-11-05 15:20:39 | 2023-11-05 15:20:41 | 1.70 | DataFrame | gene pathway weight p.value 1 RFC2 EGFR 1.470647 0.001655 2 ESRRA EGFR 0.178590 0.211838 3 HNRNPK EGFR 0.306699 0.084560 4 CBX6 EGFR -0.675507 0.017641 5 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2023-11-05 15:20:39 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2023-11-05 15:20:41 | 2023-11-05 15:20:41 | 0.37 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/proteinatlas.py", line 55, in get_proteinatlas
uniprots = mapping.map_name(l[1], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:51:20 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2023-11-05 15:20:41 | 2023-11-05 15:20:41 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/proteinatlas.py", line 120, in proteinatlas_annotations
data = get_proteinatlas(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/proteinatlas.py", line 55, in get_proteinatlas
uniprots = mapping.map_name(l[1], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:51:20 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2023-11-05 15:20:41 | 2023-11-05 15:20:41 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/proteinatlas.py", line 247, in proteinatlas_secretome_annotations
path = science.science_download(url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 18:51:20 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2023-11-05 15:20:41 | 2023-11-05 15:20:41 | 0.27 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/proteinatlas.py", line 219, in proteinatlas_subcellular_annotations
uniprots = mapping.map_name(rec['Gene name'], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 18:51:20 | |||
| ¶ | pypath.inputs.proteins.variants | 2023-11-05 15:20:41 | 2023-11-05 15:31:21 | 639.32 | list | [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) | 48,576 | {} | 2023-11-05 15:20:41 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2023-11-05 15:31:21 | 2023-11-05 15:31:30 | 8.84 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) | 2 | {} | 2023-11-05 15:31:21 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2023-11-05 15:31:31 | 2023-11-05 15:31:31 | 0.56 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'24357804', '24727247', '22304920', '25728676', '25545367'}, 'substrate': 'P15336', 'databases': {'SIGNOR', 'REACH', 'Sparser', 'PhosphoSite'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'24727247', '23708658'}, ...(truncated) | 22,139 | {} | 2023-11-05 15:31:31 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2023-11-05 15:31:31 | 2023-11-05 15:31:32 | 0.57 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2023-11-05 15:31:31 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2023-11-05 15:31:32 | 2023-11-05 15:31:35 | 3.35 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/ramilowski2015.py", line 153, in ramilowski_locations
uniprots = mapping.map_name(l[3], 'uniprot', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:03:22 | |||
| ¶ | pypath.inputs.ramp._ramp_sqldump | 2023-11-05 15:31:35 | 2023-11-05 15:31:41 | 5.51 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/cache/2ac9fe4b32649e946c59f28f74943748-38534654' encoding='utf-8'> | 0 | {} | 2023-11-05 15:31:35 | |
| ¶ | pypath.inputs.ramp.ramp_id_types | 2023-11-05 15:31:41 | 2023-11-05 15:39:16 | 455.63 | set | {'plantfa', 'pubchem', 'uniprot', 'entrez', 'swisslipids', 'wikidata', 'gene_symbol', 'kegg', 'brenda', 'hmdb', 'CAS', 'ensembl', 'EN', 'ncbiprotein', 'LIPIDMAPS', 'chebi', 'kegg_glycan', 'lipidbank', 'chemspider'} | 19 | {} | 2023-11-05 15:31:41 | |
| ¶ | pypath.inputs.ramp.ramp_id_types_2 | 2023-11-05 15:39:16 | 2023-11-05 15:39:24 | 8.10 | set | {'plantfa', 'pubchem', 'uniprot', 'entrez', 'swisslipids', 'wikidata', 'gene_symbol', 'kegg', 'polymer', 'brenda', 'hmdb', 'CAS', 'ensembl', 'EN', 'ncbiprotein', 'LIPIDMAPS', 'chebi', 'kegg_glycan', 'lipidbank', 'chemspider', 'rhea-comp'} | 21 | {} | 2023-11-05 15:39:16 | |
| ¶ | pypath.inputs.ramp.ramp_list_tables | 2023-11-05 15:39:24 | 2023-11-05 15:39:27 | 2.37 | dict | {'analyte': ['rampId', 'type'], 'analytehasontology': ['rampCompoundId', 'rampOntologyId'], 'analytehaspathway': ['rampId', 'pathwayRampId', 'pathwaySource'], 'analytesynonym': ['Synonym', 'rampId', 'geneOrCompound', 'source'], 'catalyzed': ['rampCompoundId', 'rampGeneId'], 'chem_props': ['ramp_id',...(truncated) | 13 | {} | 2023-11-05 15:39:24 | |
| ¶ | pypath.inputs.ramp.ramp_mapping |
Not calling `pypath.inputs.ramp.ramp_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_raw |
Not calling `pypath.inputs.ramp.ramp_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_show_tables | 2023-11-05 15:39:27 | 2023-11-05 15:39:29 | 2.33 | NoneType | None | 0 | {} | 2023-11-05 15:39:27 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2023-11-05 15:39:29 | 2023-11-05 15:39:29 | 0.00 | NoneType | None | 0 | {} | 2023-11-05 15:39:29 | |
| ¶ | pypath.inputs.rdata._rdata_data_frame_get_rownames |
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.rdata._rdata_list_get_names |
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._bp_collect_resources |
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._process_controls |
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_resources |
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_species |
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_compartment |
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_id |
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_res |
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_id |
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reaction |
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reactions | 2023-11-05 15:39:29 | 2023-11-05 15:39:29 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 966, in _reactome_reactions
for pw, soup in soups:
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 134, in reactome_bs
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-10-20 19:11:18 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2023-11-05 15:39:29 | 2023-11-05 15:39:29 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 1032, in _reactome_reactions_et
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-10-20 19:11:18 | |||
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2023-11-05 15:39:29 | 2023-11-05 15:39:40 | 11.03 | list | ['<?xml version="1.0" encoding="UTF-8"?>\n', '<rdf:RDF\n', ' xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n', ' xmlns:owl="http://www.w3.org/2002/07/owl#"\n', ' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n', ' xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"\n', ' xml:base="...(truncated) | 190,854 | {} | 2023-11-05 15:39:29 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2023-11-05 15:39:40 | 2023-11-05 15:39:40 | 0.09 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2023-11-05 15:39:40 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2023-11-05 15:39:40 | 2023-11-05 15:39:41 | 0.33 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/pyreact.py", line 1295, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/pyreact.py", line 1171, in load_wikipathways
len(biopaxes.result),
TypeError: object of type 'NoneType' has no len()
|
{} | 2023-10-20 19:11:20 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2023-11-05 15:39:41 | 2023-11-05 15:39:47 | 6.38 | dict | {'BioPAX/2-arachidonoylglycerol_biosynthesis.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/5-Hydroxytryptamine_biosynthesis.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypa...(truncated) | 178 | {} | 2023-11-05 15:39:41 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2023-11-05 15:39:47 | 2023-11-05 15:39:49 | 2.53 | NoneType | None | 0 | {} | 2023-11-05 15:39:47 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2023-11-05 15:39:49 | 2023-11-05 15:39:49 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 79, in reactome_biopax
url = urls.urls['reactome']['biopax_l3']
KeyError: 'biopax_l3'
|
{} | 2023-10-20 19:11:29 | |||
| ¶ | pypath.inputs.reaction.reactome_bs | 2023-11-05 15:39:49 | 2023-11-05 15:39:49 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 134, in reactome_bs
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-10-20 19:11:29 | |||
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2023-11-05 15:39:49 | 2023-11-05 15:39:49 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-10-20 19:11:29 | |||
| ¶ | pypath.inputs.reactome._reactome_data |
Not calling `pypath.inputs.reactome._reactome_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome._reactome_data_gen |
Not calling `pypath.inputs.reactome._reactome_data_gen`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome.reactome_chebis | 2023-11-05 15:39:49 | 2023-11-05 15:39:55 | 5.78 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-10-20 19:11:29 | |||
| ¶ | pypath.inputs.reactome.reactome_pathway_relations | 2023-11-05 15:39:55 | 2023-11-05 15:39:56 | 0.82 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-10-20 19:11:39 | |||
| ¶ | pypath.inputs.reactome.reactome_pathways | 2023-11-05 15:39:56 | 2023-11-05 15:39:57 | 1.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-10-20 19:11:40 | |||
| ¶ | pypath.inputs.reactome.reactome_uniprots | 2023-11-05 15:39:57 | 2023-11-05 15:40:24 | 26.96 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-10-20 19:11:41 | |||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2023-11-05 15:40:24 | 2023-11-05 15:40:25 | 0.34 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 109, in scconnect_annotations
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 110, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:03 | |||
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2023-11-05 15:40:25 | 2023-11-05 15:40:25 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 148, in scconnect_complexes
annot = scconnect_annotations(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 109, in scconnect_annotations
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 110, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:03 | |||
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2023-11-05 15:40:25 | 2023-11-05 15:40:25 | 0.81 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 258, in scconnect_interactions
for ligand_target in itertools.product(ligands, targets):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 197, in process_partner
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/scconnect.py", line 198, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:03 | |||
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2023-11-05 15:40:25 | 2023-11-05 15:40:25 | 0.13 | dict | {'CID100004044': {SiderDrug(name='mefenamic', atc='M01AG01')}, 'CID100005333': {SiderDrug(name='sulfonamide', atc='D06BA05'), SiderDrug(name='sulfonamide', atc='J01EB06')}, 'CID100003032': {SiderDrug(name='diclofenac', atc='M01AB05'), SiderDrug(name='diclofenac', atc='M02AA15'), SiderDrug(name='dicl...(truncated) | 1,430 | {} | 2023-11-05 15:40:25 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2023-11-05 15:40:25 | 2023-11-05 15:40:26 | 0.45 | list | [SiderSideeffectMeddra(cid='C0423282', meddra_id='10053781', side_effect_name='Anterior chamber cell'), SiderSideeffectMeddra(cid='C1141905', meddra_id='10057972', side_effect_name='Bone callus excessive'), SiderSideeffectMeddra(cid='C0581142', meddra_id='10051006', side_effect_name='Plasma cell cou...(truncated) | 20,307 | {} | 2023-11-05 15:40:25 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2023-11-05 15:40:26 | 2023-11-05 15:40:28 | 1.56 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0030252', umls_concept_in_meddra='C0030252', side_effect='Palpitations', frequency='3%'), SiderSideeffetFrequency(umls_concept_on_label='C0013378', umls_concept_in_meddra='C0013378', side_effect='Dysgeusia', frequency='3%'), SiderSide...(truncated) | 968 | {} | 2023-11-05 15:40:26 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2023-11-05 15:40:28 | 2023-11-05 15:40:29 | 1.37 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0042373', umls_concept_in_meddra='C0042373', side_effect='Angiopathy'), SiderSideeffect(umls_concept_on_label='C0015230', umls_concept_in_meddra='C0011603', side_effect='Dermatitis'), SiderSideeffect(umls_concept_on_label='C0025222', umls_con...(truncated) | 1,430 | {} | 2023-11-05 15:40:28 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2023-11-05 15:40:29 | 2023-11-05 15:40:30 | 1.26 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signalink.py", line 198, in signalink_annotations
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:08 | |||
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2023-11-05 15:40:30 | 2023-11-05 15:40:31 | 0.48 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signalink.py", line 223, in signalink_function_annotations
return signalink_annotations(organism = organism)['function']
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signalink.py", line 198, in signalink_annotations
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:09 | |||
| ¶ | pypath.inputs.signalink.signalink_interactions | 2023-11-05 15:40:31 | 2023-11-05 15:40:31 | 0.49 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {} | 2023-11-05 15:40:31 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2023-11-05 15:40:31 | 2023-11-05 15:40:32 | 0.48 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signalink.py", line 218, in signalink_pathway_annotations
return signalink_annotations(organism = organism)['pathway']
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signalink.py", line 198, in signalink_annotations
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:10 | |||
| ¶ | pypath.inputs.signor.signor_complexes | 2023-11-05 15:40:32 | 2023-11-05 15:40:33 | 0.64 | dict | {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4...(truncated) | 4,880 | {} | 2023-11-05 15:40:32 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2023-11-05 15:40:33 | 2023-11-05 15:40:35 | 2.19 | list | [{'typ': 'phosphorylation', 'resnum': 143, 'instance': 'RCFTRKYTLPPGVDP', 'substrate': 'P04792', 'start': 136, 'end': 150, 'kinase': 'Q13976', 'resaa': 'T', 'motif': 'RCFTRKYTLPPGVDP', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'19593530'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) | 10,713 | {} | 2023-11-05 15:40:33 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2023-11-05 15:40:35 | 2023-11-05 15:40:35 | 0.54 | list | [SignorInteraction(source='Q13976', target='P04792', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='down-regulates', mechanism='phosphorylation', ncbi_tax_id='9606', pubmeds='19593530', direct=True, ptm_type='phosphorylation', ptm_residue='Thr143', pt...(truncated) | 90,938 | {} | 2023-11-05 15:40:35 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2023-11-05 15:40:36 | 2023-11-05 15:40:37 | 1.22 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signor.py", line 330, in signor_pathway_annotations
proteins, interactions = signor_pathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/signor.py", line 307, in signor_pathways
mapping.map_name(row[4], 'uniprot', 'uniprot'),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:14 | |||
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2023-11-05 15:40:37 | 2023-11-05 15:40:37 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 90 | {} | 2023-11-05 15:40:37 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2023-11-05 15:40:37 | 2023-11-05 15:40:46 | 9.32 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/spike.py", line 187, in spike_complexes
interactions = spike_interactions(min_confidence = min_confidence)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/spike.py", line 107, in spike_interactions
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/spike.py", line 108, in <listcomp>
mapping.map_name(genes[m][0].entrez, 'entrez', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:15 | |||
| ¶ | pypath.inputs.spike.spike_interactions | 2023-11-05 15:40:46 | 2023-11-05 15:40:48 | 1.98 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/spike.py", line 107, in spike_interactions
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/spike.py", line 108, in <listcomp>
mapping.map_name(genes[m][0].entrez, 'entrez', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:12:24 | |||
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2023-11-05 15:40:48 | 2023-11-05 15:42:05 | 76.70 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {} | 2023-11-05 15:40:48 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2023-11-05 15:42:05 | 2023-11-05 15:43:32 | 87.66 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {} | 2023-11-05 15:42:05 | |
| ¶ | pypath.inputs.string.string_effects | 2023-11-05 15:43:32 | 2023-11-05 15:43:33 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/string.py", line 64, in string_effects
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-10-20 19:15:09 | |||
| ¶ | pypath.inputs.string.string_links_interactions | 2023-11-05 15:43:33 | 2023-11-05 15:43:59 | 26.87 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) | 201,712 | {} | 2023-11-05 15:43:33 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2023-11-05 15:43:59 | 2023-11-05 15:44:01 | 1.30 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {} | 2023-11-05 15:43:59 | |
| ¶ | pypath.inputs.string.string_species | 2023-11-05 15:44:01 | 2023-11-05 15:44:01 | 0.14 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {} | 2023-11-05 15:44:01 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2023-11-05 15:44:01 | 2023-11-05 15:44:03 | 2.30 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/surfaceome.py", line 37, in surfaceome_annotations
raw = inputs_common.read_xls(xlsname, 'in silico surfaceome only')[2:]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-10-20 19:15:49 | |||
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2023-11-05 15:44:03 | 2023-11-05 15:44:09 | 5.40 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2023-11-05 15:44:03 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2023-11-05 15:44:09 | 2023-11-05 15:44:09 | 0.58 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/talklr.py", line 105, in talklr_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:15:58 | |||
| ¶ | pypath.inputs.talklr.talklr_interactions | 2023-11-05 15:44:09 | 2023-11-05 15:44:09 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {} | 2023-11-05 15:44:09 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2023-11-05 15:44:09 | 2023-11-05 15:44:09 | 0.02 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2023-11-05 15:44:09 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2023-11-05 15:44:09 | 2023-11-05 15:44:14 | 5.04 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/tcdb.py", line 99, in tcdb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3592, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:15:59 | |||
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2023-11-05 15:44:14 | 2023-11-05 15:44:14 | 0.03 | dict | {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) | 23,441 | {} | 2023-11-05 15:44:14 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2023-11-05 15:44:14 | 2023-11-05 15:44:14 | 0.01 | dict | {'1.A.1': 'Voltage-gated Ion Channel (VIC)', '1.A.10': 'Glutamate-gated Ion Channel (GIC) of Neurotransmitter Receptors', '1.A.100': 'Rhabdoviridae Putative Viroporin, U5 (RV-U5)', '1.A.101': 'Peroxisomal Pore-forming Pex11 (Pex11)', '1.A.102': 'Influenza A viroporin PB1-F2 (PB1-F2)', '1.A.103': 'Si...(truncated) | 1,901 | {} | 2023-11-05 15:44:14 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2023-11-05 15:44:14 | 2023-11-05 15:44:15 | 0.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/tfcensus.py", line 67, in tfcensus_annotations
uniprots = mapping.map_names(ensg, 'ensembl', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3682, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2332, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2334, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:16:05 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2023-11-05 15:44:15 | 2023-11-05 15:44:18 | 3.87 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2023-11-05 15:44:15 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2023-11-05 15:44:19 | 2023-11-05 15:44:40 | 21.08 | set | {ThreedcomplexContact(pdb='3byz_2', uniprot_1='P28845', uniprot_2='P28845', chain_1='D', chain_2='C', n_residues=47.0, length_1=261, length_2=255, domain_s1=('51735',), domain_p1=('PF00106.20',), domain_s2=('51735',), domain_p2=('PF00106.20',), ident=True, homo=True), ThreedcomplexContact(pdb='1k9m_...(truncated) | 259,798 | {} | 2023-11-05 15:44:19 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2023-11-05 15:44:41 | 2023-11-05 15:47:28 | 167.22 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/threedcomplex.py", line 105, in threedcomplex_ddi
dom1 = intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/internals/intera.py", line 651, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 128, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 464, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3703, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2663, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2041, in map_name
uniprots = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:16:31 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2023-11-05 15:47:28 | 2023-11-05 15:47:38 | 9.78 | dict | {'3byz_2': {('P28845', 'P28845'): 47.0}, '1k9m_1': {('P22452', 'P32410'): 2.5, ('P20279', 'P29198'): 5.5, ('P12732', 'P22452'): 4.5, ('P12734', 'P14123'): 10.0, ('P12737', 'P32411'): 1.0, ('P10971', 'P12732'): 6.5, ('P14116', 'P22450'): 10.5, ('P14116', 'P20279'): 4.0, ('P20279', 'P22450'): 5.0, ('P...(truncated) | 81,192 | {} | 2023-11-05 15:47:28 | |
| ¶ | pypath.inputs.threedid.get_3did | 2023-11-05 15:47:38 | 2023-11-05 15:48:14 | 36.25 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/threedid.py", line 361, in get_3did
dom1 = intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/internals/intera.py", line 651, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 128, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/core/entity.py", line 464, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3703, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2663, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2041, in map_name
uniprots = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:19:29 | |||
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2023-11-05 15:48:14 | 2023-11-05 15:48:17 | 3.41 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/threedid.py", line 54, in get_3did_ddi
u_pfam, pfam_u = pfam_input.pfam_uniprot(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/pfam.py", line 94, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-10-20 19:20:11 | |||
| ¶ | pypath.inputs.topdb.topdb_annotations | 2023-11-05 15:48:17 | 2023-11-05 15:48:18 | 0.59 | dict | {} | 0 | {} | 2023-11-05 15:48:17 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2023-11-05 15:48:18 | 2023-11-05 15:48:19 | 1.17 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2023-11-05 15:48:18 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2023-11-05 15:48:19 | 2023-11-05 15:48:19 | 0.01 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2023-11-05 15:48:19 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2023-11-05 15:48:19 | 2023-11-05 15:48:19 | 0.01 | list | [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '12601176;11290752;11983166', 'Calcium measurement;Fusion protein-pull down assay;Patch clamp;Fl...(truncated) | 359 | {} | 2023-11-05 15:48:19 | |
| ¶ | pypath.inputs.trip.trip_process | 2023-11-05 15:48:19 | 2023-11-05 15:48:19 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'Rat aortic vascular smooth muscle cell', 'Porcine coronary artery', 'Rat vascular smooth muscle cell', 'HEK293'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2023-11-05 15:48:19 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2023-11-05 15:48:19 | 2023-11-05 15:48:23 | 3.58 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2023-11-05 15:48:19 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2023-11-05 15:48:23 | 2023-11-05 15:48:23 | 0.01 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2023-11-05 15:48:23 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2023-11-05 15:48:23 | 2023-11-05 15:48:26 | 2.87 | list | [TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bak1', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bax', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bbc3', ...(truncated) | 7,057 | {} | 2023-11-05 15:48:23 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2023-11-05 15:48:26 | 2023-11-05 15:51:52 | 206.71 | list | [TwosidesInteraction(drug1_rxnorm='10355', drug1='Temazepam', drug2_rxnorm='136411', drug2='sildenafil', condition_meddra='10003239', condition='Arthralgia', prr='2.91667', pee_error='0.421275', mean_reporting_frequency='0.0448718'), TwosidesInteraction(drug1_rxnorm='1808', drug1='Bumetanide', drug2...(truncated) | 42,920,391 | {} | 2023-11-05 15:48:26 | |
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2023-11-05 15:51:52 | 2023-11-05 15:51:53 | 0.03 | list | [UnichemSource(number='1', label='chembl', name='ChEMBL', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) | 41 | {} | 2023-11-05 15:51:52 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2023-11-05 15:51:53 | 2023-11-05 15:51:53 | 0.02 | dict | {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma', '22': 'pubc...(truncated) | 41 | {} | 2023-11-05 15:51:53 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2023-11-05 15:51:53 | 2023-11-05 15:51:53 | 0.05 | set | {'B4DFI7', 'Q8NGP0', 'A0A0G3VSP7', 'Q7Z4V5', 'A0A3S6RF51', 'B4DVE4', 'Q96S37', 'A1A4C0', 'A0A8Q3SI09', 'A0A6B7IK07', 'A0A8V8TP55', 'A0A1X6WJC9', 'A0A678ZVA1', 'A0A180H6J9', 'A0A075B720', 'A0A0A0MRH8', 'A0A6B7FV33', 'A0A059QQF0', 'A0A5C2G9Y7', 'P0C604', 'B3KN28', 'Q8N807', 'X6REY2', 'A0A059QR71', 'A0...(truncated) | 207,933 | {} | 2023-11-05 15:51:53 | |
| ¶ | pypath.inputs.uniprot._protein_datasheet |
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot._swissprot_param |
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2023-11-05 15:51:53 | 2023-11-05 15:51:53 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:23:39 | |||
| ¶ | pypath.inputs.uniprot.idmapping_idtypes | 2023-11-05 15:51:53 | 2023-11-05 15:51:53 | 0.03 | set | {('RGD', 'UniProtKB-Swiss-Prot'), ('UniProtKB_AC-ID', 'VGNC'), ('UniProtKB_AC-ID', 'RGD'), ('UniProtKB', 'PomBase'), ('UniProtKB-Swiss-Prot', 'ChEMBL'), ('UniProtKB_AC-ID', 'OMA'), ('EchoBASE', 'UniProtKB'), ('UniProtKB', 'CGD'), ('EchoBASE', 'UniProtKB-Swiss-Prot'), ('UniProtKB-Swiss-Prot', 'HOGENO...(truncated) | 491 | {} | 2023-11-05 15:51:53 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2023-11-05 15:51:53 | 2023-11-05 15:54:10 | 137.81 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 587, in uniprot_families
data = uniprot_data(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in uniprot_data
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in <genexpr>
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/curl.py", line 764, in iterfile
for line in fileobj:
File "/usr/lib/python3.10/gzip.py", line 314, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.10/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.10/gzip.py", line 496, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid stored block lengths
|
{} | 2023-10-20 19:23:39 | |||
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2023-11-05 15:54:10 | 2023-11-05 15:56:26 | 135.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 552, in uniprot_keywords
data = uniprot_data(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in uniprot_data
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in <genexpr>
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/curl.py", line 764, in iterfile
for line in fileobj:
File "/usr/lib/python3.10/gzip.py", line 314, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.10/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.10/gzip.py", line 496, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid literal/length code
|
{} | 2023-10-20 19:23:56 | |||
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2023-11-05 15:56:26 | 2023-11-05 15:58:44 | 138.18 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 520, in uniprot_locations
data = uniprot_preprocess(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 468, in uniprot_preprocess
data = uniprot_data(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in uniprot_data
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in <genexpr>
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/curl.py", line 764, in iterfile
for line in fileobj:
File "/usr/lib/python3.10/gzip.py", line 314, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.10/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.10/gzip.py", line 496, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid distance code
|
{'broke': True} | 2023-11-04 16:55:56 | |||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2023-11-05 15:58:44 | 2023-11-05 15:58:44 | 0.12 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,485 | {} | 2023-11-05 15:58:44 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2023-11-05 15:58:44 | 2023-11-05 15:58:46 | 1.64 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Pinus balsamea', 'Abies balsamea', 'Balsam fir'}, 'H8ZM71': {'Pinus balsamea', 'Abies balsamea', 'Balsam fir'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Pinus grandis', 'Grand fir', 'Abie...(truncated) | 555,648 | {} | 2023-11-05 15:58:44 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2023-11-05 15:58:46 | 2023-11-05 15:59:05 | 18.66 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Myeloid dendritic cells', level='undefined'), UniprotTissue(ti...(truncated) | 10,083 | {} | 2023-11-05 15:58:46 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2023-11-05 15:59:05 | 2023-11-05 16:02:23 | 198.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 647, in uniprot_topology
data = uniprot_data(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in uniprot_data
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 441, in <genexpr>
_id, *variables = zip(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/curl.py", line 764, in iterfile
for line in fileobj:
File "/usr/lib/python3.10/gzip.py", line 314, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.10/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.10/gzip.py", line 496, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid block type
|
{} | 2023-10-20 19:24:52 | |||
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db._cleanup | 2023-11-05 16:02:23 | 2023-11-05 16:02:23 | 0.00 | NoneType | None | 0 | {} | 2023-11-05 16:02:23 | |
| ¶ | pypath.inputs.uniprot_db._remove |
Not calling `pypath.inputs.uniprot_db._remove`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2023-11-05 16:02:23 | 2023-11-05 16:02:23 | 0.00 | set | {'Q8NGP0', 'P31153', 'Q7Z4V5', 'Q9Y3C8', 'Q96S37', 'P33241', 'Q15008', 'Q16850', 'P0DN77', 'P0C604', 'Q9BUX1', 'Q8N807', 'P54829', 'Q6P5X5', 'A2RU30', 'Q15072', 'Q32MH5', 'P40306', 'O60481', 'Q7Z3Q1', 'Q5GH70', 'P0DJD4', 'Q9UJS0', 'Q676U5', 'P25963', 'Q8IV33', 'Q08257', 'Q9Y478', 'Q6WN34', 'Q9GZS1',...(truncated) | 20,426 | {} | 2023-11-05 16:02:23 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2023-11-05 16:02:23 | 2023-11-05 16:23:04 | 1,241.58 | set | {'B4DFI7', 'A0A0G3VSP7', 'A0A3S6RF51', 'B4DVE4', 'A1A4C0', 'A0A8Q3SI09', 'A0A6B7IK07', 'A0A8V8TP55', 'A0A1X6WJC9', 'A0A678ZVA1', 'A0A180H6J9', 'A0A075B720', 'A0A0A0MRH8', 'A0A6B7FV33', 'A0A059QQF0', 'A0A5C2G9Y7', 'B3KN28', 'X6REY2', 'A0A059QR71', 'A0A0A7C743', 'B4DP73', 'A0A1U9X7L7', 'A0A2R8YE65', '...(truncated) | 187,508 | {'size': 1} | 2023-11-05 16:02:23 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2023-11-05 16:23:04 | 2023-11-05 16:23:05 | 0.04 | set | {'B4DFI7', 'Q8NGP0', 'A0A0G3VSP7', 'Q7Z4V5', 'A0A3S6RF51', 'B4DVE4', 'Q96S37', 'A1A4C0', 'A0A8Q3SI09', 'A0A6B7IK07', 'A0A8V8TP55', 'A0A1X6WJC9', 'A0A678ZVA1', 'A0A180H6J9', 'A0A075B720', 'A0A0A0MRH8', 'A0A6B7FV33', 'A0A059QQF0', 'A0A5C2G9Y7', 'P0C604', 'B3KN28', 'Q8N807', 'X6REY2', 'A0A059QR71', 'A0...(truncated) | 207,933 | {} | 2023-11-05 16:23:04 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2023-11-05 16:23:05 | 2023-11-05 16:23:05 | 0.00 | set | {'B4DFI7', 'Q8NGP0', 'A0A0G3VSP7', 'Q7Z4V5', 'A0A3S6RF51', 'B4DVE4', 'Q96S37', 'A1A4C0', 'A0A8Q3SI09', 'A0A6B7IK07', 'A0A8V8TP55', 'A0A1X6WJC9', 'A0A678ZVA1', 'A0A180H6J9', 'A0A075B720', 'A0A0A0MRH8', 'A0A6B7FV33', 'A0A059QQF0', 'A0A5C2G9Y7', 'P0C604', 'B3KN28', 'Q8N807', 'X6REY2', 'A0A059QR71', 'A0...(truncated) | 207,933 | {} | 2023-11-05 16:23:05 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2023-11-05 16:23:05 | 2023-11-05 16:23:05 | 0.05 | NoneType | None | 0 | {} | 2023-11-05 16:23:05 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang._wang_process |
Not calling `pypath.inputs.wang._wang_process`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang.cui_interactions | 2023-11-05 16:23:05 | 2023-11-05 16:23:09 | 4.56 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2023-11-05 16:23:05 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2023-11-05 16:23:09 | 2023-11-05 16:23:10 | 0.54 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2023-11-05 16:23:09 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2023-11-05 16:23:10 | 2023-11-05 16:23:10 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/wang.py", line 262, in wang_annotations
data = func()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/ca1.py", line 53, in ca1_interactions
path = science_input.science_download(url = url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 19:27:29 | |||
| ¶ | pypath.inputs.wang.wang_interactions | 2023-11-05 16:23:10 | 2023-11-05 16:23:10 | 0.45 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2023-11-05 16:23:10 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2023-11-05 16:23:10 | 2023-11-05 16:23:11 | 0.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/wojtowicz2020.py", line 79, in wojtowicz2020_interactions
for rec in wojtowicz2020_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/wojtowicz2020.py", line 37, in wojtowicz2020_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 19:27:30 | |||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2023-11-05 16:23:11 | 2023-11-05 16:23:11 | 0.19 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/wojtowicz2020.py", line 37, in wojtowicz2020_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-10-20 19:27:30 | |||
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2023-11-05 16:23:11 | 2023-11-05 16:23:11 | 0.19 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/zhong2015.py", line 57, in zhong2015_annotations
uniprot = mapping.map_name0(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3623, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1831, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2225, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2254, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2866, in primary_uniprot
primary = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/share/common.py", line 2786, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2010, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 2542, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 1602, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 3240, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/utils/mapping.py", line 561, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20231105-115102/pypath_git/pypath/inputs/uniprot.py", line 341, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
NameError: name 'all_uniprots' is not defined
|
{} | 2023-10-20 19:27:30 |
The OmniPath Team • Saez Lab • 2023-11-05