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 2024-04-08 14:56:39 and 2024-04-08 18:36:07; pypath version: 0.16.11 (from git, installed by poetry; 8784796 )
| Modules collected: | 184 |
|---|---|
| Modules failed to import: | 1 |
| Functions collected: | 623 |
| Functions run without error: | 293 |
| Functions returned empty value: | 25 |
| Functions skipped due to lack of arguments: | 179 |
| Functions run with error: | 151 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2024-04-08 14:56:43 | 2024-04-08 14:56:43 | 0.43 | 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 | {'first': True} | 2024-04-08 14:56:43 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2024-04-08 14:56:43 | 2024-04-08 14:56:44 | 0.65 | 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 | {'first': True} | 2024-04-08 14:56:43 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2024-04-08 14:56:44 | 2024-04-08 14:56:44 | 0.49 | 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 | {'first': True} | 2024-04-08 14:56:44 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2024-04-08 14:56:44 | 2024-04-08 14:58:18 | 93.88 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {'first': True} | 2024-04-08 14:56:44 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2024-04-08 14:58:18 | 2024-04-08 14:58:20 | 1.22 | 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 | {'first': True} | 2024-04-08 14:58:18 | |
| ¶ | pypath.inputs.adrecs._adrecs_base |
Not calling `pypath.inputs.adrecs._adrecs_base`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.adrecs._adrecs_drug_adr | 2024-04-08 14:58:20 | 2024-04-08 14:58:49 | 29.20 | 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 | {'first': True} | 2024-04-08 14:58:20 | |
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2024-04-08 14:58:49 | 2024-04-08 14:58:55 | 6.03 | 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 | {'first': True} | 2024-04-08 14:58:49 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2024-04-08 14:58:55 | 2024-04-08 14:58:56 | 0.80 | 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 | {'first': True} | 2024-04-08 14:58:55 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2024-04-08 14:58:56 | 2024-04-08 14:58:59 | 3.63 | 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 | {'first': True} | 2024-04-08 14:58:56 | |
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2024-04-08 14:58:59 | 2024-04-08 14:59:00 | 1.15 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='17.04.07', badd='BADD_A00388'), parent=AdrecsAdr(adr_class='17.04', badd='BADD_A01110')), AdrecsChildParent(child=AdrecsAdr(adr_class='18.08.05', badd='BADD_A06670'), parent=AdrecsAdr(adr_class='18.08', badd='BADD_A01006')), AdrecsChildParent(child=Adrec...(truncated) | 13,828 | {'first': True} | 2024-04-08 14:58:59 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2024-04-08 14:59:00 | 2024-04-08 14:59:01 | 0.78 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1978, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1562, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3208, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/ipi.py", line 40, in ipi_uniprot
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 14:59:00 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2024-04-08 14:59:01 | 2024-04-08 14:59:02 | 0.56 |
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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{'first': True} | 2024-04-08 14:59:01 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2024-04-08 14:59:02 | 2024-04-08 14:59:02 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{'first': True} | 2024-04-08 14:59:02 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2024-04-08 14:59:02 | 2024-04-08 14:59:02 | 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 | {'first': True} | 2024-04-08 14:59:02 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2024-04-08 14:59:02 | 2024-04-08 14:59:36 | 34.08 | 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 | {'first': True} | 2024-04-08 14:59:02 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2024-04-08 14:59:37 | 2024-04-08 15:00:21 | 43.78 | 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) | 8,424 | {'first': True} | 2024-04-08 14:59:37 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2024-04-08 15:00:21 | 2024-04-08 15:00:22 | 1.13 | 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) | 7,169 | {'first': True} | 2024-04-08 15:00:21 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2024-04-08 15:00:22 | 2024-04-08 15:00:51 | 29.01 | 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) | 179,834 | {'first': True} | 2024-04-08 15:00:22 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2024-04-08 15:00:51 | 2024-04-08 15:00:51 | 0.15 | list | [{'vendor': 'PHALANX', 'description': None, 'format': 'EXPRESSION', 'array': 'OneArray', 'type': 'OLIGO', 'label': 'PHALANX OneArray'}, {'type': 'OLIGO', 'array': 'CODELINK', 'format': 'EXPRESSION', 'description': None, 'vendor': 'CODELINK', 'label': 'CODELINK CODELINK'}, {'format': 'EXPRESSION', 'v...(truncated) | 35 | {'first': True} | 2024-04-08 15:00:51 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biomodels._get_biomodels | 2024-04-08 15:00:51 | 2024-04-08 15:00:51 | 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__20240408-145602/pypath_git/pypath/inputs/biomodels.py", line 101, in _get_biomodels
loginurl = urls.urls['biomodels']['login'] % t
KeyError: 'login'
|
{'first': True} | 2024-04-08 15:00:51 | |||
| ¶ | pypath.inputs.biomodels.download_single_model |
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biomodels.get_biomodels | 2024-04-08 15:00:51 | 2024-04-08 15:00:51 | 0.07 |
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__20240408-145602/pypath_git/pypath/inputs/biomodels.py", line 160, in get_biomodels
c0.perform()
pycurl.error: (77, 'error setting certificate verify locations:\n CAfile: /etc/pki/tls/certs/ca-bundle.crt\n CApath: none')
|
{'first': True} | 2024-04-08 15:00:51 | |||
| ¶ | pypath.inputs.biomodels.get_biomodels_req | 2024-04-08 15:00:51 | 2024-04-08 15:00:52 | 0.60 |
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__20240408-145602/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)
|
{'first': True} | 2024-04-08 15:00:51 | |||
| ¶ | pypath.inputs.biomodels.get_single_model |
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2024-04-08 15:00:52 | 2024-04-08 15:00:52 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 15:00:52 | |||
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2024-04-08 15:00:52 | 2024-04-08 15:00:54 | 1.35 | 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 | {'first': True} | 2024-04-08 15:00:52 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2024-04-08 15:00:54 | 2024-04-08 15:00:54 | 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__20240408-145602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 203, in cancerdrugsdb_annotations
data = cancerdrugsdb_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 114, in cancerdrugsdb_interactions
data = cancerdrugsdb_download()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 57, in cancerdrugsdb_download
return list(csv.DictReader(c.result, delimiter = '\t'))
File "/usr/lib/python3.10/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 15:00:54 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2024-04-08 15:00:54 | 2024-04-08 15:00:54 | 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__20240408-145602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 57, in cancerdrugsdb_download
return list(csv.DictReader(c.result, delimiter = '\t'))
File "/usr/lib/python3.10/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 15:00:54 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2024-04-08 15:00:54 | 2024-04-08 15:00:54 | 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__20240408-145602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 114, in cancerdrugsdb_interactions
data = cancerdrugsdb_download()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 57, in cancerdrugsdb_download
return list(csv.DictReader(c.result, delimiter = '\t'))
File "/usr/lib/python3.10/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 15:00:54 | |||
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2024-04-08 15:00:54 | 2024-04-08 15:01:14 | 20.21 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:00:54 | |||
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2024-04-08 15:01:14 | 2024-04-08 15:01:36 | 22.07 | dict | {'P08700': {CellcallAnnotation(role='ligand')}, 'P15509': {CellcallAnnotation(role='receptor')}, 'Q8IZJ0': {CellcallAnnotation(role='ligand')}, 'Q08334': {CellcallAnnotation(role='receptor')}, 'P20783': {CellcallAnnotation(role='ligand')}, 'P08138': {CellcallAnnotation(role='receptor')}, 'P43026': {...(truncated) | 460 | {'first': True} | 2024-04-08 15:01:14 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2024-04-08 15:01:36 | 2024-04-08 15:01:36 | 0.04 | 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 | {'first': True} | 2024-04-08 15:01:36 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2024-04-08 15:01:36 | 2024-04-08 15:01:37 | 0.85 | 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 | {'first': True} | 2024-04-08 15:01:36 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2024-04-08 15:01:37 | 2024-04-08 15:01:37 | 0.11 | list | [CellcallInteraction(ligand_uniprot='P08700', receptor_uniprot='P15509', core=True), CellcallInteraction(ligand_uniprot='Q8IZJ0', receptor_uniprot='Q08334', core=True), CellcallInteraction(ligand_uniprot='P20783', receptor_uniprot='P08138', core=True), CellcallInteraction(ligand_uniprot='P43026', re...(truncated) | 797 | {'first': True} | 2024-04-08 15:01:37 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2024-04-08 15:01:37 | 2024-04-08 15:01:38 | 0.79 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:01:37 | |||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2024-04-08 15:01:38 | 2024-04-08 15:01:38 | 0.00 | int | 9606 | 0 | {'first': True} | 2024-04-08 15:01:38 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_cofactors |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_complexes |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2024-04-08 15:01:38 | 2024-04-08 15:01:45 | 7.03 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 224, in cellchatdb_interactions
raw = cellchatdb_download(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 61, in cellchatdb_download
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)[key]
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 796, in _convert_next
value = convert_vector(obj, self._convert_next, attrs=attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 246, in convert_vector
value: list[Any] | StrMap = [
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 247, in <listcomp>
conversion_function(o) for o in r_vec.value
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (26827) does not match length of index (2)
|
{'first': True} | 2024-04-08 15:01:38 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2024-04-08 15:01:45 | 2024-04-08 15:01:52 | 6.83 |
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__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 139, in cellchatdb_cofactors
raw = cellchatdb_download(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 61, in cellchatdb_download
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)[key]
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 796, in _convert_next
value = convert_vector(obj, self._convert_next, attrs=attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 246, in convert_vector
value: list[Any] | StrMap = [
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 247, in <listcomp>
conversion_function(o) for o in r_vec.value
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (26827) does not match length of index (2)
|
{'first': True} | 2024-04-08 15:01:45 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2024-04-08 15:01:52 | 2024-04-08 15:01:59 | 6.67 |
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__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 93, in cellchatdb_complexes
raw = cellchatdb_download(organism = organism)['complex']
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 61, in cellchatdb_download
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)[key]
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 796, in _convert_next
value = convert_vector(obj, self._convert_next, attrs=attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 246, in convert_vector
value: list[Any] | StrMap = [
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 247, in <listcomp>
conversion_function(o) for o in r_vec.value
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (26827) does not match length of index (2)
|
{'first': True} | 2024-04-08 15:01:52 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2024-04-08 15:01:59 | 2024-04-08 15:02:06 | 7.04 |
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__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 61, in cellchatdb_download
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)[key]
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 796, in _convert_next
value = convert_vector(obj, self._convert_next, attrs=attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 246, in convert_vector
value: list[Any] | StrMap = [
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 247, in <listcomp>
conversion_function(o) for o in r_vec.value
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (26827) does not match length of index (2)
|
{'first': True} | 2024-04-08 15:01:59 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2024-04-08 15:02:06 | 2024-04-08 15:02:12 | 6.73 |
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__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 224, in cellchatdb_interactions
raw = cellchatdb_download(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/cellchatdb.py", line 61, in cellchatdb_download
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)[key]
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 796, in _convert_next
value = convert_vector(obj, self._convert_next, attrs=attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 246, in convert_vector
value: list[Any] | StrMap = [
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 247, in <listcomp>
conversion_function(o) for o in r_vec.value
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (26827) does not match length of index (2)
|
{'first': True} | 2024-04-08 15:02:06 | |||
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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 | {'first': True} | 2024-04-08 15:02:13 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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__20240408-145602/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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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 | {'first': True} | 2024-04-08 15:02:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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 | {'first': True} | 2024-04-08 15:02:13 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 313, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 384, in cellinker_smol_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cellinker.py", line 528, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2024-04-08 15:02:13 | 2024-04-08 15:02:13 | 0.00 | 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 | {'first': True} | 2024-04-08 15:02:13 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_annotations |
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_get_entity |
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_hla |
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2024-04-08 15:02:13 | 2024-04-08 15:02:14 | 0.24 | dict | {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) | 358 | {'first': True} | 2024-04-08 15:02:13 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2024-04-08 15:02:14 | 2024-04-08 15:02:14 | 0.01 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 358 | {'first': True} | 2024-04-08 15:02:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2024-04-08 15:02:14 | 2024-04-08 15:02:14 | 0.58 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {'first': True} | 2024-04-08 15:02:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2024-04-08 15:02:14 | 2024-04-08 15:02:14 | 0.03 | tuple | ({'Q9BT56', 'Q9BY67', 'P08253', 'P08311', Complex Glutamate_byGLS_and_SLC1A1: COMPLEX:O94925_P43005, 'Q8NFW1', 'Q00604', 'P12830', 'Q03405', 'Q9NZH6', 'Q9HC73', 'Q99075', Complex Glutamate_byGLS2_and_SLC1A1: COMPLEX:P43005_Q9UI32, 'Q9Y4C0', Complex Glutamate_byGLS2_and_SLC17A8: COMPLEX:Q8NDX2_Q9UI32...(truncated) | 2 | {'first': True} | 2024-04-08 15:02:14 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2024-04-08 15:02:14 | 2024-04-08 15:02:14 | 0.02 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,359 | {'first': True} | 2024-04-08 15:02:14 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2024-04-08 15:02:14 | 2024-04-08 15:02:28 | 13.85 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='15721238')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) | 1,598 | {'first': True} | 2024-04-08 15:02:14 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2024-04-08 15:02:28 | 2024-04-08 15:02:28 | 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 | {'first': True} | 2024-04-08 15:02:28 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2024-04-08 15:02:28 | 2024-04-08 15:02:28 | 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 | {'first': True} | 2024-04-08 15:02:28 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2024-04-08 15:02:28 | 2024-04-08 15:02:28 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3641, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2300, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2302, in <genexpr>
self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:02:28 | |||
| ¶ | pypath.inputs.chembl.chembl_activities |
Not calling `pypath.inputs.chembl.chembl_activities`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.chembl.chembl_documents | 2024-04-08 15:02:28 | 2024-04-08 15:04:11 | 102.91 | 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 | {'first': True} | 2024-04-08 15:02:28 | |
| ¶ | pypath.inputs.chembl.chembl_drug_indications | 2024-04-08 15:04:11 | 2024-04-08 15:05:16 | 64.71 | 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 | {'first': True} | 2024-04-08 15:04:11 | |
| ¶ | pypath.inputs.chembl.chembl_mechanisms | 2024-04-08 15:05:16 | 2024-04-08 15:05:25 | 9.19 | 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 | {'first': True} | 2024-04-08 15:05:16 | |
| ¶ | pypath.inputs.chembl.chembl_targets | 2024-04-08 15:05:25 | 2024-04-08 15:07:39 | 133.43 | 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 | {'first': True} | 2024-04-08 15:05:25 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2024-04-08 15:07:39 | 2024-04-08 15:08:13 | 33.98 | list | [Citation(allele='211908', variation_id='214690', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='1002009', variation_id='1026175', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='36191', variation_id='24850', nsv='', citation_source='PubMed', ...(truncated) | 3,530,037 | {'first': True} | 2024-04-08 15:07:39 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2024-04-08 15:08:17 | 2024-04-08 15:08:55 | 37.82 |
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__20240408-145602/pypath_git/pypath/inputs/clinvar.py", line 82, in clinvar_raw
otherids = tuple(row['OtherIDs'].replace('|', ';').replace(',', ';').split(';'))
AttributeError: 'NoneType' object has no attribute 'replace'
|
{'first': True} | 2024-04-08 15:08:17 | |||
| ¶ | pypath.inputs.collectri.collectri_interactions | 2024-04-08 15:08:55 | 2024-04-08 15:08:59 | 4.17 |
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__20240408-145602/pypath_git/pypath/inputs/collectri.py", line 224, in collectri_interactions
mapping.map_name(rec.target, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:08:55 | |||
| ¶ | pypath.inputs.collectri.collectri_raw | 2024-04-08 15:08:59 | 2024-04-08 15:08:59 | 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 | {'first': True} | 2024-04-08 15:08:59 | |
| ¶ | pypath.inputs.compath._compath_mappings | 2024-04-08 15:08:59 | 2024-04-08 15:09:00 | 0.22 | 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 | {'first': True} | 2024-04-08 15:08:59 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2024-04-08 15:09:00 | 2024-04-08 15:09:00 | 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__20240408-145602/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
|
{'first': True} | 2024-04-08 15:09:00 | |||
| ¶ | pypath.inputs.compleat.compleat_complexes | 2024-04-08 15:09:00 | 2024-04-08 15:09:02 | 1.88 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,693 | {'first': True} | 2024-04-08 15:09:00 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2024-04-08 15:09:02 | 2024-04-08 15:09:02 | 0.04 | 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 | {'first': True} | 2024-04-08 15:09:02 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2024-04-08 15:09:02 | 2024-04-08 15:10:27 | 85.17 | 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) | 1,949 | {'first': True} | 2024-04-08 15:09:02 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2024-04-08 15:10:27 | 2024-04-08 15:10:41 | 14.30 | list | [ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A024R0Y4', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A087WWR4', loc_a=(ComppiLocation(locati...(truncated) | 588,602 | {'first': True} | 2024-04-08 15:10:27 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2024-04-08 15:10:41 | 2024-04-08 15:10:56 | 14.99 | dict | {'A0A0R4J2E4': {ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='cytosol', score=0.8)}, 'A0A024R0Y4': {ComppiLocation(location='nucleus', score=0.8)}, 'A0A087WWR4': {ComppiLocation(location='nucleus', score=0.8)}, 'Q08379': {ComppiLocation(location='membrane', score=0.8), Comp...(truncated) | 22,828 | {'first': True} | 2024-04-08 15:10:41 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2024-04-08 15:10:56 | 2024-04-08 15:10:57 | 0.31 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {'first': True} | 2024-04-08 15:10:56 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2024-04-08 15:10:57 | 2024-04-08 15:10:57 | 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 | {'first': True} | 2024-04-08 15:10:57 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2024-04-08 15:10:57 | 2024-04-08 15:10:57 | 0.60 | 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 | {'first': True} | 2024-04-08 15:10:57 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2024-04-08 15:10:57 | 2024-04-08 15:10:57 | 0.00 | dict | {} | 0 | {'first': True} | 2024-04-08 15:10:57 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2024-04-08 15:10:57 | 2024-04-08 15:11:04 | 6.64 |
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__20240408-145602/pypath_git/pypath/inputs/cpad.py", line 62, in cpad_annotations
uniprot = mapping.map_name0(regulator, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3582, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1799, in map_name0
names = self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:10:57 | |||
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2024-04-08 15:11:04 | 2024-04-08 15:11:04 | 0.04 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='Hedgehog signaling pathway', cancer='Glioma', pathway_category='Hedgehog signaling pathway', effect_on_cancer='Activating', effect_on_cancer_outcome='promote GSC properties and glioma propagation'), CpadPathwayCancer(pathway='RhoA/alpha-v beta-3 signaling path...(truncated) | 2 | {'first': True} | 2024-04-08 15:11:04 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2024-04-08 15:11:04 | 2024-04-08 15:11:04 | 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 | {'first': True} | 2024-04-08 15:11:04 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2024-04-08 15:11:04 | 2024-04-08 15:11:08 | 4.04 | 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 | {'first': True} | 2024-04-08 15:11:04 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2024-04-08 15:11:08 | 2024-04-08 15:11:11 | 2.82 | 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 | {'first': True} | 2024-04-08 15:11:08 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2024-04-08 15:11:12 | 2024-04-08 15:11:12 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{'first': True} | 2024-04-08 15:11:12 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2024-04-08 15:11:12 | 2024-04-08 15:11:13 | 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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'float' object has no attribute 'value'
|
{'first': True} | 2024-04-08 15:11:12 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2024-04-08 15:11:13 | 2024-04-08 15:11:13 | 0.14 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'float' object has no attribute 'value'
|
{'first': True} | 2024-04-08 15:11:13 | |||
| ¶ | pypath.inputs.ctdbase._ctdbase_download |
Not calling `pypath.inputs.ctdbase._ctdbase_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase._map_keys |
Not calling `pypath.inputs.ctdbase._map_keys`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase._modify_dict |
Not calling `pypath.inputs.ctdbase._modify_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2024-04-08 15:11:13 | 2024-04-08 15:11:14 | 0.57 |
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__20240408-145602/pypath_git/pypath/inputs/cytosig.py", line 106, in cytosig_annotations
u_cytokine = map_to_uniprot(cytokine)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 15:11:13 | |||
| ¶ | pypath.inputs.cytosig.cytosig_df | 2024-04-08 15:11:14 | 2024-04-08 15:11:14 | 0.03 | 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 | {'first': True} | 2024-04-08 15:11:14 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2024-04-08 15:11:14 | 2024-04-08 15:11:18 | 3.82 | 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 | {'first': True} | 2024-04-08 15:11:14 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2024-04-08 15:11:18 | 2024-04-08 15:11:20 | 1.68 |
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__20240408-145602/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---jXRgP0-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'
|
{'first': True} | 2024-04-08 15:11:18 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2024-04-08 15:11:20 | 2024-04-08 15:11:21 | 1.37 | 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 | {'first': True} | 2024-04-08 15:11:20 | |
| ¶ | pypath.inputs.ddinter._ensure_hashable |
Not calling `pypath.inputs.ddinter._ensure_hashable`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2024-04-08 15:11:21 | 2024-04-08 15:35:37 | 1,455.64 | list | [{DdinterInteraction(drug1_id='DDInter1', drug1_name='Abacavir', drug2_id='DDInter411', drug2_name='Clonazepam', level=('Unknown',), actions=('unknown',)), DdinterInteraction(drug1_id='DDInter1', drug1_name='Abacavir', drug2_id='DDInter1513', drug2_name='Prednisolone', level=('Unknown',), actions=('...(truncated) | 1,972 | {'first': True} | 2024-04-08 15:11:21 | |
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2024-04-08 15:35:37 | 2024-04-08 16:08:25 | 1,967.11 | 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 | {'first': True} | 2024-04-08 15:35:37 | |
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2024-04-08 16:08:25 | 2024-04-08 16:08:25 | 0.39 | int | 1972 | 0 | {'first': True} | 2024-04-08 16:08:25 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2024-04-08 16:08:25 | 2024-04-08 16:08:25 | 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__20240408-145602/pypath_git/pypath/inputs/deathdomain.py", line 43, in deathdomain_interactions
soup = bs4.BeautifulSoup(html, 'lxml')
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-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()
|
{'first': True} | 2024-04-08 16:08:25 | |||
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2024-04-08 16:08:25 | 2024-04-08 16:08:25 | 0.24 | 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 | {'first': True} | 2024-04-08 16:08:25 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2024-04-08 16:08:25 | 2024-04-08 16:08:25 | 0.23 |
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__20240408-145602/pypath_git/pypath/inputs/depod.py", line 129, in depod_enzyme_substrate
if resaa in common.aminoa_3_to_1_letter else
TypeError: argument of type 'function' is not iterable
|
{'first': True} | 2024-04-08 16:08:25 | |||
| ¶ | pypath.inputs.depod.depod_interactions | 2024-04-08 16:08:25 | 2024-04-08 16:08:25 | 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 | {'first': True} | 2024-04-08 16:08:25 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2024-04-08 16:08:25 | 2024-04-08 16:08:26 | 0.60 | dict | {} | 0 | {'first': True} | 2024-04-08 16:08:25 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2024-04-08 16:08:26 | 2024-04-08 16:08:27 | 0.57 | list | [] | 0 | {'first': True} | 2024-04-08 16:08:26 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2024-04-08 16:08:27 | 2024-04-08 16:09:04 | 37.44 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3641, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2300, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2302, in <genexpr>
self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:08:27 | |||
| ¶ | pypath.inputs.dip.dip_interactions | 2024-04-08 16:09:04 | 2024-04-08 16:09:04 | 0.26 | 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 | {'first': True} | 2024-04-08 16:09:04 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.diseases._diseases_general |
Not calling `pypath.inputs.diseases._diseases_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2024-04-08 16:09:04 | 2024-04-08 16:09:05 | 0.39 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resource='TIGA', source_score=25, confidence=0.835), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:535', disease='Sleep disorder', resource='TIGA'...(truncated) | 28,828 | {'first': True} | 2024-04-08 16:09:04 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2024-04-08 16:09:05 | 2024-04-08 16:09:08 | 3.16 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:150', disease='Disease of mental health', resource='TIGA', source_score=18, confidence=0.723), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resou...(truncated) | 328,031 | {'first': True} | 2024-04-08 16:09:05 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2024-04-08 16:09:08 | 2024-04-08 16:09:08 | 0.23 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:1928', disease='Williams-Beuren syndrome', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Cranio...(truncated) | 7,505 | {'first': True} | 2024-04-08 16:09:08 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2024-04-08 16:09:08 | 2024-04-08 16:09:09 | 0.81 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050177', disease='Monogenic disease', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050736', disease='Autosomal...(truncated) | 95,022 | {'first': True} | 2024-04-08 16:09:08 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2024-04-08 16:09:09 | 2024-04-08 16:09:13 | 4.41 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.24, confidence=3.62, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol='...(truncated) | 286,278 | {'first': True} | 2024-04-08 16:09:09 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2024-04-08 16:09:13 | 2024-04-08 16:11:40 | 146.66 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.24, confidence=3.62, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol='...(truncated) | 11,312,436 | {'first': True} | 2024-04-08 16:09:13 | |
| ¶ | pypath.inputs.domino.domino_ddi | 2024-04-08 16:11:40 | 2024-04-08 16:11:45 | 4.47 | list | [<pypath.internals.intera.DomainDomain object at 0x7f76a06793f0>, <pypath.internals.intera.DomainDomain object at 0x7f76a0678ac0>, <pypath.internals.intera.DomainDomain object at 0x7f76a067af50>, <pypath.internals.intera.DomainDomain object at 0x7f76a067b340>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {'first': True} | 2024-04-08 16:11:40 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2024-04-08 16:11:45 | 2024-04-08 16:11:45 | 0.62 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f76d82d2a40>, <pypath.internals.intera.DomainDomain object at 0x7f76d82d0ca0>, <pypath.internals.intera.DomainDomain object at 0x7f76d82d3d90>, <pypath.internals.intera.DomainDomain object at 0x7f76d82d3520>, <pypath.internals.intera.Domain...(truncated) | 2 | {'first': True} | 2024-04-08 16:11:45 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2024-04-08 16:11:45 | 2024-04-08 16:11:46 | 0.39 | 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 | {'first': True} | 2024-04-08 16:11:45 | |
| ¶ | pypath.inputs.domino.get_domino | 2024-04-08 16:11:46 | 2024-04-08 16:11:46 | 0.37 | 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 | {'first': True} | 2024-04-08 16:11:46 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2024-04-08 16:11:46 | 2024-04-08 16:11:54 | 8.35 | 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 | {'first': True} | 2024-04-08 16:11:46 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2024-04-08 16:11:55 | 2024-04-08 16:12:08 | 13.30 | 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 | {'first': True} | 2024-04-08 16:11:55 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2024-04-08 16:12:08 | 2024-04-08 16:12:08 | 0.31 |
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__20240408-145602/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
|
{'first': True} | 2024-04-08 16:12:08 | |||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2024-04-08 16:12:08 | 2024-04-08 16:12:08 | 0.11 |
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__20240408-145602/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
|
{'first': True} | 2024-04-08 16:12:08 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2024-04-08 16:12:08 | 2024-04-08 16:12:10 | 1.76 | 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 | {'first': True} | 2024-04-08 16:12:08 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2024-04-08 16:12:10 | 2024-04-08 16:12:10 | 0.39 | 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 | {'first': True} | 2024-04-08 16:12:10 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2024-04-08 16:12:10 | 2024-04-08 16:12:12 | 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 | {'first': True} | 2024-04-08 16:12:10 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2024-04-08 16:12:12 | 2024-04-08 16:12:25 | 13.29 | 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 | {'first': True} | 2024-04-08 16:12:12 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2024-04-08 16:12:25 | 2024-04-08 16:12:25 | 0.11 |
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__20240408-145602/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
|
{'first': True} | 2024-04-08 16:12:25 | |||
| ¶ | pypath.inputs.drugbank._drugbank_credentials | 2024-04-08 16:12:25 | 2024-04-08 16:12:25 | 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__20240408-145602/pypath_git/pypath/inputs/drugbank.py", line 49, in _drugbank_credentials
return credentials.credentials(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/credentials.py", line 115, in credentials
raise RuntimeError(msg)
RuntimeError: Failed to obtain credentials for resource `DrugBank`
|
{'first': True} | 2024-04-08 16:12:25 | |||
| ¶ | pypath.inputs.drugbank._drugbank_download |
Not calling `pypath.inputs.drugbank._drugbank_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_annotations | 2024-04-08 16:12:25 | 2024-04-08 16:12:25 | 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__20240408-145602/pypath_git/pypath/inputs/drugbank.py", line 352, in drugbank_annotations
drugs = drugbank_drugs(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{'first': True} | 2024-04-08 16:12:25 | |||
| ¶ | pypath.inputs.drugbank.drugbank_drugs | 2024-04-08 16:12:25 | 2024-04-08 16:12:25 | 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__20240408-145602/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{'first': True} | 2024-04-08 16:12:25 | |||
| ¶ | pypath.inputs.drugbank.drugbank_interactions | 2024-04-08 16:12:25 | 2024-04-08 16:12:25 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{'first': True} | 2024-04-08 16:12:25 | |||
| ¶ | pypath.inputs.drugbank.drugbank_mapping |
Not calling `pypath.inputs.drugbank.drugbank_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_raw_interactions | 2024-04-08 16:12:25 | 2024-04-08 16:12:25 | 0.00 | list | [] | 0 | {'first': True} | 2024-04-08 16:12:25 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2024-04-08 16:12:25 | 2024-04-08 16:12:26 | 1.09 | 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 | {'first': True} | 2024-04-08 16:12:25 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2024-04-08 16:12:26 | 2024-04-08 16:12:28 | 1.22 | 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 | {'first': True} | 2024-04-08 16:12:26 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2024-04-08 16:12:28 | 2024-04-08 16:12:30 | 1.92 | 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 | {'first': True} | 2024-04-08 16:12:28 | |
| ¶ | pypath.inputs.elm.elm_domains | 2024-04-08 16:12:30 | 2024-04-08 16:12:30 | 0.53 | 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 | {'first': True} | 2024-04-08 16:12:30 | |
| ¶ | pypath.inputs.elm.elm_instances | 2024-04-08 16:12:30 | 2024-04-08 16:15:19 | 168.96 | list | [ELMInstance(accession='Accession', type='ELMType', identifier='ELMIdentifier', uniprot_id='ProteinName', uniprot='Primary_Acc', synonyms='Accessions', start='Start', end='End', references='References', methods='Methods', logic='InstanceLogic', pdb='PDB', organism='Organism'), ELMInstance(accession=...(truncated) | 4,252 | {'first': True} | 2024-04-08 16:12:30 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2024-04-08 16:15:19 | 2024-04-08 16:15:19 | 0.12 | 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 | {'first': True} | 2024-04-08 16:15:19 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2024-04-08 16:15:19 | 2024-04-08 16:15:19 | 0.12 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:15:19 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2024-04-08 16:15:19 | 2024-04-08 16:15:19 | 0.12 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:15:19 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2024-04-08 16:15:19 | 2024-04-08 16:15:20 | 0.12 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:15:19 | |||
| ¶ | pypath.inputs.embrace.embrace_translated | 2024-04-08 16:15:20 | 2024-04-08 16:15:20 | 0.12 |
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__20240408-145602/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:15:20 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2024-04-08 16:15:20 | 2024-04-08 16:15:20 | 0.48 | 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 | {'first': True} | 2024-04-08 16:15:20 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2024-04-08 16:15:20 | 2024-04-08 16:15:21 | 0.58 | 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 | {'first': True} | 2024-04-08 16:15:20 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2024-04-08 16:15:21 | 2024-04-08 16:15:44 | 22.77 | 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 | {'first': True} | 2024-04-08 16:15:21 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2024-04-08 16:15:44 | 2024-04-08 16:15:44 | 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 | {'first': True} | 2024-04-08 16:15:44 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2024-04-08 16:15:44 | 2024-04-08 16:17:01 | 77.28 | 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 | {'first': True} | 2024-04-08 16:15:44 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2024-04-08 16:17:01 | 2024-04-08 16:17:01 | 0.06 | 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) | 354 | {'first': True} | 2024-04-08 16:17:01 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2024-04-08 16:17:01 | 2024-04-08 16:17:02 | 0.82 | 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) | 8,236 | {'first': True} | 2024-04-08 16:17:01 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2024-04-08 16:17:02 | 2024-04-08 16:20:26 | 204.33 |
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__20240408-145602/pypath_git/pypath/inputs/go.py", line 937, in get_go_quick
terms[l[5]][l[1]].add(l[4])
KeyError: 'GO ASPECT'
|
{'first': True} | 2024-04-08 16:17:02 | |||
| ¶ | pypath.inputs.go.get_goslim | 2024-04-08 16:20:26 | 2024-04-08 16:20:27 | 1.11 | 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 | {'first': True} | 2024-04-08 16:20:26 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2024-04-08 16:20:27 | 2024-04-08 16:30:09 | 581.79 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'...(truncated) | 3 | {'first': True} | 2024-04-08 16:20:27 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2024-04-08 16:30:09 | 2024-04-08 16:30:09 | 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__20240408-145602/pypath_git/pypath/inputs/go.py", line 190, in go_ancestors_goose
sql_path = os.path.join(common.DATA, 'goose_ancestors.sql')
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2024-04-08 16:30:09 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2024-04-08 16:30:09 | 2024-04-08 16:30:14 | 5.11 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'...(truncated) | 3 | {'first': True} | 2024-04-08 16:30:09 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2024-04-08 16:30:14 | 2024-04-08 16:30:18 | 3.78 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005615', 'G...(truncated) | 3 | {'first': True} | 2024-04-08 16:30:14 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2024-04-08 16:30:18 | 2024-04-08 16:30:23 | 4.93 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='involved_in', go_id='GO:0071543', reference='GO_REF:0000033', evidence_code='IBA', with_or_from='PANTHER:PTN000290327|UniProtKB:O95989', aspect='P', db_object_name='Diphosphoinositol polypho...(truncated) | 19,670 | {'first': True} | 2024-04-08 16:30:18 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2024-04-08 16:30:25 | 2024-04-08 16:30:26 | 1.12 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005615', 'G...(truncated) | 3 | {'first': True} | 2024-04-08 16:30:25 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2024-04-08 16:30:26 | 2024-04-08 16:30:26 | 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__20240408-145602/pypath_git/pypath/inputs/go.py", line 833, in go_annotations_goose
sql_path = os.path.join(common.DATA, 'goose_annotations.sql')
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2024-04-08 16:30:26 | |||
| ¶ | pypath.inputs.go.go_annotations_solr | 2024-04-08 16:30:26 | 2024-04-08 16:30:27 | 1.25 |
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__20240408-145602/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'
|
{'first': True} | 2024-04-08 16:30:26 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2024-04-08 16:30:27 | 2024-04-08 16:30:29 | 1.83 |
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__20240408-145602/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'
|
{'first': True} | 2024-04-08 16:30:27 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2024-04-08 16:30:29 | 2024-04-08 16:30:34 | 4.54 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016014', 'part_of'), ('GO:0016011', 'part_of'), ('GO:0016013', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {'first': True} | 2024-04-08 16:30:29 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2024-04-08 16:30:34 | 2024-04-08 16:30:34 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/go.py", line 190, in go_ancestors_goose
sql_path = os.path.join(common.DATA, 'goose_ancestors.sql')
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2024-04-08 16:30:34 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2024-04-08 16:30:34 | 2024-04-08 16:30:38 | 4.57 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016014', 'part_of'), ('GO:0016011', 'part_of'), ('GO:0016013', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {'first': True} | 2024-04-08 16:30:34 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2024-04-08 16:30:38 | 2024-04-08 16:30:42 | 3.80 | 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 | {'first': True} | 2024-04-08 16:30:38 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2024-04-08 16:30:42 | 2024-04-08 16:30:42 | 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__20240408-145602/pypath_git/pypath/inputs/go.py", line 564, in go_terms_goose
sql_path = os.path.join(common.DATA, 'goose_terms.sql')
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2024-04-08 16:30:42 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2024-04-08 16:30:42 | 2024-04-08 16:30:46 | 3.75 | 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 | {'first': True} | 2024-04-08 16:30:42 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2024-04-08 16:30:46 | 2024-04-08 16:30:47 | 0.59 |
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__20240408-145602/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'
|
{'first': True} | 2024-04-08 16:30:46 | |||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2024-04-08 16:30:47 | 2024-04-08 16:30:47 | 0.24 | 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) | 426 | {'first': True} | 2024-04-08 16:30:47 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2024-04-08 16:30:47 | 2024-04-08 16:30:48 | 1.46 | 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 | {'first': True} | 2024-04-08 16:30:47 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2024-04-08 16:30:48 | 2024-04-08 16:30:50 | 1.84 |
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__20240408-145602/pypath_git/pypath/inputs/guide2pharma.py", line 232, in guide2pharma_download
ligand_uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3582, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1799, in map_name0
names = self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:30:48 | |||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2024-04-08 16:30:50 | 2024-04-08 16:30:55 | 5.24 |
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__20240408-145602/pypath_git/pypath/inputs/gutmgene.py", line 117, in gutmgene_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:30:50 | |||
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2024-04-08 16:30:55 | 2024-04-08 16:30:55 | 0.00 | list | [GutmgeneRaw(microbe_taxon='Faecalibacterium prausnitzii', microbe_ncbi_tax_id='853', gut_microbiota_id='gm0327', classification='species', genesymbol='TGFB1', entrez='7040', effect='activation', throughput='low-throughput'), GutmgeneRaw(microbe_taxon='Escherichia coli O127:H6 str. E2348/69', microb...(truncated) | 278 | {'first': True} | 2024-04-08 16:30:55 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2024-04-08 16:30:55 | 2024-04-08 16:30:56 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:30:55 | |||
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2024-04-08 16:30:56 | 2024-04-08 16:30:56 | 0.12 |
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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:30:56 | |||
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2024-04-08 16:30:56 | 2024-04-08 16:30:57 | 1.86 | dict | {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='Alpha-2-macroglobulin family')}, 'A8K2U0': {HGNCGeneGroupAnnotation(mainclass='Alpha-2...(truncated) | 15,412 | {'first': True} | 2024-04-08 16:30:56 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2024-04-08 16:30:58 | 2024-04-08 16:31:23 | 25.76 | list | [HippieInteraction(id_a='Q86VG3', id_b='Q8NEZ3', score=0.83, methods=None, references=('26186194', '28514442', '33961781'), sources=None, organisms=None), HippieInteraction(id_a='P41134', id_b='P55036', score=0.87, methods=None, references=('17891176', '9235903'), sources=None, organisms=None), Hipp...(truncated) | 102,414 | {'first': True} | 2024-04-08 16:30:58 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2024-04-08 16:31:24 | 2024-04-08 16:32:40 | 76.12 | 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 | {'first': True} | 2024-04-08 16:31:24 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2024-04-08 16:32:40 | 2024-04-08 16:32:40 | 0.00 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | {'first': True} | 2024-04-08 16:32:40 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2024-04-08 16:32:40 | 2024-04-08 16:32:40 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | {'first': True} | 2024-04-08 16:32:40 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2024-04-08 16:32:40 | 2024-04-08 16:32:40 | 0.00 | dict | {} | 0 | {'first': True} | 2024-04-08 16:32:40 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2024-04-08 16:32:40 | 2024-04-08 16:32:40 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | {'first': True} | 2024-04-08 16:32:40 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2024-04-08 16:32:40 | 2024-04-08 16:32:42 | 2.05 | dict | {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0002355'), HpoAnnotation(entrez_ge...(truncated) | 4,978 | {'first': True} | 2024-04-08 16:32:40 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2024-04-08 16:32:42 | 2024-04-08 16:32:45 | 2.68 | 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:619317', name='Developmental and epileptic encephalopat...(truncated) | 10,948 | {'first': True} | 2024-04-08 16:32:42 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2024-04-08 16:32:45 | 2024-04-08 16:32:47 | 1.70 | 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 | {'first': True} | 2024-04-08 16:32:45 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2024-04-08 16:32:47 | 2024-04-08 16:32:47 | 0.57 | 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) | 18,536 | {'first': True} | 2024-04-08 16:32:47 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2024-04-08 16:32:47 | 2024-04-08 16:32:52 | 4.68 | 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 | {'first': True} | 2024-04-08 16:32:47 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2024-04-08 16:32:52 | 2024-04-08 16:32:54 | 1.44 | 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 | {'first': True} | 2024-04-08 16:32:52 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2024-04-08 16:32:54 | 2024-04-08 16:32:55 | 1.44 | 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 | {'first': True} | 2024-04-08 16:32:54 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2024-04-08 16:32:55 | 2024-04-08 16:32:57 | 1.80 | 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 | {'first': True} | 2024-04-08 16:32:55 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2024-04-08 16:32:57 | 2024-04-08 16:33:27 | 30.28 | 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 | {'first': True} | 2024-04-08 16:32:57 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2024-04-08 16:33:27 | 2024-04-08 16:33:29 | 1.30 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='peroxisome', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,384 | {'first': True} | 2024-04-08 16:33:27 | |
| ¶ | pypath.inputs.humap.humap2_complexes | 2024-04-08 16:33:29 | 2024-04-08 16:33:30 | 1.36 | dict | {'COMPLEX:O95900_Q9BQS8': Complex: COMPLEX:O95900_Q9BQS8, 'COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9': Complex: COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9, 'COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6ZRY4_Q93062_Q96S66_Q9NZC3_Q9UF11_Q9Y6M7': Complex: COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6Z...(truncated) | 7,044 | {'first': True} | 2024-04-08 16:33:29 | |
| ¶ | pypath.inputs.humap.humap_complexes | 2024-04-08 16:33:30 | 2024-04-08 16:33:31 | 0.97 | dict | {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) | 4,493 | {'first': True} | 2024-04-08 16:33:30 | |
| ¶ | pypath.inputs.humsavar._parse_desc |
Not calling `pypath.inputs.humsavar._parse_desc`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2024-04-08 16:33:31 | 2024-04-08 16:33:34 | 3.46 | 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) | 13,068 | {'first': True} | 2024-04-08 16:33:31 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2024-04-08 16:33:35 | 2024-04-08 16:33:36 | 1.57 | list | [HuriInteraction(uniprot_a='Q8IY31', uniprot_b='Q9BQD3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='P49902', uniprot_b='P49902', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9BVJ6', uniprot_b='Q8NHQ1', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 5,650 | {'first': True} | 2024-04-08 16:33:35 | |
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2024-04-08 16:33:36 | 2024-04-08 16:33:41 | 5.00 | list | [HuriInteraction(uniprot_a='Q9H2A7', uniprot_b='Q6UY14', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q5SY16', uniprot_b='Q09666', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='Q8TAB5', uniprot_b='Q96F24', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 46,928 | {'first': True} | 2024-04-08 16:33:36 | |
| ¶ | pypath.inputs.huri.hi_iii_old | 2024-04-08 16:33:41 | 2024-04-08 16:33:41 | 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__20240408-145602/pypath_git/pypath/inputs/huri.py", line 90, in hi_iii_old
url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
|
{'first': True} | 2024-04-08 16:33:41 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2024-04-08 16:33:41 | 2024-04-08 16:34:03 | 21.82 | list | [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) | 228,501 | {'first': True} | 2024-04-08 16:33:41 | |
| ¶ | pypath.inputs.huri.huri_interactions | 2024-04-08 16:34:03 | 2024-04-08 16:34:18 | 14.85 | list | [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) | 165,139 | {'first': True} | 2024-04-08 16:34:03 | |
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2024-04-08 16:34:18 | 2024-04-08 16:34:19 | 0.93 | 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 | {'first': True} | 2024-04-08 16:34:18 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2024-04-08 16:34:19 | 2024-04-08 16:34:20 | 1.19 | 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 | {'first': True} | 2024-04-08 16:34:19 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2024-04-08 16:34:20 | 2024-04-08 16:34:21 | 0.81 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1978, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:34:20 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2024-04-08 16:34:21 | 2024-04-08 16:34:21 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:34:21 | |||
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2024-04-08 16:34:21 | 2024-04-08 16:34:22 | 1.16 | list | [HuriInteraction(uniprot_a='A0A0S2Z436', uniprot_b='Q9BQQ3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='O94989', uniprot_b='Q53EZ4', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q8NHQ1', uniprot_b='Q9H7H0', isoform_a=1, isoform_b=1, score=None), HuriIntera...(truncated) | 2,880 | {'first': True} | 2024-04-08 16:34:21 | |
| ¶ | pypath.inputs.huri.yu2011_interactions | 2024-04-08 16:34:22 | 2024-04-08 16:34:24 | 1.60 | list | [HuriInteraction(uniprot_a='Q5VUM1', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P62166', uniprot_b='Q86UW9', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9NV12', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteractio...(truncated) | 7,331 | {'first': True} | 2024-04-08 16:34:22 | |
| ¶ | pypath.inputs.i3d.get_i3d | 2024-04-08 16:34:24 | 2024-04-08 16:34:32 | 8.38 | 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 | {'first': True} | 2024-04-08 16:34:24 | |
| ¶ | pypath.inputs.icellnet._icellnet_get_components |
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_entity |
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_references |
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_resources |
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2024-04-08 16:34:32 | 2024-04-08 16:34:32 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/icellnet.py", line 64, in icellnet_interactions
references = _icellnet_get_references(line)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/icellnet.py", line 230, in _icellnet_get_references
(_ref.strip() for _ref in re.split(r'[,;]', line['PubMed ID']))
KeyError: 'PubMed ID'
|
{'first': True} | 2024-04-08 16:34:32 | |||
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2024-04-08 16:34:32 | 2024-04-08 16:34:32 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/icellnet.py", line 64, in icellnet_interactions
references = _icellnet_get_references(line)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/icellnet.py", line 230, in _icellnet_get_references
(_ref.strip() for _ref in re.split(r'[,;]', line['PubMed ID']))
KeyError: 'PubMed ID'
|
{'first': True} | 2024-04-08 16:34:32 | |||
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2024-04-08 16:34:32 | 2024-04-08 16:34:32 | 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__20240408-145602/pypath_git/pypath/inputs/icellnet.py", line 64, in icellnet_interactions
references = _icellnet_get_references(line)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/icellnet.py", line 230, in _icellnet_get_references
(_ref.strip() for _ref in re.split(r'[,;]', line['PubMed ID']))
KeyError: 'PubMed ID'
|
{'first': True} | 2024-04-08 16:34:32 | |||
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2024-04-08 16:34:32 | 2024-04-08 16:34:33 | 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__20240408-145602/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)
|
{'first': True} | 2024-04-08 16:34:32 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2024-04-08 16:34:33 | 2024-04-08 16:34:33 | 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__20240408-145602/pypath_git/pypath/inputs/imweb.py", line 105, in get_imweb
c0.perform()
pycurl.error: (77, 'error setting certificate verify locations:\n CAfile: /etc/pki/tls/certs/ca-bundle.crt\n CApath: none')
|
{'first': True} | 2024-04-08 16:34:33 | |||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2024-04-08 16:34:33 | 2024-04-08 16:34:33 | 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__20240408-145602/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)
|
{'first': True} | 2024-04-08 16:34:33 | |||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2024-04-08 16:34:33 | 2024-04-08 16:34:37 | 4.25 | 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 | {'first': True} | 2024-04-08 16:34:33 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2024-04-08 16:34:37 | 2024-04-08 16:34:38 | 0.71 | NoneType | None | 0 | {'first': True} | 2024-04-08 16:34:37 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2024-04-08 16:34:38 | 2024-04-08 16:34:38 | 0.45 | NoneType | None | 0 | {'first': True} | 2024-04-08 16:34:38 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2024-04-08 16:34:38 | 2024-04-08 16:37:55 | 196.24 | list | [IntactInteraction(id_a='P49418', id_b='Q05193', 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='P49418', id_b='Q05193', id_type_a='uniprot', i...(truncated) | 72,631 | {'first': True} | 2024-04-08 16:34:38 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2024-04-08 16:37:55 | 2024-04-08 16:37:56 | 1.31 | set | {'P06756', 'P26010', 'P08648', 'P16144', 'P26006', 'P38570', 'P23229', 'P05106', 'P20701', 'P56199', 'P20702', 'Q13349', 'P08514', 'Q9UKX5', 'P05107', 'Q13683', 'P18564', 'P05556', 'P18084', 'P53708', 'O75578', 'P26012', 'P11215', 'Q13797', 'P17301'} | 25 | {'first': True} | 2024-04-08 16:37:55 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2024-04-08 16:37:56 | 2024-04-08 16:37:58 | 2.01 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0005634', go_term_name='nucleus'), Interpro2GOAnnotation(go_term_id='GO:0008270', go_term_name='zinc ion binding'), Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term...(truncated) | 14,723 | {'first': True} | 2024-04-08 16:37:56 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2024-04-08 16:37:58 | 2024-04-08 16:38:01 | 3.20 |
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__20240408-145602/pypath_git/pypath/inputs/interpro.py", line 268, in interpro_annotations
totalrec = int(res['count'])
TypeError: 'NoneType' object is not subscriptable
|
{'first': True} | 2024-04-08 16:37:58 | |||
| ¶ | pypath.inputs.interpro.interpro_entries | 2024-04-08 16:38:01 | 2024-04-08 16:38:21 | 19.56 | list | [InterproEntry(interpro_id='IPR000001', protein_count='19394', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 44,602 | {'first': True} | 2024-04-08 16:38:01 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2024-04-08 16:38:21 | 2024-04-08 16:38:21 | 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__20240408-145602/pypath_git/pypath/inputs/intogen.py", line 51, in intogen_annotations
with settings.context(curl_connect_timeout = 100):
AttributeError: module 'pypath.share.settings' has no attribute 'context'
|
{'first': True} | 2024-04-08 16:38:21 | |||
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2024-04-08 16:38:21 | 2024-04-08 16:38:21 | 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__20240408-145602/pypath_git/pypath/inputs/ipi.py", line 40, in ipi_uniprot
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:38:21 | |||
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2024-04-08 16:38:21 | 2024-04-08 16:38:43 | 21.67 |
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__20240408-145602/pypath_git/pypath/inputs/iptmnet.py", line 118, in iptmnet_interactions
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1978, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:38:21 | |||
| ¶ | pypath.inputs.italk.italk_annotations | 2024-04-08 16:38:43 | 2024-04-08 16:38:44 | 0.66 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:38:43 | |||
| ¶ | pypath.inputs.italk.italk_interactions | 2024-04-08 16:38:44 | 2024-04-08 16:38:44 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:38:44 | |||
| ¶ | pypath.inputs.italk.italk_raw | 2024-04-08 16:38:44 | 2024-04-08 16:38:44 | 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 | {'first': True} | 2024-04-08 16:38:44 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2024-04-08 16:38:44 | 2024-04-08 16:38:46 | 2.13 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/kea.py", line 75, in kea_interactions
s_uniprots = mapping.map_name(target, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:38:44 | |||
| ¶ | pypath.inputs.kea.kea_interactions | 2024-04-08 16:38:46 | 2024-04-08 16:38:46 | 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__20240408-145602/pypath_git/pypath/inputs/kea.py", line 75, in kea_interactions
s_uniprots = mapping.map_name(target, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:38:46 | |||
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2024-04-08 16:38:46 | 2024-04-08 16:45:19 | 392.77 | list | [KeggInteraction(id_a='Q03113', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcriptional=False), KeggInteraction(id_a='O94763', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcription...(truncated) | 14,827 | {'first': True} | 2024-04-08 16:38:46 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2024-04-08 16:45:19 | 2024-04-08 16:45:42 | 23.62 | set | {KeggMedicusRawInteraction(id_a='K21050', id_b='3134', name_a='(US2) US2; HCMV unique short US2 glycoprotein', name_b='HLA-F', effect='inhibition', itype='post_translational', pw_type='pathogen', type_a='perturbant', type_b='gene', network_id='N00418'), KeggMedicusRawInteraction(id_a='C01413', id_b...(truncated) | 12,946 | {'first': True} | 2024-04-08 16:45:19 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2024-04-08 16:45:42 | 2024-04-08 16:45:43 | 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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/kegg.py", line 643, in process_partner
process_protein(ids, symbols)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/kegg.py", line 636, in process_protein
mapping.map_name(id_, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:45:42 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2024-04-08 16:45:43 | 2024-04-08 16:45:43 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/kegg.py", line 643, in process_partner
process_protein(ids, symbols)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/kegg.py", line 636, in process_protein
mapping.map_name(id_, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:45:43 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2024-04-08 16:45:43 | 2024-04-08 16:45:48 | 4.58 | dict | {'Q9Y6R4': {KeggPathway(pathway='MAPK signaling pathway')}, 'Q12988': {KeggPathway(pathway='Proteoglycans in cancer'), KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='VEGF signaling pathway')}, 'P30305': {KeggPathway(pathway='Cell cycle'), KeggPathway(pathway='MAPK signaling path...(truncated) | 2,652 | {'first': True} | 2024-04-08 16:45:43 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2024-04-08 16:45:48 | 2024-04-08 16:45:48 | 0.51 | dict | {'A8K7J7': {KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Amino suga...(truncated) | 813 | {'first': True} | 2024-04-08 16:45:48 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2024-04-08 16:45:48 | 2024-04-08 16:45:52 | 3.86 | tuple | ({'MAPK signaling pathway': {'Q9Y6R4', 'Q12988', 'P30305', 'Q9HC77', 'Q9H2K8', 'Q9UBE8', 'O75676', 'P18848', 'Q12968', 'O95267', 'P51617', 'O14733', 'P0C869', 'Q15750', 'P01375', 'P08571', 'Q8IVH8', 'Q16637', 'Q9UK32', 'P10398', 'Q9NYJ8', 'Q16644', 'P14210', 'O43318', 'Q7RTX0', 'Q5STR5', 'Q13164', '...(truncated) | 2 | {'first': True} | 2024-04-08 16:45:48 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._generate_conv_functions | 2024-04-08 16:45:52 | 2024-04-08 16:45:52 | 0.00 | NoneType | None | 0 | {'first': True} | 2024-04-08 16:45:52 | |
| ¶ | pypath.inputs.kegg_api._generate_relation_functions | 2024-04-08 16:45:52 | 2024-04-08 16:45:52 | 0.00 | NoneType | None | 0 | {'first': True} | 2024-04-08 16:45:52 | |
| ¶ | pypath.inputs.kegg_api._kegg_conv |
Not calling `pypath.inputs.kegg_api._kegg_conv`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi |
Not calling `pypath.inputs.kegg_api._kegg_ddi`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_async |
Not calling `pypath.inputs.kegg_api._kegg_ddi_async`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_sync |
Not calling `pypath.inputs.kegg_api._kegg_ddi_sync`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general |
Not calling `pypath.inputs.kegg_api._kegg_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general_async |
Not calling `pypath.inputs.kegg_api._kegg_general_async`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_link |
Not calling `pypath.inputs.kegg_api._kegg_link`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_list |
Not calling `pypath.inputs.kegg_api._kegg_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_relations |
Not calling `pypath.inputs.kegg_api._kegg_relations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2024-04-08 16:45:52 | 2024-04-08 16:45:57 | 4.86 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
return entry[0].split(':')[1]
IndexError: list index out of range
|
{'first': True} | 2024-04-08 16:45:52 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2024-04-08 16:45:57 | 2024-04-08 16:45:58 | 0.59 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:45:57 | |||
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2024-04-08 16:45:58 | 2024-04-08 16:45:58 | 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__20240408-145602/pypath_git/pypath/inputs/kirouac2010.py", line 87, in kirouac2010_interactions
tbl = embo.embopress_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/embopress.py", line 96, in embopress_supplementary
fname = c.fname
AttributeError: 'Curl' object has no attribute 'fname'
|
{'first': True} | 2024-04-08 16:45:58 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2024-04-08 16:45:58 | 2024-04-08 16:45:58 | 0.14 |
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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:45:58 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2024-04-08 16:45:58 | 2024-04-08 16:45:58 | 0.12 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 16:45:58 | |||
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2024-04-08 16:45:58 | 2024-04-08 16:45:58 | 0.39 | 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 | {'first': True} | 2024-04-08 16:45:58 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2024-04-08 16:45:58 | 2024-04-08 16:45:59 | 1.00 | 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 | {'first': True} | 2024-04-08 16:45:58 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2024-04-08 16:45:59 | 2024-04-08 16:46:09 | 9.37 | 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 | {'first': True} | 2024-04-08 16:45:59 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2024-04-08 16:46:09 | 2024-04-08 16:46:28 | 18.85 |
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__20240408-145602/pypath_git/pypath/inputs/li2012.py", line 144, in li2012_dmi
subs_resnum = int(common.non_digit.sub('', l[1].split('/')[1]))
AttributeError: module 'pypath.share.common' has no attribute 'non_digit'
|
{'first': True} | 2024-04-08 16:46:09 | |||
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2024-04-08 16:46:28 | 2024-04-08 16:46:28 | 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__20240408-145602/pypath_git/pypath/inputs/li2012.py", line 90, in li2012_enzyme_substrate
subs_resnum = int(common.non_digit.sub('', l[1].split('/')[1]))
AttributeError: module 'pypath.share.common' has no attribute 'non_digit'
|
{'first': True} | 2024-04-08 16:46:28 | |||
| ¶ | pypath.inputs.li2012.li2012_interactions | 2024-04-08 16:46:28 | 2024-04-08 16:46:28 | 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 | {'first': True} | 2024-04-08 16:46:28 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2024-04-08 16:46:28 | 2024-04-08 16:46:31 | 3.11 | 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 | {'first': True} | 2024-04-08 16:46:28 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2024-04-08 16:46:31 | 2024-04-08 16:46:32 | 0.65 | list | [] | 0 | {'first': True} | 2024-04-08 16:46:31 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2024-04-08 16:46:32 | 2024-04-08 16:46:32 | 0.35 | list | [] | 0 | {'first': True} | 2024-04-08 16:46:32 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2024-04-08 16:46:32 | 2024-04-08 16:46:32 | 0.34 | list | [] | 0 | {'first': True} | 2024-04-08 16:46:32 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2024-04-08 16:46:32 | 2024-04-08 16:46:33 | 1.06 | 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 | {'first': True} | 2024-04-08 16:46:32 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2024-04-08 16:46:33 | 2024-04-08 16:46:34 | 0.36 | list | [] | 0 | {'first': True} | 2024-04-08 16:46:33 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2024-04-08 16:46:34 | 2024-04-08 16:47:28 | 53.90 | dict | {'P27824': {LocateAnnotation(source='HPRD', location='golgi apparatus', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI', pmid=None, scor...(truncated) | 9,469 | {'first': True} | 2024-04-08 16:46:34 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2024-04-08 16:47:28 | 2024-04-08 16:47:28 | 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__20240408-145602/pypath_git/pypath/inputs/lrdb.py", line 111, in lrdb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:47:28 | |||
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2024-04-08 16:47:28 | 2024-04-08 16:47:28 | 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 | {'first': True} | 2024-04-08 16:47:28 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2024-04-08 16:47:28 | 2024-04-08 16:47:28 | 0.23 | 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 | {'first': True} | 2024-04-08 16:47:28 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2024-04-08 16:47:28 | 2024-04-08 16:47:29 | 1.10 |
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__20240408-145602/pypath_git/pypath/inputs/matrisome.py", line 86, in __matrisome_annotations_2
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2024-04-08 16:47:28 | |||
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2024-04-08 16:47:29 | 2024-04-08 16:47:30 | 0.81 | dict | {'H0YCP4': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C4X4': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C4S3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,504 | {'first': True} | 2024-04-08 16:47:29 | |
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2024-04-08 16:47:30 | 2024-04-08 16:47:34 | 3.20 | dict | {'O15440': {MatrixdbAnnotation(mainclass='membrane')}, 'O14641': {MatrixdbAnnotation(mainclass='membrane')}, 'O43657': {MatrixdbAnnotation(mainclass='membrane')}, 'Q969V3': {MatrixdbAnnotation(mainclass='membrane')}, 'Q08289': {MatrixdbAnnotation(mainclass='membrane')}, 'P47775': {MatrixdbAnnotation...(truncated) | 10,128 | {'first': True} | 2024-04-08 16:47:30 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2024-04-08 16:47:34 | 2024-04-08 16:47:34 | 0.01 | set | {'Q8N145', 'P08253', 'Q9Y5R2', 'Q9UKP5', 'P25391', 'Q8NFW1', 'Q9NRM1', 'P51693', 'Q9BQB4', 'Q7Z304', 'Q6ZMI3', 'Q96GW7', 'P24043', 'Q9GZV7', 'Q99715', 'O00300', 'Q96CG8', 'Q9NZV1', 'Q92832', 'Q9UBM4', 'Q99542', 'Q7Z7G0', 'Q6W4X9', 'P51512', 'P51511', 'Q8TB73', 'Q99727', 'Q6UXK5', 'O75339', 'P39060',...(truncated) | 482 | {'first': True} | 2024-04-08 16:47:34 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2024-04-08 16:47:34 | 2024-04-08 16:47:34 | 0.12 | 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 | {'first': True} | 2024-04-08 16:47:34 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2024-04-08 16:47:34 | 2024-04-08 16:47:36 | 1.94 | set | {'O15440', 'O14641', 'O43657', 'Q969V3', 'Q08289', 'P47775', 'Q6NXT6', 'Q7Z695', 'Q9Y3D7', 'P12931', 'P34741', 'Q96LB8', 'P33260', 'Q8N9I5', 'P03901', 'Q00325', 'Q86Y34', 'Q6ZUJ8', 'Q9UK28', 'P0DN84', 'Q96KK4', 'O14492', 'A0A0B4J273', 'Q8NH42', 'Q70Z44', 'Q7Z403', 'O00148', 'Q9BUP3', 'Q9BT76', 'Q8NF...(truncated) | 8,269 | {'first': True} | 2024-04-08 16:47:34 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2024-04-08 16:47:36 | 2024-04-08 16:47:36 | 0.32 | set | {'Q5W0Q7', 'Q8N145', 'Q9UBB4', 'A6NHM9', 'P0DPK3', 'P10619', 'Q9BZD6', 'P19883', 'Q9HBJ0', 'Q6UWE3', 'P05013', 'P34741', 'Q96LB8', 'P05362', 'P09871', 'P08294', 'P04216', 'P0DUB6', 'P17693', 'Q6WN34', 'P0C869', 'O95399', 'Q9BSG0', 'Q6PDA7', 'Q5JXM2', 'Q9BU76', 'P19652', 'Q9H7B7', 'P00488', 'Q86YQ2',...(truncated) | 2,924 | {'first': True} | 2024-04-08 16:47:36 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2024-04-08 16:47:36 | 2024-04-08 16:47:37 | 1.31 | set | {'Q9NZ94', 'Q9BY67', 'P28827', 'O14525', 'Q9Y5Y7', 'Q4G160', 'Q15223', 'Q9Y4C0', 'Q9BX90', 'Q6ZW63', 'P56748', 'P34741', 'Q96BL7', 'Q8IUX7', 'Q04900', 'O60759', 'O15394', 'Q13895', 'Q9BRX2', 'Q86WK6', 'P08F94', 'P50895', 'Q9NY15', 'P42771', 'Q96KR4', 'Q13308', 'P07359', 'Q6MZM7', 'Q9BYD3', 'Q6UWL6',...(truncated) | 112 | {'first': True} | 2024-04-08 16:47:36 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2024-04-08 16:47:37 | 2024-04-08 16:48:04 | 26.66 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,433 | {'first': True} | 2024-04-08 16:47:37 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2024-04-08 16:48:04 | 2024-04-08 16:48:04 | 0.15 | 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 | {'first': True} | 2024-04-08 16:48:04 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2024-04-08 16:48:04 | 2024-04-08 16:48:07 | 2.46 | 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 | {'first': True} | 2024-04-08 16:48:04 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2024-04-08 16:48:07 | 2024-04-08 16:48:07 | 0.20 | 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 | {'first': True} | 2024-04-08 16:48:07 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2024-04-08 16:48:07 | 2024-04-08 16:48:07 | 0.19 | 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 | {'first': True} | 2024-04-08 16:48:07 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2024-04-08 16:48:07 | 2024-04-08 16:48:07 | 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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:07 | |||
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2024-04-08 16:48:07 | 2024-04-08 16:48:07 | 0.13 |
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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 141, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:07 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2024-04-08 16:48:07 | 2024-04-08 16:48:07 | 0.13 |
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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 77, in mirbase_mature
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:07 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2024-04-08 16:48:07 | 2024-04-08 16:48:08 | 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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 168, in mirbase_mature_all
return [i[0] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 168, in <listcomp>
return [i[0] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 141, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:07 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2024-04-08 16:48:08 | 2024-04-08 16:48:08 | 0.13 |
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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 90, in mirbase_precursor
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:08 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2024-04-08 16:48:08 | 2024-04-08 16:48:08 | 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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 173, in mirbase_precursor_all
return [i[1] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 173, in <listcomp>
return [i[1] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 141, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:08 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2024-04-08 16:48:08 | 2024-04-08 16:48:08 | 0.14 |
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__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 109, in mirbase_precursor_to_mature
for mmat, mpre in ids:
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 141, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/mirbase.py", line 57, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:48:08 | |||
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2024-04-08 16:48:08 | 2024-04-08 16:48:08 | 0.29 | 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 | {'first': True} | 2024-04-08 16:48:08 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2024-04-08 16:48:08 | 2024-04-08 16:48:09 | 0.57 | 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 | {'first': True} | 2024-04-08 16:48:08 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2024-04-08 16:48:09 | 2024-04-08 16:48:15 | 5.65 |
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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{'first': True} | 2024-04-08 16:48:09 | |||
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2024-04-08 16:48:15 | 2024-04-08 16:48:15 | 0.30 | 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 | {'first': True} | 2024-04-08 16:48:15 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2024-04-08 16:48:15 | 2024-04-08 16:49:03 | 48.24 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3641, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2300, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2302, in <genexpr>
self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 16:48:15 | |||
| ¶ | pypath.inputs.msigdb.msigdb_download | 2024-04-08 16:49:03 | 2024-04-08 16:49:16 | 13.29 | dict | {'chr1p11': {'FAM72B', 'PPIAL4A', 'SRGAP2-AS1', 'NOTCH2NLR', 'EMBP1', 'NBPF26', 'LINC00623', 'RPL22P6', 'FCGR1BP', 'MTIF2P1', 'H3P4', 'H2BP1', 'PDE4DIPP4', 'RNVU1-4', 'RNVU1-19', 'LINC02798', 'NBPF8', 'PDE4DIPP2', 'SRGAP2C', 'LINC01691', 'PFN1P2'}, 'chr1p12': {'PSMC1P12', 'HSD3BP4', 'NBPF7P', 'GAPDH...(truncated) | 33,591 | {'first': True} | 2024-04-08 16:49:03 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2024-04-08 16:49:17 | 2024-04-08 16:49:17 | 0.47 | dict | {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'NFIL3', 'PER1', 'CLCF1', 'CXCL10', 'CDKN1A', 'LAMB3', 'SPSB1', 'MARCKS', 'SPHK1', 'KLF6', 'RNF19B', 'DUSP1', 'HBEGF', 'RHOB', 'TNFSF9', 'BHLHE40', 'TNFRSF9', 'CD69', 'GFPT2', 'REL', 'EGR2', 'NINJ1', 'LITAF', 'TNIP2', 'MAP3K8', 'TNF', 'RE...(truncated) | 18 | {'first': True} | 2024-04-08 16:49:17 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2024-04-08 16:49:18 | 2024-04-08 16:49:18 | 0.39 | 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 | {'first': True} | 2024-04-08 16:49:18 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2024-04-08 16:49:18 | 2024-04-08 16:49:48 | 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__20240408-145602/pypath_git/pypath/inputs/negatome.py", line 49, in negatome_interactions
for l in f:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 16:49:18 | |||
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2024-04-08 16:49:48 | 2024-04-08 16:49:48 | 0.16 | 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 | {'first': True} | 2024-04-08 16:49:48 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2024-04-08 16:49:48 | 2024-04-08 16:49:48 | 0.13 | 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 | {'first': True} | 2024-04-08 16:49:48 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2024-04-08 16:49:48 | 2024-04-08 16:52:50 | 181.31 |
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__20240408-145602/pypath_git/pypath/inputs/netpath.py", line 43, in netpath_interactions
pwnames = netpath_names()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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---jXRgP0-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()
|
{'first': True} | 2024-04-08 16:49:48 | |||
| ¶ | pypath.inputs.netpath.netpath_names | 2024-04-08 16:52:50 | 2024-04-08 16:55:51 | 180.83 |
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__20240408-145602/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---jXRgP0-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()
|
{'first': True} | 2024-04-08 16:52:50 | |||
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2024-04-08 16:55:51 | 2024-04-08 17:01:52 | 361.81 |
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__20240408-145602/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__20240408-145602/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---jXRgP0-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()
|
{'first': True} | 2024-04-08 16:55:51 | |||
| ¶ | pypath.inputs.offsides._sides_base |
Not calling `pypath.inputs.offsides._sides_base`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2024-04-08 17:01:52 | 2024-04-08 17:01:53 | 0.20 |
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__20240408-145602/pypath_git/pypath/inputs/offsides.py", line 70, in _sides_base
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2024-04-08 17:01:52 | |||
| ¶ | pypath.inputs.oma._id_translate |
Not calling `pypath.inputs.oma._id_translate`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.oma.oma_orthologs | 2024-04-08 17:01:53 | 2024-04-08 17:03:19 | 86.86 | list | [OmaOrthology(a=OmaGene(id='OR6B2_HUMAN', oma_group=350582, hog='HOG:D0615686.2b.14b', taxon=9606, chr='2', start=240029491, end=240030429, strand=-1, main_isoform=True), b=OmaGene(id='Q8VGU5', oma_group=906496, hog='HOG:D0615686.2b.11b.5a', taxon=10090, chr='1', start=92438810, end=92439748, strand...(truncated) | 22,379 | {'first': True} | 2024-04-08 17:01:53 | |
| ¶ | pypath.inputs.oma.oma_table | 2024-04-08 17:03:19 | 2024-04-08 17:03:26 | 6.81 | defaultdict | defaultdict(<class 'set'>, {'OR6B2_HUMAN': {'Q8VGU5', 'A0A0N4SV77'}, 'PE2R3_HUMAN': {'G3UYL9'}, 'RIDA_HUMAN': {'RIDA_MOUSE'}, 'S31F1_HUMAN': {'A2AKP6', '31F12_MOUSE', 'D3YZF6'}, 'CREG2_HUMAN': {'CREG2_MOUSE'}, 'DRC9_HUMAN': {'DRC9_MOUSE'}, 'HDAC3_HUMAN': {'HDAC3_MOUSE'}, 'P2Y10_HUMAN': {'P2Y10_MOUSE...(truncated) | 17,896 | {'first': True} | 2024-04-08 17:03:19 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2024-04-08 17:03:26 | 2024-04-08 17:03:27 | 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__20240408-145602/pypath_git/pypath/inputs/ontology.py", line 118, in listof_ontologies
result = ebi.ebi_rest(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/ebi.py", line 141, in ebi_rest
res = inputs_common.json_extract(c.result, fields)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 333, in json_extract
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 334, in <listcomp>
glom.glom(rec, spec, default = _cons.GLOM_ERROR)
NameError: name '_cons' is not defined
|
{'first': True} | 2024-04-08 17:03:26 | |||
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.opentargets._opentargets_general |
Not calling `pypath.inputs.opentargets._opentargets_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2024-04-08 17:03:27 | 2024-04-08 17:03:49 | 22.18 | 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 | {'first': True} | 2024-04-08 17:03:27 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2024-04-08 17:03:49 | 2024-04-08 17:10:41 | 411.56 | 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 | {'first': True} | 2024-04-08 17:03:49 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2024-04-08 17:10:41 | 2024-04-08 17:12:20 | 99.13 | 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 | {'first': True} | 2024-04-08 17:10:41 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2024-04-08 17:12:20 | 2024-04-08 17:16:30 | 249.86 | 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 | {'first': True} | 2024-04-08 17:12:20 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2024-04-08 17:16:30 | 2024-04-08 17:16:55 | 25.26 |
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__20240408-145602/pypath_git/pypath/inputs/opm.py", line 101, in opm_annotations
mapping.map_name0(this_name, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3582, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1799, in map_name0
names = self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 17:16:30 | |||
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2024-04-08 17:16:55 | 2024-04-08 17:17:25 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2024-04-08 17:16:55 | |||
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2024-04-08 17:17:25 | 2024-04-08 17:17:55 | 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__20240408-145602/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2024-04-08 17:17:25 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2024-04-08 17:17:55 | 2024-04-08 17:17:55 | 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__20240408-145602/pypath_git/pypath/inputs/panglaodb.py", line 80, in panglaodb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 17:17:55 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2024-04-08 17:17:55 | 2024-04-08 17:17:55 | 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 | {'first': True} | 2024-04-08 17:17:55 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2024-04-08 17:17:55 | 2024-04-08 17:17:55 | 0.00 | list | [] | 0 | {'first': True} | 2024-04-08 17:17:55 | |
| ¶ | pypath.inputs.pathwaycommons._create_single_resource_method |
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2024-04-08 17:17:55 | 2024-04-08 17:18:08 | 12.32 |
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__20240408-145602/pypath_git/pypath/inputs/pathwaycommons.py", line 120, in pathwaycommons_interactions
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2024-04-08 17:17:55 | |||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2024-04-08 17:18:08 | 2024-04-08 17:18:08 | 0.37 | 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 | {'first': True} | 2024-04-08 17:18:08 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2024-04-08 17:18:08 | 2024-04-08 17:18:15 | 7.08 | 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 | {'first': True} | 2024-04-08 17:18:08 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2024-04-08 17:18:18 | 2024-04-08 17:18:26 | 8.17 | 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) | 44,851 | {'first': True} | 2024-04-08 17:18:18 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2024-04-08 17:18:26 | 2024-04-08 17:18:33 | 6.70 | tuple | ({'P02185': {('3h58', 'X-ray', 1.8), ('1cp0', 'X-ray', 2.0), ('2w6x', 'X-ray', 1.73), ('7cez', 'X-ray', 1.57), ('5ilm', 'X-ray', 1.7), ('2myb', 'X-ray', 1.9), ('1vxa', 'X-ray', 2.0), ('4nxa', 'X-ray', 1.6), ('5zeo', 'X-ray', 1.77), ('1ufp', 'X-ray', 2.1), ('5hlx', 'X-ray', 1.5), ('7slh', 'X-ray', 1....(truncated) | 2 | {'first': True} | 2024-04-08 17:18:26 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2024-04-08 17:18:33 | 2024-04-08 17:18:34 | 0.63 | 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 | {'first': True} | 2024-04-08 17:18:33 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2024-04-08 17:18:34 | 2024-04-08 17:31:07 | 752.99 | 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 | {'first': True} | 2024-04-08 17:18:34 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2024-04-08 17:31:07 | 2024-04-08 17:31:08 | 1.23 | 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 | {'first': True} | 2024-04-08 17:31:07 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2024-04-08 17:31:08 | 2024-04-08 17:31:08 | 0.12 |
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__20240408-145602/pypath_git/pypath/inputs/pfam.py", line 316, in pfam_pdb
start = int(common.non_digit.sub('', l[2]))
AttributeError: module 'pypath.share.common' has no attribute 'non_digit'
|
{'first': True} | 2024-04-08 17:31:08 | |||
| ¶ | pypath.inputs.pfam.pfam_regions | 2024-04-08 17:31:08 | 2024-04-08 17:35:49 | 280.97 | tuple | ({}, {}) | 2 | {'first': True} | 2024-04-08 17:31:08 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2024-04-08 17:35:49 | 2024-04-08 17:35:57 | 7.98 |
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__20240408-145602/pypath_git/pypath/inputs/pfam.py", line 94, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{'first': True} | 2024-04-08 17:35:49 | |||
| ¶ | pypath.inputs.pharos._create_query_functions | 2024-04-08 17:35:57 | 2024-04-08 17:35:57 | 0.00 | NoneType | None | 0 | {'first': True} | 2024-04-08 17:35:57 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2024-04-08 17:35:57 | 2024-04-08 18:08:16 | 1,938.96 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2024-04-08 17:35:57 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2024-04-08 18:08:17 | 2024-04-08 18:08:21 | 3.56 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2024-04-08 18:08:17 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2024-04-08 18:08:22 | 2024-04-08 18:08:25 | 3.41 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2024-04-08 18:08:22 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2024-04-08 18:08:26 | 2024-04-08 18:08:30 | 3.50 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2024-04-08 18:08:26 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2024-04-08 18:08:31 | 2024-04-08 18:08:34 | 3.25 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2024-04-08 18:08:31 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2024-04-08 18:08:35 | 2024-04-08 18:19:28 | 653.54 | 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 | {'first': True} | 2024-04-08 18:08:35 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2024-04-08 18:19:28 | 2024-04-08 18:19:31 | 2.96 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2024-04-08 18:19:28 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2024-04-08 18:19:32 | 2024-04-08 18:19:33 | 0.59 | 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 | {'first': True} | 2024-04-08 18:19:32 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2024-04-08 18:19:33 | 2024-04-08 18:19:33 | 0.14 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 18:19:33 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2024-04-08 18:19:33 | 2024-04-08 18:19:35 | 1.54 | 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 | {'first': True} | 2024-04-08 18:19:33 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2024-04-08 18:19:35 | 2024-04-08 18:19:35 | 0.51 | 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 | {'first': True} | 2024-04-08 18:19:35 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2024-04-08 18:19:35 | 2024-04-08 18:19:35 | 0.11 | 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 | {'first': True} | 2024-04-08 18:19:35 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2024-04-08 18:19:35 | 2024-04-08 18:19:37 | 1.43 | 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 | {'first': True} | 2024-04-08 18:19:35 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2024-04-08 18:19:37 | 2024-04-08 18:19:37 | 0.02 | list | [['RAF1', 'RNUXA'], ['WEE1', 'EIF4A3'], ['PRKACA', 'STUB1'], ['CDK4', 'C14orf106'], ['DYRK1B', 'ERF'], ['MAP4K5', 'STUB1'], ['PAK6', 'MDM2'], ['MAPK3', 'NCF1'], ['FYN', 'FCGR2A'], ['ADRBK1', 'TP53'], ['LCK', 'ITK'], ['NEK4', 'DDX39'], ['DCLK1', 'PRKACB'], ['CDK6', 'LIG1'], ['MAPK8', 'SNRP70'], ['CDK...(truncated) | 1,821 | {'first': True} | 2024-04-08 18:19:37 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2024-04-08 18:19:37 | 2024-04-08 18:19:37 | 0.25 | 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 | {'first': True} | 2024-04-08 18:19:37 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2024-04-08 18:19:37 | 2024-04-08 18:19:37 | 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 | {'first': True} | 2024-04-08 18:19:37 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2024-04-08 18:19:37 | 2024-04-08 18:19:37 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) | 9,094 | {'first': True} | 2024-04-08 18:19:37 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2024-04-08 18:19:37 | 2024-04-08 18:19:38 | 0.46 | 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 | {'first': True} | 2024-04-08 18:19:37 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2024-04-08 18:19:38 | 2024-04-08 18:19:38 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {'first': True} | 2024-04-08 18:19:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2024-04-08 18:19:38 | 2024-04-08 18:19:38 | 0.07 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 9,164 | {'first': True} | 2024-04-08 18:19:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2024-04-08 18:19:38 | 2024-04-08 18:19:38 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 4,374 | {'first': True} | 2024-04-08 18:19:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2024-04-08 18:19:38 | 2024-04-08 18:19:38 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {'first': True} | 2024-04-08 18:19:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2024-04-08 18:19:38 | 2024-04-08 18:19:38 | 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', 'WB;MA;AB'...(truncated) | 4,790 | {'first': True} | 2024-04-08 18:19:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2024-04-08 18:19:38 | 2024-04-08 18:19:38 | 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__20240408-145602/pypath_git/pypath/inputs/phosphosite.py", line 213, in phosphosite_ptm_orthology
for typ in common.psite_mod_types:
TypeError: 'function' object is not iterable
|
{'first': True} | 2024-04-08 18:19:38 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2024-04-08 18:19:38 | 2024-04-08 18:19:57 | 19.24 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {'first': True} | 2024-04-08 18:19:38 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2024-04-08 18:19:57 | 2024-04-08 18:19:58 | 0.50 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'protein degradation', 'phosphorylation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {'first': True} | 2024-04-08 18:19:57 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2024-04-08 18:19:58 | 2024-04-08 18:19:58 | 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__20240408-145602/pypath_git/pypath/inputs/phosphosite.py", line 504, in phosphosite_regsites_one_organism
mod_types = dict(common.psite_mod_types2)
TypeError: 'function' object is not iterable
|
{'first': True} | 2024-04-08 18:19:58 | |||
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2024-04-08 18:19:58 | 2024-04-08 18:20:36 | 37.78 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {'first': True} | 2024-04-08 18:19:58 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2024-04-08 18:20:36 | 2024-04-08 18:20:41 | 5.27 | 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) | 391,447 | {'first': True} | 2024-04-08 18:20:36 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2024-04-08 18:20:41 | 2024-04-08 18:20:45 | 3.81 |
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__20240408-145602/pypath_git/pypath/inputs/progeny.py", line 97, in progeny_annotations
raw = progeny_raw(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/progeny.py", line 67, in progeny_raw
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (274143) does not match length of index (2)
|
{'first': True} | 2024-04-08 18:20:41 | |||
| ¶ | pypath.inputs.progeny.progeny_raw | 2024-04-08 18:20:45 | 2024-04-08 18:20:47 | 1.86 |
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__20240408-145602/pypath_git/pypath/inputs/progeny.py", line 67, in progeny_raw
rdata_converted = rdata.rdata.conversion.convert(rdata_parsed)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 933, in convert
return SimpleConverter(*args, **kwargs).convert(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 699, in convert
return self._convert_next(data)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 728, in _convert_next
value = convert_list(obj, self._convert_next)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 141, in convert_list
return {tag: conversion_function(r_list.value[0]), **cdr}
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 866, in _convert_next
new_value = constructor(value, attrs)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/rdata/conversion/_conversion.py", line 472, in dataframe_constructor
return pandas.DataFrame(obj, columns=obj, index=index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 767, in __init__
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 119, in arrays_to_mgr
arrays, refs = _homogenize(arrays, index, dtype)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 630, in _homogenize
com.require_length_match(val, index)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pandas/core/common.py", line 571, in require_length_match
raise ValueError(
ValueError: Length of values (274143) does not match length of index (2)
|
{'first': True} | 2024-04-08 18:20:45 | |||
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2024-04-08 18:20:47 | 2024-04-08 18:20:47 | 0.56 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:20:47 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2024-04-08 18:20:47 | 2024-04-08 18:20:48 | 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__20240408-145602/pypath_git/pypath/inputs/proteinatlas.py", line 120, in proteinatlas_annotations
data = get_proteinatlas(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:20:47 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2024-04-08 18:20:48 | 2024-04-08 18:20:48 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 18:20:48 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2024-04-08 18:20:48 | 2024-04-08 18:20:48 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:20:48 | |||
| ¶ | pypath.inputs.proteins.variants | 2024-04-08 18:20:48 | 2024-04-08 18:20:56 | 7.63 |
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__20240408-145602/pypath_git/pypath/inputs/proteins.py", line 130, in variants
result = ebi.ebi_rest(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/ebi.py", line 141, in ebi_rest
res = inputs_common.json_extract(c.result, fields)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 333, in json_extract
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 334, in <listcomp>
glom.glom(rec, spec, default = _cons.GLOM_ERROR)
NameError: name '_cons' is not defined
|
{'first': True} | 2024-04-08 18:20:48 | |||
| ¶ | pypath.inputs.protmapper.get_protmapper | 2024-04-08 18:20:56 | 2024-04-08 18:20:58 | 2.07 | 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 | {'first': True} | 2024-04-08 18:20:56 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2024-04-08 18:20:58 | 2024-04-08 18:20:58 | 0.52 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'24357804', '25728676', '22304920', '24727247', '25545367'}, 'substrate': 'P15336', 'databases': {'REACH', 'PhosphoSite', 'SIGNOR', 'Sparser'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'23708658', '24727247'}, ...(truncated) | 22,139 | {'first': True} | 2024-04-08 18:20:58 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2024-04-08 18:20:59 | 2024-04-08 18:20:59 | 0.52 | 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 | {'first': True} | 2024-04-08 18:20:59 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2024-04-08 18:20:59 | 2024-04-08 18:21:05 | 5.95 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), Ram...(truncated) | 18,885 | {'first': True} | 2024-04-08 18:20:59 | |
| ¶ | pypath.inputs.ramp._ramp_sqldump | 2024-04-08 18:21:05 | 2024-04-08 18:21:10 | 5.06 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/cache/2ac9fe4b32649e946c59f28f74943748-38534654' encoding='utf-8'> | 0 | {'first': True} | 2024-04-08 18:21:05 | |
| ¶ | pypath.inputs.ramp.ramp_id_types | 2024-04-08 18:21:10 | 2024-04-08 18:21:10 | 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__20240408-145602/pypath_git/pypath/inputs/ramp.py", line 172, in ramp_id_types
con = ramp_raw(tables = 'source', sqlite = True)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/ramp.py", line 83, in ramp_raw
return sqldump.tables(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/formats/sqldump.py", line 79, in tables
common.log_memory_usage()
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 1924, in log_memory_usage
pypath.session.log.msg(
AttributeError: 'function' object has no attribute 'msg'
|
{'first': True} | 2024-04-08 18:21:10 | |||
| ¶ | pypath.inputs.ramp.ramp_id_types_2 | 2024-04-08 18:21:10 | 2024-04-08 18:21:19 | 8.72 | set | {'uniprot', 'gene_symbol', 'pubchem', 'plantfa', 'rhea-comp', 'chemspider', 'swisslipids', 'LIPIDMAPS', 'entrez', 'kegg', 'lipidbank', 'EN', 'wikidata', 'hmdb', 'CAS', 'kegg_glycan', 'polymer', 'brenda', 'chebi', 'ensembl', 'ncbiprotein'} | 21 | {'first': True} | 2024-04-08 18:21:10 | |
| ¶ | pypath.inputs.ramp.ramp_list_tables | 2024-04-08 18:21:19 | 2024-04-08 18:21:21 | 2.35 | 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 | {'first': True} | 2024-04-08 18:21:19 | |
| ¶ | pypath.inputs.ramp.ramp_mapping |
Not calling `pypath.inputs.ramp.ramp_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_raw |
Not calling `pypath.inputs.ramp.ramp_raw`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_show_tables | 2024-04-08 18:21:21 | 2024-04-08 18:21:24 | 2.35 | NoneType | None | 0 | {'first': True} | 2024-04-08 18:21:21 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2024-04-08 18:21:24 | 2024-04-08 18:21:24 | 0.00 | NoneType | None | 0 | {'first': True} | 2024-04-08 18:21:24 | |
| ¶ | pypath.inputs.rdata._rdata_data_frame_get_rownames |
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.rdata._rdata_list_get_names |
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._bp_collect_resources |
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._process_controls |
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_resources |
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_species |
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_compartment |
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_id |
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_res |
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_id |
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reaction |
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reactions | 2024-04-08 18:21:24 | 2024-04-08 18:21:24 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 134, in reactome_bs
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{'first': True} | 2024-04-08 18:21:24 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2024-04-08 18:21:24 | 2024-04-08 18:21:24 | 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__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 1032, in _reactome_reactions_et
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{'first': True} | 2024-04-08 18:21:24 | |||
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2024-04-08 18:21:24 | 2024-04-08 18:21:33 | 9.32 | NoneType | None | 0 | {'first': True} | 2024-04-08 18:21:24 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2024-04-08 18:21:33 | 2024-04-08 18:21:33 | 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 | {'first': True} | 2024-04-08 18:21:33 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2024-04-08 18:21:33 | 2024-04-08 18:21:33 | 0.34 |
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__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/pyreact.py", line 1172, in load_wikipathways
len(biopaxes.result),
TypeError: object of type 'NoneType' has no len()
|
{'first': True} | 2024-04-08 18:21:33 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2024-04-08 18:21:33 | 2024-04-08 18:21:40 | 6.44 | dict | {'BioPAX/2-arachidonoylglycerol_biosynthesis.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/5-Hydroxytryptamine_biosynthesis.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypa...(truncated) | 178 | {'first': True} | 2024-04-08 18:21:33 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2024-04-08 18:21:40 | 2024-04-08 18:21:42 | 1.94 | NoneType | None | 0 | {'first': True} | 2024-04-08 18:21:40 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2024-04-08 18:21:42 | 2024-04-08 18:21:42 | 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__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 79, in reactome_biopax
url = urls.urls['reactome']['biopax_l3']
KeyError: 'biopax_l3'
|
{'first': True} | 2024-04-08 18:21:42 | |||
| ¶ | pypath.inputs.reaction.reactome_bs | 2024-04-08 18:21:42 | 2024-04-08 18:21:42 | 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__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 134, in reactome_bs
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{'first': True} | 2024-04-08 18:21:42 | |||
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2024-04-08 18:21:42 | 2024-04-08 18:21:42 | 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__20240408-145602/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{'first': True} | 2024-04-08 18:21:42 | |||
| ¶ | pypath.inputs.reactome._reactome_data |
Not calling `pypath.inputs.reactome._reactome_data`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reactome._reactome_data_gen |
Not calling `pypath.inputs.reactome._reactome_data_gen`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reactome.reactome_chebis | 2024-04-08 18:21:42 | 2024-04-08 18:21:48 | 6.26 |
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__20240408-145602/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{'first': True} | 2024-04-08 18:21:42 | |||
| ¶ | pypath.inputs.reactome.reactome_pathway_relations | 2024-04-08 18:21:48 | 2024-04-08 18:21:49 | 0.83 |
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__20240408-145602/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{'first': True} | 2024-04-08 18:21:48 | |||
| ¶ | pypath.inputs.reactome.reactome_pathways | 2024-04-08 18:21:49 | 2024-04-08 18:21:50 | 1.04 |
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__20240408-145602/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{'first': True} | 2024-04-08 18:21:49 | |||
| ¶ | pypath.inputs.reactome.reactome_uniprots | 2024-04-08 18:21:50 | 2024-04-08 18:22:06 | 16.29 |
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__20240408-145602/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{'first': True} | 2024-04-08 18:21:50 | |||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2024-04-08 18:22:06 | 2024-04-08 18:22:07 | 0.77 |
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__20240408-145602/pypath_git/pypath/inputs/scconnect.py", line 109, in scconnect_annotations
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/scconnect.py", line 110, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:22:06 | |||
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2024-04-08 18:22:07 | 2024-04-08 18:22:07 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/scconnect.py", line 109, in scconnect_annotations
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/scconnect.py", line 110, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:22:07 | |||
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2024-04-08 18:22:07 | 2024-04-08 18:23:34 | 87.44 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/scconnect.py", line 197, in process_partner
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/scconnect.py", line 198, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:22:07 | |||
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2024-04-08 18:23:34 | 2024-04-08 18:23:35 | 0.13 | dict | {'CID100000271': {SiderDrug(name='calcium', atc='A12AA20'), SiderDrug(name='calcium', atc='A07XA03')}, 'CID100003381': {SiderDrug(name='fluocinolone', atc='C05AA10'), SiderDrug(name='fluocinolone', atc='D07AC04'), SiderDrug(name='fluocinolone', atc='S02BA08'), SiderDrug(name='fluocinolone', atc='S01...(truncated) | 1,430 | {'first': True} | 2024-04-08 18:23:34 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2024-04-08 18:23:35 | 2024-04-08 18:23:35 | 0.43 | list | [SiderSideeffectMeddra(cid='C0278500', meddra_id='10002136', side_effect_name='Anal cancer stage II'), SiderSideeffectMeddra(cid='C0860280', meddra_id='10014894', side_effect_name='Enterocolitis AIDS'), SiderSideeffectMeddra(cid='C1735603', meddra_id='10066418', side_effect_name="Tenon's cyst"), Sid...(truncated) | 20,307 | {'first': True} | 2024-04-08 18:23:35 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2024-04-08 18:23:35 | 2024-04-08 18:23:37 | 1.69 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0013404', umls_concept_in_meddra='C0013404', side_effect='Dyspnoea', frequency='7%'), SiderSideeffetFrequency(umls_concept_on_label='C0031350', umls_concept_in_meddra='C0031350', side_effect='Pharyngitis', frequency='33%'), SiderSidee...(truncated) | 968 | {'first': True} | 2024-04-08 18:23:35 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2024-04-08 18:23:37 | 2024-04-08 18:23:38 | 1.14 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0002418', umls_concept_in_meddra='C0002418', side_effect='Amblyopia'), SiderSideeffect(umls_concept_on_label='C0019080', umls_concept_in_meddra='C0019080', side_effect='Haemorrhage'), SiderSideeffect(umls_concept_on_label='C0546817', umls_con...(truncated) | 1,430 | {'first': True} | 2024-04-08 18:23:37 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2024-04-08 18:23:38 | 2024-04-08 18:23:39 | 1.35 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway...(truncated) | 2 | {'first': True} | 2024-04-08 18:23:38 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2024-04-08 18:23:40 | 2024-04-08 18:23:40 | 0.44 | dict | {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 785 | {'first': True} | 2024-04-08 18:23:40 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2024-04-08 18:23:40 | 2024-04-08 18:23:41 | 0.95 | 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 | {'first': True} | 2024-04-08 18:23:40 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2024-04-08 18:23:41 | 2024-04-08 18:23:41 | 0.45 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='T-cell receptor')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='To...(truncated) | 839 | {'first': True} | 2024-04-08 18:23:41 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2024-04-08 18:23:41 | 2024-04-08 18:23:42 | 0.74 | 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) | 4,886 | {'first': True} | 2024-04-08 18:23:41 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2024-04-08 18:23:42 | 2024-04-08 18:23:42 | 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__20240408-145602/pypath_git/pypath/inputs/signor.py", line 200, in signor_enzyme_substrate
for k, v in iteritems(common.aaletters))
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
AttributeError: 'function' object has no attribute 'items'
|
{'first': True} | 2024-04-08 18:23:42 | |||
| ¶ | pypath.inputs.signor.signor_interactions | 2024-04-08 18:23:42 | 2024-04-08 18:23:44 | 2.04 | list | [SignorInteraction(source='Q99608', target='Q9UBK2', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates quantity by stabilization', mechanism='binding', ncbi_tax_id='9606', pubmeds='26971449', direct=True, ptm_type='binding', ptm_residue='', ...(truncated) | 92,249 | {'first': True} | 2024-04-08 18:23:42 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2024-04-08 18:23:44 | 2024-04-08 18:24:02 | 17.44 | dict | {'O60674': {SignorPathway(pathway='EBV infection'), SignorPathway(pathway='Leptin Signaling'), SignorPathway(pathway='EGFR Signaling'), SignorPathway(pathway='Macrophage polarization'), SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q5H9F3': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P1...(truncated) | 694 | {'first': True} | 2024-04-08 18:23:44 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2024-04-08 18:24:02 | 2024-04-08 18:24:02 | 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 | {'first': True} | 2024-04-08 18:24:02 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2024-04-08 18:24:02 | 2024-04-08 18:24:06 | 4.39 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/spike.py", line 101, in spike_interactions
if all(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/spike.py", line 103, in <genexpr>
genes[m][0].type != 'complex'
IndexError: list index out of range
|
{'first': True} | 2024-04-08 18:24:02 | |||
| ¶ | pypath.inputs.spike.spike_interactions | 2024-04-08 18:24:06 | 2024-04-08 18:24:09 | 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__20240408-145602/pypath_git/pypath/inputs/spike.py", line 101, in spike_interactions
if all(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/spike.py", line 103, in <genexpr>
genes[m][0].type != 'complex'
IndexError: list index out of range
|
{'first': True} | 2024-04-08 18:24:06 | |||
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2024-04-08 18:24:09 | 2024-04-08 18:25:28 | 79.49 | 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 | {'first': True} | 2024-04-08 18:24:09 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2024-04-08 18:25:28 | 2024-04-08 18:26:55 | 87.30 | 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 | {'first': True} | 2024-04-08 18:25:28 | |
| ¶ | pypath.inputs.string.string_effects | 2024-04-08 18:26:55 | 2024-04-08 18:26:56 | 0.14 |
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__20240408-145602/pypath_git/pypath/inputs/string.py", line 64, in string_effects
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2024-04-08 18:26:55 | |||
| ¶ | pypath.inputs.string.string_links_interactions | 2024-04-08 18:26:56 | 2024-04-08 18:27:23 | 27.50 | 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 | {'first': True} | 2024-04-08 18:26:56 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2024-04-08 18:27:23 | 2024-04-08 18:27:24 | 1.37 | 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 | {'first': True} | 2024-04-08 18:27:23 | |
| ¶ | pypath.inputs.string.string_species | 2024-04-08 18:27:25 | 2024-04-08 18:27:25 | 0.15 | 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 | {'first': True} | 2024-04-08 18:27:25 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2024-04-08 18:27:25 | 2024-04-08 18:27:27 | 2.34 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{'first': True} | 2024-04-08 18:27:25 | |||
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2024-04-08 18:27:27 | 2024-04-08 18:27:28 | 1.23 |
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__20240408-145602/pypath_git/pypath/inputs/switches_elm.py", line 91, in get_switches_elm
mod_ont = ontology.ontology('MOD')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/ontology.py", line 68, in ontology
result = ebi.ebi_rest(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/ebi.py", line 141, in ebi_rest
res = inputs_common.json_extract(c.result, fields)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 333, in json_extract
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 334, in <listcomp>
glom.glom(rec, spec, default = _cons.GLOM_ERROR)
NameError: name '_cons' is not defined
|
{'first': True} | 2024-04-08 18:27:27 | |||
| ¶ | pypath.inputs.talklr.talklr_annotations | 2024-04-08 18:27:28 | 2024-04-08 18:27:29 | 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__20240408-145602/pypath_git/pypath/inputs/talklr.py", line 105, in talklr_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:27:28 | |||
| ¶ | pypath.inputs.talklr.talklr_interactions | 2024-04-08 18:27:29 | 2024-04-08 18:27:29 | 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 | {'first': True} | 2024-04-08 18:27:29 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2024-04-08 18:27:29 | 2024-04-08 18:27:29 | 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 | {'first': True} | 2024-04-08 18:27:29 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2024-04-08 18:27:29 | 2024-04-08 18:27:35 | 6.52 | dict | {'B1B1G6': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(family='Synaptosomal Vesicle Fusion Pore (SVF-Pore)', tcid='1.F.1.1.1')}, 'O00299'...(truncated) | 2,327 | {'first': True} | 2024-04-08 18:27:29 | |
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2024-04-08 18:27:35 | 2024-04-08 18:27:35 | 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) | 23,535 | {'first': True} | 2024-04-08 18:27:35 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2024-04-08 18:27:35 | 2024-04-08 18:27:35 | 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) | 1,920 | {'first': True} | 2024-04-08 18:27:35 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2024-04-08 18:27:35 | 2024-04-08 18:27:36 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3641, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2300, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2302, in <genexpr>
self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1978, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:27:35 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2024-04-08 18:27:36 | 2024-04-08 18:27:39 | 3.76 | 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 | {'first': True} | 2024-04-08 18:27:36 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2024-04-08 18:27:39 | 2024-04-08 18:28:01 | 21.40 | set | {ThreedcomplexContact(pdb='2x2v_1', uniprot_1='P22483', uniprot_2='P22483', chain_1='C', chain_2='D', n_residues=29.5, length_1=68, length_2=68, domain_s1=('',), domain_p1=('PF00137.16',), domain_s2=('',), domain_p2=('PF00137.16',), ident=True, homo=True), ThreedcomplexContact(pdb='2yzc_1', uniprot_...(truncated) | 259,354 | {'first': True} | 2024-04-08 18:27:39 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2024-04-08 18:28:02 | 2024-04-08 18:31:24 | 202.24 | list | [<pypath.internals.intera.DomainDomain object at 0x7f766b672350>, <pypath.internals.intera.DomainDomain object at 0x7f766b672470>, <pypath.internals.intera.DomainDomain object at 0x7f766b6724d0>, <pypath.internals.intera.DomainDomain object at 0x7f766b672590>, <pypath.internals.intera.DomainDomain o...(truncated) | 523,776 | {'first': True} | 2024-04-08 18:28:02 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2024-04-08 18:31:25 | 2024-04-08 18:31:35 | 9.80 | dict | {'2x2v_1': {('P22483', 'P22483'): 29.0}, '2yzc_1': {('D0VWQ1', 'D0VWQ1'): 66.5}, '1jof_1': {('P38677', 'P38677'): 15.0}, '1lrl_1': {('P09147', 'P09147'): 20.0}, '5jz9_1': {('P9WNH5', 'P9WNH5'): 20.0}, '2qkp_1': {('Q8DU08', 'Q8DU08'): 42.0}, '3sm3_1': {('Q8PUK2', 'Q8PUK2'): 15.0}, '5l68_1': {('P30656...(truncated) | 81,061 | {'first': True} | 2024-04-08 18:31:25 | |
| ¶ | pypath.inputs.threedid.get_3did | 2024-04-08 18:31:35 | 2024-04-08 18:32:13 | 38.17 |
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__20240408-145602/pypath_git/pypath/inputs/threedid.py", line 329, in get_3did
common.non_digit.sub('', l[2][2:].split('-')[0])
AttributeError: module 'pypath.share.common' has no attribute 'non_digit'
|
{'first': True} | 2024-04-08 18:31:35 | |||
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2024-04-08 18:32:13 | 2024-04-08 18:32:24 | 11.39 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/pfam.py", line 94, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{'first': True} | 2024-04-08 18:32:13 | |||
| ¶ | pypath.inputs.topdb.topdb_annotations | 2024-04-08 18:32:24 | 2024-04-08 18:32:25 | 0.66 |
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__20240408-145602/pypath_git/pypath/inputs/topdb.py", line 50, in topdb_annotations
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 18:32:24 | |||
| ¶ | pypath.inputs.transmir.transmir_interactions | 2024-04-08 18:32:25 | 2024-04-08 18:32:26 | 0.99 | 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 | {'first': True} | 2024-04-08 18:32:25 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2024-04-08 18:32:26 | 2024-04-08 18:32:26 | 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 | {'first': True} | 2024-04-08 18:32:26 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2024-04-08 18:32:26 | 2024-04-08 18:32:26 | 0.01 | list | [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '12601176;11290752;11983166', 'Fluorescence probe labeling;Calcium measurement;Fusion protein-pu...(truncated) | 359 | {'first': True} | 2024-04-08 18:32:26 | |
| ¶ | pypath.inputs.trip.trip_process | 2024-04-08 18:32:26 | 2024-04-08 18:32:26 | 0.00 | dict | {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'HEK293', 'Porcine coronary artery', 'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {'first': True} | 2024-04-08 18:32:26 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2024-04-08 18:32:26 | 2024-04-08 18:32:30 | 4.08 | 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 | {'first': True} | 2024-04-08 18:32:26 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2024-04-08 18:32:30 | 2024-04-08 18:32:30 | 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 | {'first': True} | 2024-04-08 18:32:30 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2024-04-08 18:32:30 | 2024-04-08 18:32:34 | 3.44 | 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 | {'first': True} | 2024-04-08 18:32:30 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2024-04-08 18:32:34 | 2024-04-08 18:32:34 | 0.20 |
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__20240408-145602/pypath_git/pypath/inputs/offsides.py", line 70, in _sides_base
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2024-04-08 18:32:34 | |||
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2024-04-08 18:32:34 | 2024-04-08 18:32:34 | 0.31 | 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 | {'first': True} | 2024-04-08 18:32:34 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2024-04-08 18:32:34 | 2024-04-08 18:32:34 | 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 | {'first': True} | 2024-04-08 18:32:34 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2024-04-08 18:32:34 | 2024-04-08 18:32:34 | 0.05 | set | {'G1EQ61', 'K7ELL7', 'C6K4F4', 'A8MYV2', 'Q8N1E9', 'A0A286MCD0', 'A0A5C2G6J2', 'A0A6B9VU45', 'A0A343DWP9', 'A0A7S5C0X8', 'A0A0G2JHI0', 'B4DSW0', 'H0YDI2', 'A0A7S5BXW1', 'P12931', 'Q6IEW6', 'Q9GZN1', 'F5GZS7', 'Q86VW0', 'A0A288QA90', 'H3BQU6', 'B4DR25', 'A0A7S5C555', 'B4DH11', 'I3L455', 'N0A0I9', 'A0...(truncated) | 204,063 | {'first': True} | 2024-04-08 18:32:34 | |
| ¶ | pypath.inputs.uniprot._protein_datasheet |
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot._swissprot_param |
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2024-04-08 18:32:34 | 2024-04-08 18:32:35 | 0.60 | list | [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ13', 'K7EN86'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZ66', 'K7EQ86'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZK0', 'A0A024QZP7'], ['A0A024Q...(truncated) | 72,277 | {'first': True} | 2024-04-08 18:32:34 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.query_builder |
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2024-04-08 18:32:35 | 2024-04-08 18:32:54 | 19.55 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0B4J2F2': {UniprotFamily(family='Protein kinase superfamily, CAMK Ser/Thr protein kinase', subfamily='AMPK')}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M...(truncated) | 14,445 | {'first': True} | 2024-04-08 18:32:35 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2024-04-08 18:32:55 | 2024-04-08 18:33:11 | 16.69 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Glycoprotein'), UniprotKeyword(keyword='Reference proteome'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Transmembrane'), Unipro...(truncated) | 20,434 | {'first': True} | 2024-04-08 18:32:55 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2024-04-08 18:33:11 | 2024-04-08 18:33:32 | 20.24 | dict | {'A0A087X1C5': {UniprotLocation(location='Mitochondrion', features=None), UniprotLocation(location='Cytoplasm', features=None), UniprotLocation(location='Membrane', features=('Multi-pass membrane protein',))}, 'A0A0B4J2F0': {UniprotLocation(location='Mitochondrion outer membrane', features=('Single-...(truncated) | 17,129 | {'first': True} | 2024-04-08 18:33:11 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2024-04-08 18:33:32 | 2024-04-08 18:33:32 | 0.08 | 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) | 27,585 | {'first': True} | 2024-04-08 18:33:32 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_query |
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2024-04-08 18:33:32 | 2024-04-08 18:33:33 | 1.77 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Abies balsamea', 'Balsam fir', 'Pinus balsamea'}, 'H8ZM71': {'Abies balsamea', 'Balsam fir', 'Pinus balsamea'}, 'Q9MV51': {'Momi fir', 'Abies firma'}, 'O81086': {'Grand fir', 'Abies grandis', 'Pinu...(truncated) | 556,678 | {'first': True} | 2024-04-08 18:33:32 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2024-04-08 18:33:34 | 2024-04-08 18:33:54 | 19.81 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Lymphocytes nor granulocytes', level='none'), UniprotTissue(ti...(truncated) | 10,122 | {'first': True} | 2024-04-08 18:33:34 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2024-04-08 18:33:54 | 2024-04-08 18:35:16 | 82.45 | dict | {'A0A087X1C5': {UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Extracellular', ...(truncated) | 5,241 | {'first': True} | 2024-04-08 18:33:54 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db._cleanup | 2024-04-08 18:35:16 | 2024-04-08 18:35:16 | 0.00 | NoneType | None | 0 | {'first': True} | 2024-04-08 18:35:16 | |
| ¶ | pypath.inputs.uniprot_db._remove |
Not calling `pypath.inputs.uniprot_db._remove`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2024-04-08 18:35:16 | 2024-04-08 18:35:16 | 0.00 | set | {'O15440', 'O14641', 'A6NHM9', 'Q6NXT6', 'Q9BSU3', 'A0A1B0GV22', 'Q07955', 'A0A1W2PP81', 'P12931', 'P33260', 'Q9GZN1', 'Q86VW0', 'Q86Y34', 'Q6B8I1', 'Q8TC57', 'A0A0B4J273', 'Q8NH42', 'P78549', 'Q15327', 'Q9NQ92', 'Q15256', 'P0C1H6', 'O60930', 'P61006', 'Q6ZS72', 'Q16513', 'Q96BR6', 'Q9H1L0', 'Q6ZUT1...(truncated) | 20,434 | {'first': True} | 2024-04-08 18:35:16 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2024-04-08 18:35:16 | 2024-04-08 18:36:02 | 45.79 | set | {'G1EQ61', 'K7ELL7', 'C6K4F4', 'A8MYV2', 'Q8N1E9', 'A0A286MCD0', 'A0A5C2G6J2', 'A0A6B9VU45', 'A0A343DWP9', 'A0A7S5C0X8', 'A0A0G2JHI0', 'B4DSW0', 'H0YDI2', 'A0A7S5BXW1', 'Q6IEW6', 'F5GZS7', 'A0A288QA90', 'H3BQU6', 'B4DR25', 'A0A7S5C555', 'B4DH11', 'I3L455', 'N0A0I9', 'A0A5C2G984', 'A0A8V8TLH8', 'F8WD...(truncated) | 183,629 | {'first': True} | 2024-04-08 18:35:16 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2024-04-08 18:36:02 | 2024-04-08 18:36:02 | 0.00 | set | {'G1EQ61', 'K7ELL7', 'C6K4F4', 'A8MYV2', 'Q8N1E9', 'A0A286MCD0', 'A0A5C2G6J2', 'A0A6B9VU45', 'A0A343DWP9', 'A0A7S5C0X8', 'A0A0G2JHI0', 'B4DSW0', 'H0YDI2', 'A0A7S5BXW1', 'P12931', 'Q6IEW6', 'Q9GZN1', 'F5GZS7', 'Q86VW0', 'A0A288QA90', 'H3BQU6', 'B4DR25', 'A0A7S5C555', 'B4DH11', 'I3L455', 'N0A0I9', 'A0...(truncated) | 204,063 | {'first': True} | 2024-04-08 18:36:02 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2024-04-08 18:36:02 | 2024-04-08 18:36:02 | 0.00 | set | {'G1EQ61', 'K7ELL7', 'C6K4F4', 'A8MYV2', 'Q8N1E9', 'A0A286MCD0', 'A0A5C2G6J2', 'A0A6B9VU45', 'A0A343DWP9', 'A0A7S5C0X8', 'A0A0G2JHI0', 'B4DSW0', 'H0YDI2', 'A0A7S5BXW1', 'P12931', 'Q6IEW6', 'Q9GZN1', 'F5GZS7', 'Q86VW0', 'A0A288QA90', 'H3BQU6', 'B4DR25', 'A0A7S5C555', 'B4DH11', 'I3L455', 'N0A0I9', 'A0...(truncated) | 204,063 | {'first': True} | 2024-04-08 18:36:02 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2024-04-08 18:36:02 | 2024-04-08 18:36:02 | 0.05 | NoneType | None | 0 | {'first': True} | 2024-04-08 18:36:02 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_idmapping.idtypes | 2024-04-08 18:36:02 | 2024-04-08 18:36:02 | 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__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:36:02 | |||
| ¶ | pypath.inputs.wang._wang_process |
Not calling `pypath.inputs.wang._wang_process`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.wang.cui_interactions | 2024-04-08 18:36:02 | 2024-04-08 18:36:05 | 2.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 114, in read_xls
book = openpyxl.load_workbook(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 344, in load_workbook
reader = ExcelReader(filename, read_only, keep_vba,
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 123, in __init__
self.archive = _validate_archive(fn)
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 95, in _validate_archive
archive = ZipFile(filename, 'r')
File "/usr/lib/python3.10/zipfile.py", line 1269, in __init__
self._RealGetContents()
File "/usr/lib/python3.10/zipfile.py", line 1336, in _RealGetContents
raise BadZipFile("File is not a zip file")
zipfile.BadZipFile: File is not a zip file
During handling of the above exception, another exception occurred:
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__20240408-145602/pypath_git/pypath/inputs/wang.py", line 139, in cui_interactions
raw = embo.embopress_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/embopress.py", line 102, in embopress_supplementary
inputs_common.read_xls(fname, sheet = sheet)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/common.py", line 124, in read_xls
raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: <_io.BufferedReader name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/cache/e2b39a322462f0f9978a1e2965dba6e1-downloadSupplement'>
|
{'first': True} | 2024-04-08 18:36:02 | |||
| ¶ | pypath.inputs.wang.hsn_interactions | 2024-04-08 18:36:05 | 2024-04-08 18:36:06 | 0.96 | 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 | {'first': True} | 2024-04-08 18:36:05 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2024-04-08 18:36:06 | 2024-04-08 18:36:06 | 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__20240408-145602/pypath_git/pypath/inputs/wang.py", line 262, in wang_annotations
data = func()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 18:36:06 | |||
| ¶ | pypath.inputs.wang.wang_interactions | 2024-04-08 18:36:06 | 2024-04-08 18:36:06 | 0.40 | 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 | {'first': True} | 2024-04-08 18:36:06 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2024-04-08 18:36:06 | 2024-04-08 18:36:07 | 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__20240408-145602/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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 18:36:06 | |||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2024-04-08 18:36:07 | 2024-04-08 18:36:07 | 0.12 |
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__20240408-145602/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__20240408-145602/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2024-04-08 18:36:07 | |||
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2024-04-08 18:36:07 | 2024-04-08 18:36:07 | 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__20240408-145602/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__20240408-145602/pypath_git/pypath/utils/mapping.py", line 3582, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1799, in map_name0
names = self.map_name(
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath---jXRgP0-py3.10/lib/python3.10/site-packages/pypath_common/_misc.py", line 2935, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2181, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/utils/mapping.py", line 1587, in which_table
input_cls.possible(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/internals/input_formats.py", line 540, in possible
pairs = uniprot_idmapping.idtypes()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20240408-145602/pypath_git/pypath/inputs/uniprot_idmapping.py", line 42, in idtypes
url = urls.urls['uniprot_idmapping']['fields']
NameError: name 'urls' is not defined
|
{'first': True} | 2024-04-08 18:36:07 |
The OmniPath Team • Saez Lab • 2024-04-08