Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2023-06-14 18:26:47 and 2023-06-18 13:52:22; pypath version: 0.15.4 (from git, installed by poetry; 7455e32 )
| Modules collected: | 169 |
|---|---|
| Modules failed to import: | 0 |
| Functions collected: | 568 |
| Functions run without error: | 282 |
| Functions returned empty value: | 57 |
| Functions skipped due to lack of arguments: | 165 |
| Functions run with error: | 121 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2023-06-14 18:26:48 | 2023-06-14 18:26:49 | 0.37 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2023-06-14 18:26:48 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2023-06-14 18:26:49 | 2023-06-14 18:26:49 | 0.50 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2023-06-14 18:26:49 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2023-06-14 18:26:49 | 2023-06-14 18:26:49 | 0.36 | list | [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) | 9,570 | {} | 2023-06-14 18:26:49 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2023-06-14 18:26:49 | 2023-06-14 18:42:35 | 945.77 | dict | {} | 0 | {'size': -239} | 2023-06-14 18:26:49 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2023-06-14 18:42:35 | 2023-06-14 18:42:37 | 1.30 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2023-06-14 18:42:35 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2023-06-14 18:42:37 | 2023-06-14 20:59:08 | 8,191.13 | dict | {} | 0 | {'size': -4825} | 2023-06-14 18:42:37 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2023-06-14 20:59:08 | 2023-06-14 21:13:10 | 842.19 |
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__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 196, in baccin2019_annotations
ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 137, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 84, in raw_to_uniprots
itertools.product(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 85, in <genexpr>
*(id_translate(comp) for comp in components)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 56, in id_translate
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 623, in read_mapping_uniprot_list
self.set_uniprot_space()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 699, in set_uniprot_space
self.uniprots = uniprot_input.all_uniprots(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 91, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 131, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 117, in init_db
globals()['db'][key] = _all_uniprots(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 85, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2023-06-13 18:30:59 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2023-06-14 21:13:10 | 2023-06-14 21:35:52 | 1,361.73 |
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__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 137, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 84, in raw_to_uniprots
itertools.product(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 85, in <genexpr>
*(id_translate(comp) for comp in components)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/baccin2019.py", line 56, in id_translate
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2203, in map_name
mapped_names = self.uniprot_cleanup(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2252, in uniprot_cleanup
uniprots = self.only_valid_uniprots(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2993, in only_valid_uniprots
return {
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2996, in <setcomp>
if uniprot_input.is_uniprot(uniprot, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 165, in is_uniprot
return name in get_db(organism = organism, swissprot = swissprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 131, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 117, in init_db
globals()['db'][key] = _all_uniprots(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/uniprot.py", line 85, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2023-06-13 18:37:16 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2023-06-14 21:35:52 | 2023-06-14 21:35:52 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2023-06-14 21:35:52 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2023-06-14 21:35:52 | 2023-06-14 21:36:25 | 33.07 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2023-06-14 21:35:52 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2023-06-14 21:36:25 | 2023-06-14 21:38:09 | 104.08 | 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) | 8,246 | {} | 2023-06-14 21:36:25 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2023-06-14 21:38:10 | 2023-06-14 21:38:11 | 1.15 | 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) | 7,004 | {} | 2023-06-14 21:38:10 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2023-06-14 21:38:11 | 2023-06-14 21:38:44 | 32.97 | 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) | 178,164 | {} | 2023-06-14 21:38:11 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2023-06-14 21:38:44 | 2023-06-14 21:38:44 | 0.28 | list | [{'type': 'OLIGO', 'format': 'EXPRESSION', 'array': 'OneArray', 'vendor': 'PHALANX', 'description': None, 'label': 'PHALANX OneArray'}, {'type': 'OLIGO', 'format': 'EXPRESSION', 'array': 'CODELINK', 'vendor': 'CODELINK', 'description': None, 'label': 'CODELINK CODELINK'}, {'description': None, 'type...(truncated) | 35 | {} | 2023-06-14 21:38:44 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomodels._get_biomodels | 2023-06-14 21:38:44 | 2023-06-14 21:38:44 | 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__20230614-182602/pypath_git/pypath/inputs/biomodels.py", line 106, in _get_biomodels
loginurl = urls.urls['biomodels']['login'] % t
KeyError: 'login'
|
{} | 2023-06-12 18:37:15 | |||
| ¶ | pypath.inputs.biomodels.download_single_model |
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomodels.get_biomodels | 2023-06-14 21:38:44 | 2023-06-14 21:38:44 | 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__20230614-182602/pypath_git/pypath/inputs/biomodels.py", line 165, in get_biomodels
c0.perform()
pycurl.error: (3, '')
|
{} | 2023-06-12 18:37:15 | |||
| ¶ | pypath.inputs.biomodels.get_biomodels_req | 2023-06-14 21:38:44 | 2023-06-14 21:38:45 | 0.82 |
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__20230614-182602/pypath_git/pypath/inputs/biomodels.py", line 198, in get_biomodels_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-06-12 18:37:15 | |||
| ¶ | pypath.inputs.biomodels.get_single_model |
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2023-06-14 21:38:45 | 2023-06-14 21:38:48 | 3.36 | list | [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) | 1,788 | {} | 2023-06-14 21:38:45 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2023-06-14 21:38:48 | 2023-06-14 21:38:50 | 1.97 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2023-06-14 21:38:48 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2023-06-14 21:38:50 | 2023-06-14 21:46:40 | 469.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 204, in cancerdrugsdb_annotations
data = cancerdrugsdb_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 136, in cancerdrugsdb_interactions
target_uniprots = mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2191, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1710, in which_table
self.load_genesymbol5(ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3292, in load_genesymbol5
for genesymbol, uniprots in iteritems(table.data):
AttributeError: 'NoneType' object has no attribute 'data'
|
{'broke': True} | 2023-06-13 18:39:15 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2023-06-14 21:46:40 | 2023-06-14 21:46:40 | 0.00 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 297 | {} | 2023-06-14 21:46:40 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2023-06-14 21:46:40 | 2023-06-14 21:46:40 | 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__20230614-182602/pypath_git/pypath/inputs/cancerdrugsdb.py", line 136, in cancerdrugsdb_interactions
target_uniprots = mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2191, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1710, in which_table
self.load_genesymbol5(ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3292, in load_genesymbol5
for genesymbol, uniprots in iteritems(table.data):
AttributeError: 'NoneType' object has no attribute 'data'
|
{'broke': True} | 2023-06-13 18:39:27 | |||
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2023-06-14 21:46:40 | 2023-06-14 21:48:46 | 126.18 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cancersea.py", line 68, in cancersea_annotations
uniprots = mapping.map_name(line[1], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2191, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1710, in which_table
self.load_genesymbol5(ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3292, in load_genesymbol5
for genesymbol, uniprots in iteritems(table.data):
AttributeError: 'NoneType' object has no attribute 'data'
|
{'broke': True} | 2023-06-13 18:39:27 | |||
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2023-06-14 21:48:46 | 2023-06-14 21:54:50 | 364.13 | dict | {} | 0 | {'size': -460} | 2023-06-14 21:48:46 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2023-06-14 21:54:50 | 2023-06-14 21:54:50 | 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 | {} | 2023-06-14 21:54:50 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2023-06-14 21:54:50 | 2023-06-14 21:54:51 | 0.82 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2023-06-14 21:54:50 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2023-06-14 21:54:51 | 2023-06-14 21:54:51 | 0.11 | list | [] | 0 | {'size': -797} | 2023-06-14 21:54:51 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2023-06-14 21:54:51 | 2023-06-14 21:54:52 | 0.67 |
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__20230614-182602/pypath_git/pypath/inputs/cellcellinteractions.py", line 55, in cellcellinteractions_annotations
uniprots = mapping.map_name(row[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:39:41 | |||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2023-06-14 21:54:52 | 2023-06-14 21:54:52 | 0.00 | int | 9606 | 0 | {} | 2023-06-14 21:54:52 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_cofactors |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_complexes |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2023-06-14 21:54:52 | 2023-06-14 21:54:57 | 5.40 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 328, in cellchatdb_annotations
interactions = cellchatdb_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 232, in cellchatdb_interactions
_complexes = _cellchatdb_process_complexes(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 118, in _cellchatdb_process_complexes
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 119, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:39:41 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2023-06-14 21:54:57 | 2023-06-14 21:55:02 | 5.21 |
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__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 147, in cellchatdb_cofactors
return _cellchatdb_process_cofactors(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 164, in _cellchatdb_process_cofactors
uniprots = mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:39:50 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2023-06-14 21:55:02 | 2023-06-14 21:55:08 | 5.44 |
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__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 101, in cellchatdb_complexes
return _cellchatdb_process_complexes(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 118, in _cellchatdb_process_complexes
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 119, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:39:56 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2023-06-14 21:55:08 | 2023-06-14 21:55:13 | 5.15 | dict | {'interaction': interaction_name ... rownames TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 TGFB1_ACVR1B_TGF...(truncated) | 4 | {} | 2023-06-14 21:55:08 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2023-06-14 21:55:13 | 2023-06-14 21:55:18 | 5.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 232, in cellchatdb_interactions
_complexes = _cellchatdb_process_complexes(raw, organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 118, in _cellchatdb_process_complexes
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellchatdb.py", line 119, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:07 | |||
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2023-06-14 21:55:18 | 2023-06-14 21:55:19 | 0.57 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2023-06-14 21:55:18 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 0.09 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 461, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 318, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 321, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 168, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 169, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 533, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 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__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 518, in cellinker_complex_annotations
return cellinker_annotations(organism = organism, entity_type = 'complex')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 461, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 318, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 321, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 168, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 169, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 533, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 202, in cellinker_complexes
for cplex in components_to_complex(c.components, organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 168, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 169, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 533, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2023-06-14 21:55:19 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 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__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 318, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 321, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 168, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 169, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 533, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2023-06-14 21:55:19 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 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__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 500, in cellinker_protein_annotations
return cellinker_annotations(organism = organism, entity_type = 'protein')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 461, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 318, in cellinker_lr_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 321, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 168, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 169, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 533, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 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__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 389, in cellinker_smol_interactions
complexes = dict(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 392, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 168, in components_to_complex
for uniprots in itertools.product(*(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 169, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellinker.py", line 533, in _cellinker_uniprots
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 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 | {} | 2023-06-14 21:55:19 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_annotations |
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_get_entity |
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_hla |
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 0.20 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 225, in cellphonedb_complex_annotations
return _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 133, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 214, in name_method
comp = get_stoichiometry(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 208, in get_stoichiometry
return tuple(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 209, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:13 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2023-06-14 21:55:19 | 2023-06-14 21:55:19 | 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__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 353, in cellphonedb_complexes
annot = cellphonedb_complex_annotations()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 225, in cellphonedb_complex_annotations
return _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 133, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 214, in name_method
comp = get_stoichiometry(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 208, in get_stoichiometry
return tuple(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 209, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:14 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2023-06-14 21:55:19 | 2023-06-14 21:56:07 | 47.36 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 289, in cellphonedb_interactions
ligands, receptors = cellphonedb_ligands_receptors()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 68, in cellphonedb_ligands_receptors
proteins = cellphonedb_protein_annotations()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 168, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 133, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 163, in name_method
uniprot = _cellphonedb_hla(uniprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 187, in _cellphonedb_hla
uniprots = mapping.map_name(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:14 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2023-06-14 21:56:07 | 2023-06-14 21:56:07 | 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__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 68, in cellphonedb_ligands_receptors
proteins = cellphonedb_protein_annotations()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 168, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 133, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 163, in name_method
uniprot = _cellphonedb_hla(uniprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 187, in _cellphonedb_hla
uniprots = mapping.map_name(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:14 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2023-06-14 21:56:07 | 2023-06-14 21:56:07 | 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__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 168, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 133, in _cellphonedb_annotations
names = name_method(rec)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 163, in name_method
uniprot = _cellphonedb_hla(uniprot)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cellphonedb.py", line 187, in _cellphonedb_hla
uniprots = mapping.map_name(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:14 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2023-06-14 21:56:07 | 2023-06-14 21:56:21 | 14.70 |
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__20230614-182602/pypath_git/pypath/inputs/celltalkdb.py", line 188, in celltalkdb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:14 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2023-06-14 21:56:21 | 2023-06-14 21:56:21 | 0.00 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2023-06-14 21:56:21 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2023-06-14 21:56:21 | 2023-06-14 21:56:21 | 0.01 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2023-06-14 21:56:21 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2023-06-14 21:56:21 | 2023-06-14 21:56:22 | 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__20230614-182602/pypath_git/pypath/inputs/celltypist.py", line 76, in celltypist_annotations
uniprots = mapping.map_names(genesymbols, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:40:40 | |||
| ¶ | pypath.inputs.chembl.chembl_activities |
Not calling `pypath.inputs.chembl.chembl_activities`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.chembl.chembl_documents | 2023-06-14 21:56:22 | 2023-06-14 21:57:50 | 88.37 | dict | {'CHEMBL1139451': 14695813, 'CHEMBL1148466': 14695814, 'CHEMBL1139452': 14695824, 'CHEMBL1139453': 14695825, 'CHEMBL1139454': 14695826, 'CHEMBL1139455': 14695827, 'CHEMBL1139456': 14695815, 'CHEMBL1139457': 14695828, 'CHEMBL1139458': 14695816, 'CHEMBL1148467': 14695833, 'CHEMBL1139459': 14695834, 'C...(truncated) | 80,293 | {} | 2023-06-14 21:56:22 | |
| ¶ | pypath.inputs.chembl.chembl_drug_indications | 2023-06-14 21:57:50 | 2023-06-14 21:58:46 | 55.59 | list | [ChemblIndication(efo_id='EFO:0000404', efo_term='diffuse scleroderma', max_phase=2.0, mesh_heading='Scleroderma, Diffuse', mesh_id='D045743', molecule_chembl='CHEMBL1201823'), ChemblIndication(efo_id='EFO:0000685', efo_term='rheumatoid arthritis', max_phase=4.0, mesh_heading='Arthritis, Rheumatoid'...(truncated) | 51,582 | {} | 2023-06-14 21:57:50 | |
| ¶ | pypath.inputs.chembl.chembl_mechanisms | 2023-06-14 21:58:46 | 2023-06-14 21:58:55 | 9.70 | list | [ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_action='Carbonic anhydrase VII inhibitor', chembl='CHEMBL19', target_chembl='CHEMBL2326'), ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_acti...(truncated) | 7,098 | {} | 2023-06-14 21:58:46 | |
| ¶ | pypath.inputs.chembl.chembl_targets | 2023-06-14 21:58:55 | 2023-06-14 22:00:51 | 115.83 | list | [ChemblTarget(accession='O43451', target_chembl_id='CHEMBL2074'), ChemblTarget(accession='O60706', target_chembl_id='CHEMBL1971'), ChemblTarget(accession='O76074', target_chembl_id='CHEMBL1827'), ChemblTarget(accession='O95180', target_chembl_id='CHEMBL1859'), ChemblTarget(accession='O96760', target...(truncated) | 15,398 | {} | 2023-06-14 21:58:55 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2023-06-14 22:00:51 | 2023-06-14 22:01:16 | 24.60 | list | [Citation(allele='1117481', variation_id='1134511', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='54633', variation_id='45466', nsv='', citation_source='PubMed', citation_id='22162582'), Citation(allele='532034', variation_id='531107', nsv='', citation_source='PubMed', ...(truncated) | 2,715,961 | {} | 2023-06-14 22:00:51 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2023-06-14 22:01:19 | 2023-06-14 22:03:10 | 110.97 | list | [Variant(allele='350271', type='single nucleotide variant', variant='NM_001145809.2(MYH14):c.3427C>T (p.Leu1143=)', entrez='79784', genesymbol='MYH14', clinical_significance='Conflicting interpretations of pathogenicity', review_status='criteria provided, conflicting interpretations', rs='770366755'...(truncated) | 4,464,832 | {} | 2023-06-14 22:01:19 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2023-06-14 22:10:17 | 2023-06-14 22:10:18 | 1.05 |
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__20230614-182602/pypath_git/pypath/inputs/collectri.py", line 224, in collectri_interactions
mapping.map_name(rec.tf, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:55:36 | |||
| ¶ | pypath.inputs.collectri.collectri_raw | 2023-06-14 22:10:18 | 2023-06-14 22:10:18 | 0.07 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2023-06-14 22:10:18 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2023-06-14 22:10:18 | 2023-06-14 22:20:14 | 595.45 | dict | {} | 0 | {'size': -9693} | 2023-06-14 22:10:18 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2023-06-14 22:20:14 | 2023-06-14 22:20:14 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2023-06-14 22:20:14 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2023-06-14 22:20:14 | 2023-06-14 22:21:28 | 73.99 | 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) | 1,620 | {} | 2023-06-14 22:20:14 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2023-06-14 22:21:28 | 2023-06-15 05:37:55 | 26,186.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 18:56:58 | |||
| ¶ | pypath.inputs.comppi.comppi_locations | 2023-06-15 05:37:55 | 2023-06-15 05:38:03 | 8.03 | dict | {} | 0 | {'size': -18254} | 2023-06-15 05:37:55 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2023-06-15 05:38:03 | 2023-06-15 05:38:03 | 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__20230614-182602/pypath_git/pypath/inputs/connectomedb.py", line 98, in connectomedb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:57:29 | |||
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2023-06-15 05:38:03 | 2023-06-15 05:38:03 | 0.02 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2023-06-15 05:38:03 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2023-06-15 05:38:03 | 2023-06-15 05:38:04 | 0.68 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2023-06-15 05:38:03 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2023-06-15 05:38:04 | 2023-06-15 05:38:06 | 1.85 |
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__20230614-182602/pypath_git/pypath/inputs/cosmic.py", line 137, in cancer_gene_census_annotations
data = csv.DictReader(c.fileobj, delimiter = ',')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 18:55:36 | |||
| ¶ | pypath.inputs.cpad.cpad_annotations | 2023-06-15 05:38:06 | 2023-06-15 05:38:10 | 4.76 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cpad.py", line 68, in cpad_annotations
uniprot = mapping.map_name0(regulator, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:57:33 | |||
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2023-06-15 05:38:10 | 2023-06-15 05:38:10 | 0.06 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='Akt signaling pathway', cancer='Glioma', pathway_category='PI3K-Akt signaling pathway', effect_on_cancer='Activating', effect_on_cancer_outcome='promote progression'), CpadPathwayCancer(pathway='Akt signaling pathway', cancer='Glioma', pathway_category='PI3K-A...(truncated) | 2 | {} | 2023-06-15 05:38:10 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2023-06-15 05:38:10 | 2023-06-15 05:38:10 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2023-06-15 05:38:10 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2023-06-15 05:38:10 | 2023-06-15 05:38:16 | 5.27 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | {} | 2023-06-15 05:38:10 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2023-06-15 05:38:16 | 2023-06-15 05:38:19 | 3.13 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {} | 2023-06-15 05:38:16 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2023-06-15 05:38:19 | 2023-06-15 05:38:53 | 34.03 | dict | {} | 0 | {'size': -1446} | 2023-06-15 05:38:19 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2023-06-15 05:38:53 | 2023-06-15 05:38:54 | 0.83 | dict | {} | 0 | {'size': -1407} | 2023-06-15 05:38:53 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2023-06-15 05:38:54 | 2023-06-15 05:38:55 | 0.66 | dict | {} | 0 | {'size': -47} | 2023-06-15 05:38:54 | |
| ¶ | pypath.inputs.ctdbase._ctdbase_download |
Not calling `pypath.inputs.ctdbase._ctdbase_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase._map_keys |
Not calling `pypath.inputs.ctdbase._map_keys`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase._modify_dict |
Not calling `pypath.inputs.ctdbase._modify_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2023-06-15 05:38:55 | 2023-06-15 05:38:56 | 0.91 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cytosig.py", line 110, in cytosig_annotations
u_target = map_to_uniprot(target)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cytosig.py", line 90, in map_to_uniprot
uniprots = mapping.map_name(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:57:51 | |||
| ¶ | pypath.inputs.cytosig.cytosig_df | 2023-06-15 05:38:56 | 2023-06-15 05:38:56 | 0.04 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {} | 2023-06-15 05:38:56 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2023-06-15 05:38:56 | 2023-06-15 05:38:59 | 3.06 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2023-06-15 05:38:56 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2023-06-15 05:38:59 | 2023-06-15 05:39:01 | 1.52 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/dbptm.py", line 102, in dbptm_enzyme_substrate_old
for k, data in iteritems(extra):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-A-OJreq1-py3.10/lib/python3.10/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2023-06-12 18:56:01 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2023-06-15 05:39:01 | 2023-06-15 05:39:02 | 1.14 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2023-06-15 05:39:01 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2023-06-15 05:39:02 | 2023-06-15 05:39:03 | 0.83 | list | [] | 0 | {} | 2023-06-15 05:39:02 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2023-06-15 05:39:03 | 2023-06-15 05:39:03 | 0.16 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2023-06-15 05:39:03 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2023-06-15 05:39:03 | 2023-06-15 05:39:03 | 0.07 | list | [] | 0 | {'size': -537} | 2023-06-15 05:39:03 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2023-06-15 05:39:03 | 2023-06-15 05:39:03 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {} | 2023-06-15 05:39:03 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2023-06-15 05:39:03 | 2023-06-15 05:39:05 | 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__20230614-182602/pypath_git/pypath/inputs/dgidb.py", line 105, in dgidb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:58:01 | |||
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2023-06-15 05:39:05 | 2023-06-15 05:39:09 | 4.24 | list | [DgidbInteraction(genesymbol='PLD1', entrez='5337', resource='TTD', type=None, drug_name='ML272', drug_chembl=None, score=None, pmid=None), DgidbInteraction(genesymbol='CYP3A4', entrez='1576', resource='DTC', type=None, drug_name='AM-404', drug_chembl='chembl:CHEMBL39878', score='0.01', pmid=None), ...(truncated) | 85,022 | {} | 2023-06-15 05:39:05 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2023-06-15 05:39:09 | 2023-06-15 05:40:12 | 62.19 |
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__20230614-182602/pypath_git/pypath/inputs/dgidb.py", line 148, in get_dgidb_old
return mapping.map_names(genesymbols, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:58:07 | |||
| ¶ | pypath.inputs.dip.dip_interactions | 2023-06-15 05:40:12 | 2023-06-15 05:40:12 | 0.27 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2023-06-15 05:40:12 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.disgenet.wrapper |
Not calling `pypath.inputs.disgenet.wrapper`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.disgenet.wrapper |
Not calling `pypath.inputs.disgenet.wrapper`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.disgenet.wrapper |
Not calling `pypath.inputs.disgenet.wrapper`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.domino.domino_ddi | 2023-06-15 05:40:12 | 2023-06-15 05:40:17 | 5.26 |
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__20230614-182602/pypath_git/pypath/inputs/domino.py", line 244, in domino_ddi
domi = domino_enzsub()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/domino.py", line 418, in domino_enzsub
intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/internals/intera.py", line 656, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 132, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 468, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3681, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2641, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:59:11 | |||
| ¶ | pypath.inputs.domino.domino_enzsub | 2023-06-15 05:40:17 | 2023-06-15 05:40:18 | 0.51 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/domino.py", line 418, in domino_enzsub
intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/internals/intera.py", line 656, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 132, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 468, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3681, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2641, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 18:59:16 | |||
| ¶ | pypath.inputs.domino.domino_interactions | 2023-06-15 05:40:18 | 2023-06-15 05:40:18 | 0.40 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2023-06-15 05:40:18 | |
| ¶ | pypath.inputs.domino.get_domino | 2023-06-15 05:40:18 | 2023-06-15 05:40:19 | 0.51 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2023-06-15 05:40:18 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2023-06-15 05:40:19 | 2023-06-15 05:40:27 | 8.10 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2023-06-15 05:40:19 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2023-06-15 05:40:27 | 2023-06-15 05:40:41 | 13.82 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2023-06-15 05:40:27 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-06-15 05:40:41 | 2023-06-15 05:40:41 | 0.27 |
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__20230614-182602/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-06-15 05:40:41 | 2023-06-15 05:40:41 | 0.09 |
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__20230614-182602/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2023-06-15 05:40:41 | 2023-06-15 05:40:43 | 1.75 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2023-06-15 05:40:41 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2023-06-15 05:40:43 | 2023-06-15 05:40:43 | 0.33 | list | [['AHR', 'CYP1A1', '0', 'A', True, False, True, False, 'HTRIdb,trrust_signed', '', 'hocomoco_v11', '', 'HTRIdb,trrust_signed,hocomoco_v11'], ['AHR', 'CYP1A2', '0', 'A', True, False, False, False, 'HTRIdb,trrust_signed', '', '', '', 'HTRIdb,trrust_signed'], ['AHR', 'CYP1B1', '0', 'A', True, False, Tr...(truncated) | 14,260 | {} | 2023-06-15 05:40:43 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2023-06-15 05:40:43 | 2023-06-15 05:40:44 | 1.21 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2023-06-15 05:40:43 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2023-06-15 05:40:44 | 2023-06-15 05:40:58 | 13.84 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2023-06-15 05:40:44 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-06-15 05:40:58 | 2023-06-15 05:40:59 | 0.46 |
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__20230614-182602/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.drugbank._drugbank_credentials | 2023-06-15 05:40:59 | 2023-06-15 05:40:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/drugbank.py", line 55, in _drugbank_credentials
return credentials.credentials(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/credentials.py", line 120, in credentials
raise RuntimeError(msg)
RuntimeError: Failed to obtain credentials for resource `DrugBank`
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.drugbank._drugbank_download |
Not calling `pypath.inputs.drugbank._drugbank_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_annotations | 2023-06-15 05:40:59 | 2023-06-15 05:40:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/drugbank.py", line 358, in drugbank_annotations
drugs = drugbank_drugs(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/drugbank.py", line 309, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.drugbank.drugbank_drugs | 2023-06-15 05:40:59 | 2023-06-15 05:40:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/drugbank.py", line 309, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.drugbank.drugbank_interactions | 2023-06-15 05:40:59 | 2023-06-15 05:40:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/drugbank.py", line 204, in drugbank_interactions
for d in drugbank_drugs(user = user, passwd = passwd)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/drugbank.py", line 309, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-06-12 18:58:05 | |||
| ¶ | pypath.inputs.drugbank.drugbank_mapping |
Not calling `pypath.inputs.drugbank.drugbank_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_raw_interactions | 2023-06-15 05:40:59 | 2023-06-15 05:40:59 | 0.00 | list | [] | 0 | {} | 2023-06-15 05:40:59 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2023-06-15 05:40:59 | 2023-06-15 05:41:00 | 1.11 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2023-06-15 05:40:59 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2023-06-15 05:41:00 | 2023-06-15 05:41:01 | 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 | {} | 2023-06-15 05:41:00 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2023-06-15 05:41:01 | 2023-06-15 05:41:17 | 15.42 | 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) | 321 | {} | 2023-06-15 05:41:01 | |
| ¶ | pypath.inputs.elm.elm_domains | 2023-06-15 05:41:17 | 2023-06-15 05:41:17 | 0.52 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2023-06-15 05:41:17 | |
| ¶ | pypath.inputs.elm.elm_instances | 2023-06-15 05:41:17 | 2023-06-15 05:43:03 | 105.82 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 3,977 | {} | 2023-06-15 05:41:17 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2023-06-15 05:43:03 | 2023-06-15 05:44:20 | 77.32 | 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) | 2,442 | {} | 2023-06-15 05:43:03 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2023-06-15 05:44:20 | 2023-06-15 05:44:20 | 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__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 163, in embrace_annotations
for rec in embrace_translated(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 87, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:02:19 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2023-06-15 05:44:20 | 2023-06-15 05:44:20 | 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__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 129, in embrace_interactions
for rec in embrace_translated(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 87, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:02:19 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2023-06-15 05:44:20 | 2023-06-15 05:44:20 | 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__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:02:19 | |||
| ¶ | pypath.inputs.embrace.embrace_translated | 2023-06-15 05:44:20 | 2023-06-15 05:44:21 | 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__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 87, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:02:20 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2023-06-15 05:44:21 | 2023-06-15 05:44:21 | 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 | {} | 2023-06-15 05:44:21 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2023-06-15 05:44:21 | 2023-06-15 05:44:22 | 0.72 | 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) | 314 | {} | 2023-06-15 05:44:21 | |
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2023-06-15 05:44:22 | 2023-06-15 05:44:31 | 8.75 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {} | 2023-06-15 05:44:22 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2023-06-15 05:44:31 | 2023-06-15 05:44:31 | 0.03 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {} | 2023-06-15 05:44:31 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2023-06-15 05:44:31 | 2023-06-15 05:45:24 | 53.53 | list | [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) | 290,197 | {} | 2023-06-15 05:44:31 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2023-06-15 05:45:24 | 2023-06-15 05:49:15 | 230.84 |
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__20230614-182602/pypath_git/pypath/inputs/go.py", line 943, in get_go_quick
terms[l[5]][l[1]].add(l[4])
KeyError: 'GO ASPECT'
|
{} | 2023-06-12 19:03:23 | |||
| ¶ | pypath.inputs.go.get_goslim | 2023-06-15 05:49:15 | 2023-06-15 05:49:16 | 1.09 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 141 | {} | 2023-06-15 05:49:15 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2023-06-15 05:49:16 | 2023-06-15 06:01:43 | 746.49 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016014': {('GO:0098797', 'is_a'), ...(truncated) | 3 | {} | 2023-06-15 05:49:16 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2023-06-15 06:01:43 | 2023-06-15 06:01:43 | 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__20230614-182602/pypath_git/pypath/inputs/go.py", line 211, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-06-12 19:18:26 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2023-06-15 06:01:43 | 2023-06-15 06:01:47 | 4.13 | dict | {'C': {'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016014': {('GO:0098797', 'is_a'), ...(truncated) | 3 | {} | 2023-06-15 06:01:43 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2023-06-15 06:01:47 | 2023-06-15 06:01:51 | 4.55 | dict | {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2023-06-15 06:01:47 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2023-06-15 06:01:51 | 2023-06-15 06:01:57 | 5.23 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0046872', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0479', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) | 19,625 | {} | 2023-06-15 06:01:51 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2023-06-15 06:01:59 | 2023-06-15 06:02:00 | 1.04 | dict | {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005737', 'GO:0005634'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2023-06-15 06:01:59 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2023-06-15 06:02:00 | 2023-06-15 06:02:00 | 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__20230614-182602/pypath_git/pypath/inputs/go.py", line 858, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-06-12 19:18:48 | |||
| ¶ | pypath.inputs.go.go_annotations_solr | 2023-06-15 06:02:00 | 2023-06-15 06:02:01 | 1.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/go.py", line 744, in go_annotations_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:18:51 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2023-06-15 06:02:01 | 2023-06-15 06:02:01 | 0.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/go.py", line 67, in go_annotations_uniprot
for x in [x.split('\t') for x in data.split('\n')]
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-06-12 19:18:52 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2023-06-15 06:02:01 | 2023-06-15 06:02:05 | 4.09 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2023-06-15 06:02:01 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2023-06-15 06:02:05 | 2023-06-15 06:02:05 | 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__20230614-182602/pypath_git/pypath/inputs/go.py", line 289, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/go.py", line 211, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-06-12 19:18:57 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2023-06-15 06:02:05 | 2023-06-15 06:02:09 | 3.96 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016008', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2023-06-15 06:02:05 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2023-06-15 06:02:09 | 2023-06-15 06:02:13 | 3.32 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2023-06-15 06:02:09 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2023-06-15 06:02:13 | 2023-06-15 06:02:13 | 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__20230614-182602/pypath_git/pypath/inputs/go.py", line 584, in go_terms_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-06-12 19:19:08 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2023-06-15 06:02:13 | 2023-06-15 06:02:16 | 3.28 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2023-06-15 06:02:13 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2023-06-15 06:02:16 | 2023-06-15 06:02:17 | 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__20230614-182602/pypath_git/pypath/inputs/go.py", line 442, in go_terms_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:19:15 | |||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2023-06-15 06:02:17 | 2023-06-15 06:02:17 | 0.22 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 424 | {} | 2023-06-15 06:02:17 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2023-06-15 06:02:17 | 2023-06-15 06:02:18 | 1.37 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2023-06-15 06:02:17 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2023-06-15 06:02:18 | 2023-06-15 06:02:21 | 2.86 |
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__20230614-182602/pypath_git/pypath/inputs/guide2pharma.py", line 237, in guide2pharma_download
ligand_uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/guide2pharma.py", line 238, in <listcomp>
mapping.map_name0(ligand, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:18:00 | |||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.havugimana.get_havugimana | 2023-06-15 06:02:21 | 2023-06-15 06:02:21 | 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__20230614-182602/pypath_git/pypath/inputs/havugimana.py", line 44, in get_havugimana
path = cell_input.cell_supplementary(supp_url, article_url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:19:20 | |||
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2023-06-15 06:02:21 | 2023-06-15 06:02:21 | 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__20230614-182602/pypath_git/pypath/inputs/havugimana.py", line 59, in havugimana_complexes
for rec in get_havugimana():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/havugimana.py", line 44, in get_havugimana
path = cell_input.cell_supplementary(supp_url, article_url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:19:20 | |||
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2023-06-15 06:02:21 | 2023-06-15 07:12:33 | 4,211.93 | dict | {} | 0 | {'size': -15143} | 2023-06-15 06:02:21 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2023-06-15 07:12:33 | 2023-06-15 07:17:46 | 312.99 | list | [] | 0 | {'size': -102282} | 2023-06-15 07:12:33 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2023-06-15 07:17:46 | 2023-06-15 07:17:54 | 8.30 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2023-06-15 07:17:46 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2023-06-15 07:17:55 | 2023-06-15 07:17:55 | 0.01 | dict | {'interactions': [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462...(truncated) | 3 | {} | 2023-06-15 07:17:55 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2023-06-15 07:17:55 | 2023-06-15 07:17:55 | 0.00 | dict | {'P26992': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='CICYTR (Cytokine Type 1 receptors)', subsubclass=None)}, 'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P42...(truncated) | 1,141 | {} | 2023-06-15 07:17:55 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2023-06-15 07:17:55 | 2023-06-15 07:17:55 | 0.00 | dict | {} | 0 | {} | 2023-06-15 07:17:55 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2023-06-15 07:17:55 | 2023-06-15 07:17:55 | 0.00 | list | [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462', 'Ligand', 'P26...(truncated) | 619 | {} | 2023-06-15 07:17:55 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2023-06-15 07:17:55 | 2023-06-15 07:17:56 | 1.67 | defaultdict | defaultdict(<class 'set'>, {}) | 0 | {'size': -4858} | 2023-06-15 07:17:55 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2023-06-15 07:17:56 | 2023-06-15 07:17:59 | 2.66 | 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:614254', name='Neurodevelopmental disorder with or with...(truncated) | 10,644 | {} | 2023-06-15 07:17:56 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2023-06-15 07:17:59 | 2023-06-15 07:18:01 | 1.27 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {} | 2023-06-15 07:17:59 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2023-06-15 07:18:01 | 2023-06-15 07:18:01 | 0.56 | dict | {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) | 17,610 | {} | 2023-06-15 07:18:01 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2023-06-15 07:18:01 | 2023-06-15 07:18:05 | 3.52 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2023-06-15 07:18:01 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2023-06-15 07:18:05 | 2023-06-15 07:18:07 | 1.67 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {} | 2023-06-15 07:18:05 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2023-06-15 07:18:07 | 2023-06-15 07:18:08 | 1.66 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {} | 2023-06-15 07:18:07 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2023-06-15 07:18:08 | 2023-06-15 07:18:10 | 1.53 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2023-06-15 07:18:08 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2023-06-15 07:18:10 | 2023-06-15 07:18:13 | 2.77 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2023-06-15 07:18:10 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2023-06-15 07:18:13 | 2023-06-15 07:18:14 | 1.16 | dict | {} | 0 | {'size': -4371} | 2023-06-15 07:18:13 | |
| ¶ | pypath.inputs.humap.humap2_complexes | 2023-06-15 07:18:14 | 2023-06-15 07:18:38 | 24.06 | dict | {} | 0 | {'size': -6944} | 2023-06-15 07:18:14 | |
| ¶ | pypath.inputs.humap.humap_complexes | 2023-06-15 07:18:38 | 2023-06-15 07:18:39 | 0.85 | dict | {} | 0 | {'size': -4508} | 2023-06-15 07:18:38 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2023-06-15 07:18:39 | 2023-06-15 07:21:06 | 147.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:18:54 | |||
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2023-06-15 07:21:06 | 2023-06-15 07:27:50 | 403.67 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:18:55 | |||
| ¶ | pypath.inputs.huri.hi_iii_old | 2023-06-15 07:27:50 | 2023-06-15 07:27:50 | 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__20230614-182602/pypath_git/pypath/inputs/huri.py", line 95, in hi_iii_old
url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
|
{} | 2023-06-12 19:20:23 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2023-06-15 07:27:50 | 2023-06-15 07:39:23 | 693.53 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:18:59 | |||
| ¶ | pypath.inputs.huri.huri_interactions | 2023-06-15 07:39:23 | 2023-06-15 07:39:38 | 14.99 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:19:18 | |||
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2023-06-15 07:39:38 | 2023-06-15 07:39:39 | 0.87 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2023-06-15 07:39:38 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2023-06-15 07:39:39 | 2023-06-15 07:39:40 | 1.10 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2023-06-15 07:39:39 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2023-06-15 07:39:40 | 2023-06-15 07:39:45 | 4.52 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{} | 2023-06-12 19:20:59 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2023-06-15 07:39:45 | 2023-06-15 07:39:45 | 0.18 |
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__20230614-182602/pypath_git/pypath/inputs/huri.py", line 43, in rolland_hi_ii_14
xlsname = cell.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:21:14 | |||
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2023-06-15 07:39:45 | 2023-06-15 07:39:46 | 1.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:19:36 | |||
| ¶ | pypath.inputs.huri.yu2011_interactions | 2023-06-15 07:39:46 | 2023-06-15 07:39:47 | 1.47 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:19:38 | |||
| ¶ | pypath.inputs.i3d.get_i3d | 2023-06-15 07:39:47 | 2023-06-15 07:39:56 | 8.60 | list | [{'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P02647': {'pfam': None, 'chain': 'A', 'seq': [[68, 265]]}, 'uniprots': ['A0A024RAV5', 'P02647'], 'source': 'I3D', 'pdb': ['2mse'], 'references': []}, {'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P10398': {'pfam': N...(truncated) | 15,984 | {} | 2023-06-15 07:39:47 | |
| ¶ | pypath.inputs.icellnet._icellnet_get_components |
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_entity |
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_references |
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_resources |
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2023-06-15 07:39:56 | 2023-06-15 07:39:56 | 0.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 171, in icellnet_annotations
for ia in icellnet_interactions():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 77, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 201, in _icellnet_get_components
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 201, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 205, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:19:53 | |||
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2023-06-15 07:39:56 | 2023-06-15 07:39:56 | 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__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 108, in icellnet_complexes
for ia in icellnet_interactions():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 77, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 201, in _icellnet_get_components
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 201, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 205, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:19:54 | |||
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2023-06-15 07:39:56 | 2023-06-15 07:39:56 | 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__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 77, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 201, in _icellnet_get_components
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 201, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/icellnet.py", line 205, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:19:54 | |||
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2023-06-15 07:39:56 | 2023-06-15 07:39:58 | 1.89 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/imweb.py", line 77, in _get_imweb
hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
File "/usr/lib/python3.10/json/__init__.py", line 339, in loads
raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not NoneType
|
{} | 2023-06-12 19:21:27 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2023-06-15 07:39:58 | 2023-06-15 07:39:58 | 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__20230614-182602/pypath_git/pypath/inputs/imweb.py", line 110, in get_imweb
c0.perform()
pycurl.error: (3, '')
|
{} | 2023-06-12 19:21:29 | |||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2023-06-15 07:39:58 | 2023-06-15 07:39:59 | 0.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/imweb.py", line 143, in get_imweb_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-06-12 19:21:29 | |||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2023-06-15 07:39:59 | 2023-06-15 07:40:01 | 1.75 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2023-06-15 07:39:59 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2023-06-15 07:40:01 | 2023-06-15 07:40:01 | 0.65 | NoneType | None | 0 | {} | 2023-06-15 07:40:01 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2023-06-15 07:40:01 | 2023-06-15 07:40:02 | 0.43 | NoneType | None | 0 | {} | 2023-06-15 07:40:01 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2023-06-15 07:40:02 | 2023-06-15 07:41:06 | 64.18 | 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) | 71,496 | {} | 2023-06-15 07:40:02 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2023-06-15 07:41:06 | 2023-06-15 07:41:10 | 3.77 | set | set() | 0 | {'size': -25} | 2023-06-15 07:41:06 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2023-06-15 07:41:10 | 2023-06-15 07:41:11 | 0.94 | 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:0006355', go_term_name='regulation of DNA-templated transcription'),...(truncated) | 14,657 | {'size': 30} | 2023-06-15 07:41:10 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2023-06-15 07:41:11 | 2023-06-15 07:42:11 | 60.22 |
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__20230614-182602/pypath_git/pypath/inputs/interpro.py", line 274, in interpro_annotations
totalrec = int(res['count'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-06-12 19:22:37 | |||
| ¶ | pypath.inputs.interpro.interpro_entries | 2023-06-15 07:42:11 | 2023-06-15 07:42:30 | 19.04 | list | [InterproEntry(interpro_id='IPR000001', protein_count='18450', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 38,816 | {} | 2023-06-15 07:42:11 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2023-06-15 07:42:30 | 2023-06-15 07:42:31 | 0.46 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/intogen.py", line 78, in intogen_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:22:29 | |||
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2023-06-15 07:42:31 | 2023-06-15 07:42:32 | 1.77 | dict | {'IPI00807623': {'A0A183'}, 'IPI00396341': {'A0AUZ9'}, 'IPI00884975': {'A0AUZ9'}, 'IPI00884987': {'A0AUZ9'}, 'IPI00885003': {'A0AUZ9'}, 'IPI00855723': {'A0AV02'}, 'IPI00867607': {'A0AV02'}, 'IPI00793608': {'A0AV02'}, 'IPI00867726': {'A0AV02'}, 'IPI00867740': {'A0AV02'}, 'IPI00169342': {'A0AV96'}, 'I...(truncated) | 51,106 | {} | 2023-06-15 07:42:31 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2023-06-15 07:42:32 | 2023-06-15 07:46:50 | 258.04 | list | [IptmnetInteraction(enzyme='P41227', substrate='P41227', enzyme_isoform=None, substrate_isoform=None, ptm_type='acetylation', resaa='136', resnum='K', score=None, references=['27708256']), IptmnetInteraction(enzyme='Q00403', substrate='Q00403', enzyme_isoform=None, substrate_isoform=None, ptm_type='...(truncated) | 16,874 | {'size': -207} | 2023-06-15 07:42:32 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2023-06-15 07:46:50 | 2023-06-15 07:46:51 | 0.65 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/italk.py", line 110, in italk_annotations
mapping.map_name(row[2], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:25:35 | |||
| ¶ | pypath.inputs.italk.italk_interactions | 2023-06-15 07:46:51 | 2023-06-15 07:46:51 | 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__20230614-182602/pypath_git/pypath/inputs/italk.py", line 75, in italk_interactions
ligands = mapping.map_name(row[2], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:25:35 | |||
| ¶ | pypath.inputs.italk.italk_raw | 2023-06-15 07:46:51 | 2023-06-15 07:46:51 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2023-06-15 07:46:51 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2023-06-15 07:46:51 | 2023-06-15 07:46:53 | 1.78 |
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__20230614-182602/pypath_git/pypath/inputs/kea.py", line 112, in kea_enzyme_substrate
for rec in kea_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kea.py", line 79, in kea_interactions
e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:25:35 | |||
| ¶ | pypath.inputs.kea.kea_interactions | 2023-06-15 07:46:53 | 2023-06-15 07:46:53 | 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__20230614-182602/pypath_git/pypath/inputs/kea.py", line 79, in kea_interactions
e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:25:38 | |||
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2023-06-15 07:46:53 | 2023-06-15 07:46:57 | 3.83 |
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__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 130, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 131, in <listcomp>
common.flat_list([
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 132, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:25:38 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus | 2023-06-15 07:46:57 | 2023-06-15 07:47:13 | 16.21 | set | {KeggMedicusRawInteraction(id_a='5894', id_b='5604', name_a='RAF1', name_b='MAP2K1', effect='stimulation', itype='post_translational', pw_type='factor', type_a='gene', type_b='gene', network_id='N01408'), KeggMedicusRawInteraction(id_a='808', id_b='8536', name_a='CALM3', name_b='CAMK1', effect='stim...(truncated) | 12,578 | {} | 2023-06-15 07:46:57 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2023-06-15 07:47:13 | 2023-06-15 07:47:13 | 0.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 690, in kegg_medicus_complexes
cplexes = kegg_medicus_interactions(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 657, in kegg_medicus_interactions
process_partner(rec.id_a, rec.name_a, rec.type_a),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 648, in process_partner
process_protein(ids, symbols)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 641, in process_protein
mapping.map_name(id_, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:29:57 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2023-06-15 07:47:13 | 2023-06-15 07:47:14 | 0.52 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 657, in kegg_medicus_interactions
process_partner(rec.id_a, rec.name_a, rec.type_a),
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 648, in process_partner
process_protein(ids, symbols)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 641, in process_protein
mapping.map_name(id_, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:29:57 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2023-06-15 07:47:14 | 2023-06-15 07:47:14 | 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__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 199, in kegg_pathway_annotations
proteins, interactions = kegg_pathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 180, in kegg_pathways
data = kegg_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 130, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 131, in <listcomp>
common.flat_list([
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 132, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:29:58 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2023-06-15 07:47:14 | 2023-06-15 07:47:14 | 0.47 | dict | {'A8K7J7': {KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='B...(truncated) | 813 | {} | 2023-06-15 07:47:14 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2023-06-15 07:47:14 | 2023-06-15 07:47:15 | 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__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 180, in kegg_pathways
data = kegg_interactions()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 130, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 131, in <listcomp>
common.flat_list([
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg.py", line 132, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:30:04 | |||
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._generate_conv_functions | 2023-06-15 07:47:15 | 2023-06-15 07:47:15 | 0.00 | NoneType | None | 0 | {} | 2023-06-15 07:47:15 | |
| ¶ | pypath.inputs.kegg_api._generate_relation_functions | 2023-06-15 07:47:15 | 2023-06-15 07:47:15 | 0.00 | NoneType | None | 0 | {} | 2023-06-15 07:47:15 | |
| ¶ | pypath.inputs.kegg_api._kegg_conv |
Not calling `pypath.inputs.kegg_api._kegg_conv`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi |
Not calling `pypath.inputs.kegg_api._kegg_ddi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_async |
Not calling `pypath.inputs.kegg_api._kegg_ddi_async`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_sync |
Not calling `pypath.inputs.kegg_api._kegg_ddi_sync`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general |
Not calling `pypath.inputs.kegg_api._kegg_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general_async |
Not calling `pypath.inputs.kegg_api._kegg_general_async`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_link |
Not calling `pypath.inputs.kegg_api._kegg_link`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_list |
Not calling `pypath.inputs.kegg_api._kegg_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_relations |
Not calling `pypath.inputs.kegg_api._kegg_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2023-06-15 07:47:15 | 2023-06-15 07:47:15 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kegg_api.py", line 133, in drug_to_drug
entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
TypeError: Can't instantiate abstract class _Drug with abstract methods __init__, load
|
{} | 2023-06-12 19:35:59 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2023-06-15 07:47:15 | 2023-06-15 07:47:15 | 0.37 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/kinasedotcom.py", line 68, in kinasedotcom_annotations
uniprots = mapping.map_name(rec[23].strip(), 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:30:09 | |||
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2023-06-15 07:47:15 | 2023-06-15 07:47:18 | 3.24 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {'fixed': True} | 2023-06-15 07:47:15 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2023-06-15 07:47:18 | 2023-06-15 07:47:18 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/lambert2018.py", line 104, in lambert2018_annotations
for r in lambert2018_s1_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/lambert2018.py", line 44, in lambert2018_s1_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:36:00 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2023-06-15 07:47:18 | 2023-06-15 07:47:18 | 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__20230614-182602/pypath_git/pypath/inputs/lambert2018.py", line 44, in lambert2018_s1_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 19:36:00 | |||
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2023-06-15 07:47:18 | 2023-06-15 07:47:19 | 0.37 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2023-06-15 07:47:18 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2023-06-15 07:47:19 | 2023-06-15 07:47:19 | 0.54 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2023-06-15 07:47:19 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2023-06-15 07:47:19 | 2023-06-15 07:47:29 | 9.47 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2023-06-15 07:47:19 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2023-06-15 07:47:29 | 2023-06-15 07:47:30 | 0.82 |
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__20230614-182602/pypath_git/pypath/inputs/li2012.py", line 133, in li2012_dmi
se = seq.swissprot_seq(isoforms = True)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/seq.py", line 55, in swissprot_seq
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-06-12 19:36:10 | |||
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2023-06-15 07:47:30 | 2023-06-15 07:47:30 | 0.03 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2023-06-15 07:47:30 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2023-06-15 07:47:30 | 2023-06-15 07:47:30 | 0.03 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2023-06-15 07:47:30 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2023-06-15 07:47:30 | 2023-06-15 07:47:34 | 4.36 | dict | {'10001': LincsCompound(lincs='LSM-1001', chembl='CHEMBL14762', chebi='CHEBI:354.22', inchi='InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1', inchi_key='BTIHMVBBUGXLCJ-OAHLLOKOSA-N', smil...(truncated) | 1,320 | {} | 2023-06-15 07:47:30 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2023-06-15 07:47:34 | 2023-06-15 07:47:35 | 0.61 | list | [] | 0 | {} | 2023-06-15 07:47:34 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2023-06-15 07:47:35 | 2023-06-15 07:47:35 | 0.61 | list | [] | 0 | {} | 2023-06-15 07:47:35 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2023-06-15 07:47:35 | 2023-06-15 07:47:36 | 0.62 | list | [] | 0 | {} | 2023-06-15 07:47:35 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2023-06-15 07:47:36 | 2023-06-15 07:47:36 | 0.20 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism='human', pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism='human', pmid='22244333')...(truncated) | 478 | {} | 2023-06-15 07:47:36 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2023-06-15 07:47:36 | 2023-06-15 07:47:37 | 0.34 | list | [] | 0 | {} | 2023-06-15 07:47:36 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2023-06-15 07:47:37 | 2023-06-15 11:58:36 | 15,059.33 | dict | {} | 0 | {'size': -9496} | 2023-06-15 07:47:37 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2023-06-15 11:58:36 | 2023-06-15 11:58:36 | 0.38 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/lrdb.py", line 117, in lrdb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:31:08 | |||
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2023-06-15 11:58:36 | 2023-06-15 11:58:36 | 0.03 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {} | 2023-06-15 11:58:36 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2023-06-15 11:58:36 | 2023-06-15 11:58:37 | 0.20 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2023-06-15 11:58:36 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2023-06-15 11:58:37 | 2023-06-15 11:58:38 | 1.53 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/matrisome.py", line 91, in __matrisome_annotations_2
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-06-12 19:36:56 | |||
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2023-06-15 11:58:38 | 2023-06-15 12:40:19 | 2,501.20 | dict | {} | 0 | {'size': -1067} | 2023-06-15 11:58:38 | |
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2023-06-15 12:40:19 | 2023-06-16 14:28:10 | 92,870.77 | dict | {} | 0 | {'size': -10094} | 2023-06-15 12:40:19 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2023-06-16 14:28:10 | 2023-06-16 14:28:10 | 0.00 | set | set() | 0 | {'size': -483} | 2023-06-16 14:28:10 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2023-06-16 14:28:10 | 2023-06-16 14:28:10 | 0.14 | list | [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) | 425 | {} | 2023-06-16 14:28:10 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2023-06-16 14:28:10 | 2023-06-17 12:19:36 | 78,685.47 | set | set() | 0 | {'size': -8238} | 2023-06-16 14:28:10 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2023-06-17 12:19:36 | 2023-06-17 16:07:56 | 13,700.46 | set | set() | 0 | {'size': -2922} | 2023-06-17 12:19:36 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2023-06-17 16:07:56 | 2023-06-17 16:08:04 | 7.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/mcam.py", line 36, in mcam_cell_adhesion_molecules
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'broke': True} | 2023-06-13 19:31:16 | |||
| ¶ | pypath.inputs.membranome.membranome_annotations | 2023-06-17 16:08:04 | 2023-06-17 17:56:32 | 6,508.22 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 19:31:17 | |||
| ¶ | pypath.inputs.mimp.get_kinase_class | 2023-06-17 17:56:32 | 2023-06-17 17:56:32 | 0.16 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2023-06-17 17:56:32 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2023-06-17 17:56:32 | 2023-06-17 17:56:43 | 10.49 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2023-06-17 17:56:32 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2023-06-17 17:56:43 | 2023-06-17 17:56:43 | 0.56 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2023-06-17 17:56:43 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2023-06-17 17:56:43 | 2023-06-17 17:56:44 | 0.20 | list | [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) | 805 | {} | 2023-06-17 17:56:43 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2023-06-17 17:56:44 | 2023-06-17 17:56:44 | 0.50 | tuple | ({'MIMAT0000062': {'hsa-let-7a', 'hsa-let-7a-5p'}, 'MIMAT0000063': {'hsa-let-7b-5p', 'hsa-let-7b'}, 'MIMAT0000064': {'hsa-let-7c-5p', 'hsa-let-7c'}, 'MIMAT0000065': {'hsa-let-7d-5p', 'hsa-let-7d'}, 'MIMAT0000066': {'hsa-let-7e', 'hsa-let-7e-5p'}, 'MIMAT0000067': {'hsa-let-7f', 'hsa-let-7f-5p'}, 'MIM...(truncated) | 2 | {} | 2023-06-17 17:56:44 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2023-06-17 17:56:44 | 2023-06-17 17:56:44 | 0.08 | list | [('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000068', 'MI...(truncated) | 3,027 | {} | 2023-06-17 17:56:44 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2023-06-17 17:56:44 | 2023-06-17 17:56:44 | 0.06 | list | [('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0000064', 'hsa-let-7c-5p'), ('MIMAT0000064', 'hsa-let-7c'), ('MIMAT0000065', 'hsa-let-7d-5p'), ('MIMAT0000065', 'hsa-let-7d'), ('MIMAT0000066', 'hsa-let-7e'),...(truncated) | 3,487 | {} | 2023-06-17 17:56:44 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2023-06-17 17:56:44 | 2023-06-17 17:56:44 | 0.24 | list | ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) | 3,027 | {} | 2023-06-17 17:56:44 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2023-06-17 17:56:44 | 2023-06-17 17:56:44 | 0.06 | list | [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7bL'), ('MI0000063', 'hsa-let-7b'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,173 | {} | 2023-06-17 17:56:44 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2023-06-17 17:56:44 | 2023-06-17 17:56:45 | 0.08 | list | ['MI0000060', 'MI0000062', 'MI0000061', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000070', 'MI0000115', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) | 3,027 | {} | 2023-06-17 17:56:44 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2023-06-17 17:56:45 | 2023-06-17 17:56:45 | 0.14 | list | [('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0010195'), ('hsa-let-7a-2L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMA...(truncated) | 3,361 | {} | 2023-06-17 17:56:45 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2023-06-17 17:56:45 | 2023-06-17 17:56:45 | 0.20 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2023-06-17 17:56:45 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2023-06-17 17:56:45 | 2023-06-17 17:56:45 | 0.42 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism='Homo sapiens', target_organism='Homo sapiens', pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organ...(truncated) | 3,106 | {} | 2023-06-17 17:56:45 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2023-06-17 17:56:45 | 2023-06-17 17:57:01 | 15.46 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism='Mus musculus', target_genesymbol='Cd320', target_entrez='54219', target_organism='Mus musculus', target_site='AGAGACTGGGGTCCTCAGACACTCCC', method='Luciferase reporter assay//qRT-PCR//Western blot', catego...(truncated) | 21,560 | {} | 2023-06-17 17:56:45 | |
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2023-06-17 17:57:01 | 2023-06-17 17:57:01 | 0.46 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2023-06-17 17:57:01 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2023-06-17 17:57:01 | 2023-06-17 17:57:54 | 52.53 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/msigdb.py", line 369, in msigdb_annotations
for uniprot in mapping.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:32:01 | |||
| ¶ | pypath.inputs.msigdb.msigdb_download | 2023-06-17 17:57:54 | 2023-06-17 17:58:10 | 15.92 | dict | {'chr1p11': {'NOTCH2NLR', 'PPIAL4A', 'MTIF2P1', 'NBPF8', 'RPL22P6', 'PFN1P2', 'RNVU1-4', 'H2BP1', 'NBPF26', 'LINC02798', 'SRGAP2C', 'FAM72B', 'H3P4', 'PDE4DIPP2', 'LINC00623', 'SRGAP2-AS1', 'LINC01691', 'FCGR1BP', 'RNVU1-19', 'PDE4DIPP4', 'EMBP1'}, 'chr1p12': {'HSD3B2', 'NBPF7P', 'VDAC2P3', 'VTCN1',...(truncated) | 33,591 | {} | 2023-06-17 17:57:54 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2023-06-17 17:58:11 | 2023-06-17 17:58:11 | 0.48 | dict | {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'DUSP1', 'PPP1R15A', 'SDC4', 'CSF2', 'CLCF1', 'SMAD3', 'EGR3', 'FOSL2', 'CXCL1', 'SERPINB8', 'LDLR', 'SIK1', 'IL15RA', 'ID2', 'CDKN1A', 'CEBPB', 'TNIP1', 'EGR2', 'ACKR3', 'SPSB1', 'G0S2', 'KLF2', 'DENND5A', 'BCL2A1', 'CSF1', 'BCL6', 'KYNU...(truncated) | 18 | {} | 2023-06-17 17:58:11 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2023-06-17 17:58:11 | 2023-06-17 17:58:12 | 0.37 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2023-06-17 17:58:11 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2023-06-17 17:58:12 | 2023-06-17 17:58:42 | 30.00 |
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__20230614-182602/pypath_git/pypath/inputs/negatome.py", line 54, in negatome_interactions
for l in f:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-06-12 19:39:07 | |||
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2023-06-17 17:58:42 | 2023-06-17 17:58:42 | 0.13 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2023-06-17 17:58:42 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2023-06-17 17:58:42 | 2023-06-17 17:58:42 | 0.12 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {} | 2023-06-17 17:58:42 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2023-06-17 17:58:42 | 2023-06-17 17:58:45 | 2.50 | list | [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) | 7,555 | {} | 2023-06-17 17:58:42 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2023-06-17 17:58:45 | 2023-06-17 17:58:45 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2023-06-17 17:58:45 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2023-06-17 17:58:45 | 2023-06-17 17:58:46 | 0.91 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/netpath.py", line 215, in netpath_pathway_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:33:52 | |||
| ¶ | pypath.inputs.oma.oma_orthologs |
Not calling `pypath.inputs.oma.oma_orthologs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ontology.listof_ontologies | 2023-06-17 17:58:46 | 2023-06-17 17:58:46 | 0.69 | dict | {'rs': 'Rat Strain Ontology', 'sbo': 'Systems Biology Ontology', 'scdo': 'Sickle Cell Disease Ontology', 'sdgio': 'Sustainable Development Goals Interface Ontology', 'sepio': 'Scientific Evidence and Provenance Information Ontology', 'sibo': 'Social Insect Behavior Ontology', 'spd': 'Spider Ontology...(truncated) | 280 | {} | 2023-06-17 17:58:46 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opm.opm_annotations | 2023-06-17 17:58:46 | 2023-06-17 17:59:05 | 19.05 |
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__20230614-182602/pypath_git/pypath/inputs/opm.py", line 106, in opm_annotations
mapping.map_name0(this_name, 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:34:11 | |||
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2023-06-17 17:59:05 | 2023-06-17 18:01:25 | 139.41 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | {} | 2023-06-17 17:59:05 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2023-06-17 18:01:25 | 2023-06-17 18:01:36 | 11.72 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 5,688,970 | {} | 2023-06-17 18:01:25 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2023-06-17 18:01:36 | 2023-06-17 18:01:37 | 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__20230614-182602/pypath_git/pypath/inputs/panglaodb.py", line 85, in panglaodb_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:36:55 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2023-06-17 18:01:37 | 2023-06-17 18:01:37 | 0.04 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2023-06-17 18:01:37 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2023-06-17 18:01:37 | 2023-06-17 18:01:37 | 0.00 | list | [] | 0 | {} | 2023-06-17 18:01:37 | |
| ¶ | pypath.inputs.pathwaycommons._create_single_resource_method |
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2023-06-17 18:01:37 | 2023-06-17 18:01:53 | 16.41 | list | [PathwayCommonsInteraction(id_a='ABAT', interaction_type='catalysis-precedes', id_b='ALDH5A1', resource='PANTHER'), PathwayCommonsInteraction(id_a='ABAT', interaction_type='catalysis-precedes', id_b='ALDH6A1', resource='PANTHER'), PathwayCommonsInteraction(id_a='ABAT', interaction_type='catalysis-pr...(truncated) | 1,261,865 | {} | 2023-06-17 18:01:37 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2023-06-17 18:01:55 | 2023-06-17 18:01:55 | 0.25 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2023-06-17 18:01:55 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2023-06-17 18:01:55 | 2023-06-17 18:02:09 | 13.68 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2023-06-17 18:01:55 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2023-06-17 18:02:12 | 2023-06-17 18:02:21 | 8.14 | 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) | 42,870 | {'size': 73} | 2023-06-17 18:02:12 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2023-06-17 18:02:21 | 2023-06-17 18:03:01 | 40.46 | tuple | ({'P02185': {('2mgk', 'X-ray', 2.0), ('3m3a', 'X-ray', 1.37), ('6krc', 'X-ray', 1.39), ('1ch2', 'X-ray', 1.8), ('5zzf', 'X-ray', 1.6), ('1jpb', 'X-ray', 1.7), ('1ofk', 'X-ray', 1.8), ('1vxa', 'X-ray', 2.0), ('5ut7', 'X-ray', 1.85), ('1vxg', 'X-ray', 1.7), ('6krf', 'X-ray', 1.86), ('1bzr', 'X-ray', 1...(truncated) | 2 | {} | 2023-06-17 18:02:21 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2023-06-17 18:03:01 | 2023-06-17 18:03:02 | 0.77 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {} | 2023-06-17 18:03:01 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2023-06-17 18:03:02 | 2023-06-17 18:14:41 | 699.15 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2023-06-17 18:03:02 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2023-06-17 18:14:41 | 2023-06-17 18:14:43 | 1.13 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2023-06-17 18:14:41 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2023-06-17 18:14:43 | 2023-06-17 18:14:46 | 3.90 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': PfamDomain(chain='A', star...(truncated) | 2 | {} | 2023-06-17 18:14:43 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2023-06-17 18:14:47 | 2023-06-17 18:19:14 | 266.60 | tuple | ({}, {}) | 2 | {} | 2023-06-17 18:14:47 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2023-06-17 18:19:14 | 2023-06-17 18:19:14 | 0.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/pfam.py", line 100, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-06-12 19:59:27 | |||
| ¶ | pypath.inputs.pharos._create_query_functions | 2023-06-17 18:19:14 | 2023-06-17 18:19:14 | 0.00 | NoneType | None | 0 | {} | 2023-06-17 18:19:14 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2023-06-17 18:19:14 | 2023-06-17 18:20:16 | 61.49 | 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 | {} | 2023-06-17 18:19:14 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2023-06-17 18:20:17 | 2023-06-17 18:20:20 | 3.34 | 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 | {} | 2023-06-17 18:20:17 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2023-06-17 18:20:21 | 2023-06-17 18:20:25 | 3.84 | 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 | {} | 2023-06-17 18:20:21 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2023-06-17 18:20:26 | 2023-06-17 18:20:30 | 3.10 | 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 | {} | 2023-06-17 18:20:26 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2023-06-17 18:20:31 | 2023-06-17 18:20:34 | 3.01 | 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 | {} | 2023-06-17 18:20:31 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2023-06-17 18:20:35 | 2023-06-17 18:21:10 | 35.19 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2023-06-17 18:20:35 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2023-06-17 18:21:10 | 2023-06-17 18:21:13 | 3.12 | 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 | {} | 2023-06-17 18:21:10 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2023-06-17 18:21:14 | 2023-06-17 18:21:15 | 0.33 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2023-06-17 18:21:14 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2023-06-17 18:21:15 | 2023-06-17 18:21:19 | 4.78 |
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__20230614-182602/pypath_git/pypath/inputs/phosphatome.py", line 68, in phosphatome_annotations
uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:56:27 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2023-06-17 18:21:19 | 2023-06-17 18:21:22 | 2.26 | list | [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) | 2,426 | {} | 2023-06-17 18:21:19 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2023-06-17 18:21:22 | 2023-06-17 18:21:22 | 0.68 | list | [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) | 2,426 | {} | 2023-06-17 18:21:22 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2023-06-17 18:21:22 | 2023-06-17 18:21:22 | 0.12 | dict | {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) | 247 | {} | 2023-06-17 18:21:22 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2023-06-17 18:21:22 | 2023-06-17 18:21:25 | 2.20 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2023-06-17 18:21:22 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.02 | list | [['SIK1', 'DDEF2'], ['DYRK4', 'BMX'], ['STK17A', 'NCL'], ['CDK4', 'SMARCC2'], ['CDK4', 'BCL3'], ['CHEK2', 'CDC25C'], ['PAK4', 'LUC7L2'], ['FGFR1', 'BCAR1'], ['DYRK1B', 'CDKN1A'], ['SRPK2', 'EIF4B'], ['STK3', 'WWTR1'], ['MAP3K7', 'TRIM28'], ['NEK6', 'SGK'], ['NEK2', 'SERBP1'], ['CSNK2A2', 'NFATC4'], ...(truncated) | 1,821 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.22 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P45984', 'P46937'], ['P06493', 'Q9GZV5'], ['P11309', 'P52907'], ['O14757', 'Q...(truncated) | 8,971 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.35 | list | [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) | 13,459 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) | 2 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.01 | list | [] | 0 | {'size': -9041} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.00 | list | [] | 0 | {'size': -4309} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) | 2 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2023-06-17 18:21:25 | 2023-06-17 18:21:25 | 0.00 | list | [] | 0 | {'size': -4732} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2023-06-17 18:21:25 | 2023-06-17 18:21:31 | 5.42 | dict | {('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('Q9CQV8', 1, 'S', 6, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'S', 6, 9606,...(truncated) | 198,635 | {} | 2023-06-17 18:21:25 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2023-06-17 18:21:31 | 2023-06-17 18:21:31 | 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__20230614-182602/pypath_git/pypath/inputs/phosphosite.py", line 336, in phosphosite_ptms
res = intera.Residue(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/internals/intera.py", line 91, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 132, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 468, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3681, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2641, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 19:56:43 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2023-06-17 18:21:31 | 2023-06-17 18:21:32 | 0.64 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'phosphorylation', 'protein degradation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {} | 2023-06-17 18:21:31 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2023-06-17 18:21:32 | 2023-06-17 18:26:16 | 284.25 | dict | {} | 0 | {'size': -3619} | 2023-06-17 18:21:32 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2023-06-17 18:26:16 | 2023-06-17 18:32:16 | 360.02 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2023-06-17 18:26:16 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2023-06-17 18:32:16 | 2023-06-17 18:32:17 | 0.43 | list | [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) | 320,143 | {} | 2023-06-17 18:32:16 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2023-06-17 18:32:17 | 2023-06-17 18:32:20 | 2.91 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/progeny.py", line 109, in progeny_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:04:49 | |||
| ¶ | pypath.inputs.progeny.progeny_raw | 2023-06-17 18:32:20 | 2023-06-17 18:32:22 | 1.82 | DataFrame | gene pathway weight p.value 1 RFC2 EGFR 1.470647 0.001655 2 ESRRA EGFR 0.178590 0.211838 3 HNRNPK EGFR 0.306699 0.084560 4 CBX6 EGFR -0.675507 0.017641 5 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2023-06-17 18:32:20 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2023-06-17 18:32:22 | 2023-06-17 18:32:23 | 0.83 |
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__20230614-182602/pypath_git/pypath/inputs/proteinatlas.py", line 60, in get_proteinatlas
uniprots = mapping.map_name(l[1], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:04:57 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2023-06-17 18:32:23 | 2023-06-17 18:32:23 | 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__20230614-182602/pypath_git/pypath/inputs/proteinatlas.py", line 125, in proteinatlas_annotations
data = get_proteinatlas(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/proteinatlas.py", line 60, in get_proteinatlas
uniprots = mapping.map_name(l[1], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:05:04 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2023-06-17 18:32:23 | 2023-06-17 18:43:06 | 643.79 | dict | {} | 0 | {'size': -2590} | 2023-06-17 18:32:23 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2023-06-17 18:43:06 | 2023-06-17 18:43:07 | 0.40 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/proteinatlas.py", line 224, in proteinatlas_subcellular_annotations
uniprots = mapping.map_name(rec['Gene name'], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:05:22 | |||
| ¶ | pypath.inputs.proteins.variants | 2023-06-17 18:43:07 | 2023-06-17 19:05:37 | 1,349.87 | list | [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) | 48,453 | {} | 2023-06-17 18:43:07 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2023-06-17 19:05:38 | 2023-06-17 19:05:42 | 4.72 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) | 2 | {} | 2023-06-17 19:05:38 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2023-06-17 19:05:43 | 2023-06-17 19:05:43 | 0.81 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'24357804', '24727247', '25728676', '25545367', '22304920'}, 'substrate': 'P15336', 'databases': {'SIGNOR', 'Sparser', 'PhosphoSite', 'REACH'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'24727247', '23708658'}, ...(truncated) | 22,139 | {} | 2023-06-17 19:05:43 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2023-06-17 19:05:43 | 2023-06-17 19:05:44 | 0.68 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2023-06-17 19:05:43 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2023-06-17 19:05:44 | 2023-06-18 00:24:17 | 19,113.28 | dict | {} | 0 | {'size': -18852} | 2023-06-17 19:05:44 | |
| ¶ | pypath.inputs.ramp._ramp_sqldump | 2023-06-18 00:24:17 | 2023-06-18 00:24:22 | 4.16 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/cache/2ac9fe4b32649e946c59f28f74943748-38534654' encoding='utf-8'> | 0 | {} | 2023-06-18 00:24:17 | |
| ¶ | pypath.inputs.ramp.ramp_id_types | 2023-06-18 00:24:22 | 2023-06-18 00:32:26 | 484.26 | set | {'wikidata', 'kegg_glycan', 'ncbiprotein', 'LIPIDMAPS', 'chebi', 'entrez', 'pubchem', 'brenda', 'kegg', 'chemspider', 'lipidbank', 'swisslipids', 'hmdb', 'gene_symbol', 'plantfa', 'EN', 'CAS', 'ensembl', 'uniprot'} | 19 | {} | 2023-06-18 00:24:22 | |
| ¶ | pypath.inputs.ramp.ramp_id_types_2 | 2023-06-18 00:32:26 | 2023-06-18 00:32:33 | 7.21 | set | {'wikidata', 'kegg_glycan', 'ncbiprotein', 'LIPIDMAPS', 'chebi', 'entrez', 'pubchem', 'brenda', 'kegg', 'chemspider', 'lipidbank', 'swisslipids', 'hmdb', 'gene_symbol', 'plantfa', 'EN', 'CAS', 'ensembl', 'uniprot'} | 19 | {} | 2023-06-18 00:32:26 | |
| ¶ | pypath.inputs.ramp.ramp_list_tables | 2023-06-18 00:32:33 | 2023-06-18 00:32:36 | 2.60 | dict | {'analyte': ['rampId', 'type'], 'analytehasontology': ['rampCompoundId', 'rampOntologyId'], 'analytehaspathway': ['rampId', 'pathwayRampId', 'pathwaySource'], 'analytesynonym': ['Synonym', 'rampId', 'geneOrCompound', 'source'], 'catalyzed': ['rampCompoundId', 'rampGeneId'], 'chem_props': ['ramp_id',...(truncated) | 13 | {} | 2023-06-18 00:32:33 | |
| ¶ | pypath.inputs.ramp.ramp_mapping |
Not calling `pypath.inputs.ramp.ramp_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_raw |
Not calling `pypath.inputs.ramp.ramp_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_show_tables | 2023-06-18 00:32:36 | 2023-06-18 00:32:38 | 2.58 | NoneType | None | 0 | {} | 2023-06-18 00:32:36 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2023-06-18 00:32:38 | 2023-06-18 00:32:38 | 0.00 | NoneType | None | 0 | {} | 2023-06-18 00:32:38 | |
| ¶ | pypath.inputs.rdata._rdata_data_frame_get_rownames |
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.rdata._rdata_list_get_names |
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._bp_collect_resources |
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._process_controls |
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_resources |
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_species |
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_compartment |
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_id |
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_res |
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_id |
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reaction |
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reactions | 2023-06-18 00:32:38 | 2023-06-18 00:32:54 | 15.80 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/reaction.py", line 986, in _reactome_reactions
for i in sp.find('bqbiol:haspart').find_all('rdf:li'):
AttributeError: 'NoneType' object has no attribute 'find_all'
|
{} | 2023-06-12 20:55:06 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2023-06-18 00:32:54 | 2023-06-18 00:32:56 | 2.33 | tuple | ({}, {}, {}) | 3 | {} | 2023-06-18 00:32:54 | |
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2023-06-18 00:32:56 | 2023-06-18 00:32:57 | 0.81 | list | ['<?xml version="1.0" encoding="UTF-8"?>\n', '<rdf:RDF\n', ' xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n', ' xmlns:owl="http://www.w3.org/2002/07/owl#"\n', ' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n', ' xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"\n', ' xml:base="...(truncated) | 190,854 | {} | 2023-06-18 00:32:56 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2023-06-18 00:32:57 | 2023-06-18 00:32:57 | 0.09 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2023-06-18 00:32:57 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2023-06-18 00:32:57 | 2023-06-18 00:33:00 | 2.84 |
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__20230614-182602/pypath_git/pypath/inputs/reaction.py", line 1187, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/pyreact.py", line 1300, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/pyreact.py", line 1193, in load_wikipathways
self.add_dataset(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/pyreact.py", line 1314, in add_dataset
self.merge()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/pyreact.py", line 1350, in merge
self.merge_modifications()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/pyreact.py", line 1582, in merge_modifications
self.load_sequences()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/pyreact.py", line 2333, in load_sequences
self.seq = seq.swissprot_seq(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/seq.py", line 55, in swissprot_seq
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-06-12 20:55:22 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2023-06-18 00:33:00 | 2023-06-18 00:33:06 | 6.01 | dict | {'BioPAX/Fructose_galactose_metabolism.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/B_cell_activation.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__202...(truncated) | 178 | {} | 2023-06-18 00:33:00 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2023-06-18 00:33:06 | 2023-06-18 00:33:08 | 1.76 | NoneType | None | 0 | {} | 2023-06-18 00:33:06 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2023-06-18 00:33:08 | 2023-06-18 00:33:34 | 26.28 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {} | 2023-06-18 00:33:08 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2023-06-18 00:33:34 | 2023-06-18 00:40:42 | 427.96 | list | [('R-HSA-1059683', <?xml version='1.0' encoding='utf-8' standalone='no'?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 85 on 5/30/23, 5:13 PM using JSBML version 1....(truncated) | 2,629 | {} | 2023-06-18 00:33:34 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2023-06-18 00:41:06 | 2023-06-18 00:41:08 | 2.29 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/cache/9c...(truncated) | 2,629 | {} | 2023-06-18 00:41:06 | |
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2023-06-18 00:41:08 | 2023-06-18 00:41:09 | 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__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 114, in scconnect_annotations
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 115, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:35:00 | |||
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2023-06-18 00:41:09 | 2023-06-18 00:41:09 | 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__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 153, in scconnect_complexes
annot = scconnect_annotations(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 114, in scconnect_annotations
uniprots = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 115, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:35:14 | |||
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2023-06-18 00:41:09 | 2023-06-18 00:41:10 | 1.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 263, in scconnect_interactions
for ligand_target in itertools.product(ligands, targets):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 202, in process_partner
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/scconnect.py", line 203, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:35:14 | |||
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signalink.signalink_annotations | 2023-06-18 00:41:10 | 2023-06-18 00:41:31 | 20.92 | dict | {'pathway': {}, 'function': {}} | 2 | {} | 2023-06-18 00:41:10 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2023-06-18 00:41:31 | 2023-06-18 00:41:31 | 0.62 | dict | {} | 0 | {'size': -783} | 2023-06-18 00:41:31 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2023-06-18 00:41:31 | 2023-06-18 00:41:32 | 0.62 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {} | 2023-06-18 00:41:31 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2023-06-18 00:41:32 | 2023-06-18 00:41:32 | 0.64 | dict | {} | 0 | {'size': -835} | 2023-06-18 00:41:32 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2023-06-18 00:41:32 | 2023-06-18 00:41:33 | 0.61 | 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) | 4,867 | {} | 2023-06-18 00:41:32 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2023-06-18 00:41:33 | 2023-06-18 00:41:35 | 2.19 | list | [{'typ': 'dephosphorylation', 'resnum': 164, 'instance': 'STDTVEHSLDNKDGP', 'substrate': 'P42575', 'start': 157, 'end': 171, 'kinase': 'P62136', 'resaa': 'S', 'motif': 'STDTVEHSLDNKDGP', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'19531356'}}, {'typ': 'phosphorylation', 'resnu...(truncated) | 10,295 | {'size': 4} | 2023-06-18 00:41:33 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2023-06-18 00:41:35 | 2023-06-18 00:41:36 | 0.70 | list | [SignorInteraction(source=Complex NAE: COMPLEX:Q13564_Q8TBC4, target='Q9UJX6', source_isoform=None, target_isoform=None, source_type='complex', target_type='protein', effect='up-regulates activity', mechanism='neddylation', ncbi_tax_id='9606', pubmeds='25504797', direct=True, ptm_type='neddylation',...(truncated) | 90,172 | {'size': 58} | 2023-06-18 00:41:35 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2023-06-18 00:41:36 | 2023-06-18 00:58:35 | 1,019.06 | dict | {} | 0 | {'size': -672} | 2023-06-18 00:41:36 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2023-06-18 00:58:35 | 2023-06-18 00:58:35 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 90 | {} | 2023-06-18 00:58:35 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2023-06-18 00:58:35 | 2023-06-18 01:00:55 | 140.01 |
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__20230614-182602/pypath_git/pypath/inputs/spike.py", line 192, in spike_complexes
interactions = spike_interactions(min_confidence = min_confidence)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/spike.py", line 55, in spike_interactions
xml = ET.parse(spikexml['LatestSpikeDB.xml'])
TypeError: 'NoneType' object is not subscriptable
|
{'broke': True} | 2023-06-13 20:48:07 | |||
| ¶ | pypath.inputs.spike.spike_interactions | 2023-06-18 01:00:55 | 2023-06-18 01:01:25 | 30.00 |
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__20230614-182602/pypath_git/pypath/inputs/spike.py", line 55, in spike_interactions
xml = ET.parse(spikexml['LatestSpikeDB.xml'])
TypeError: 'NoneType' object is not subscriptable
|
{'broke': True} | 2023-06-13 20:54:02 | |||
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2023-06-18 01:01:25 | 2023-06-18 01:02:42 | 76.81 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {} | 2023-06-18 01:01:25 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2023-06-18 01:02:42 | 2023-06-18 01:04:13 | 91.12 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {} | 2023-06-18 01:02:42 | |
| ¶ | pypath.inputs.string.string_effects | 2023-06-18 01:04:13 | 2023-06-18 01:04:21 | 8.08 | list | [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) | 2,250,122 | {} | 2023-06-18 01:04:13 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2023-06-18 01:04:23 | 2023-06-18 01:04:52 | 29.56 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000440005', neighborhood_score=0, fusion=0, cooccurence=50, coexpression=99, experimental=679, database=900, textmining=59, combined_score=969, physical_combined_score=740), StringLinksInteraction(protein_a='ENSP00000000233', prot...(truncated) | 247,200 | {} | 2023-06-18 01:04:23 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2023-06-18 01:04:52 | 2023-06-18 01:04:54 | 1.65 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000221957', experimental=483, database=600, textmining=821, combined_score=959), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=932, database=0, textmining=0, combined_score=932...(truncated) | 83,896 | {} | 2023-06-18 01:04:52 | |
| ¶ | pypath.inputs.string.string_species | 2023-06-18 01:04:54 | 2023-06-18 01:04:54 | 0.12 | 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) | 14,094 | {} | 2023-06-18 01:04:54 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2023-06-18 01:04:54 | 2023-06-18 01:07:31 | 157.12 | dict | {} | 0 | {'size': -2808} | 2023-06-18 01:04:54 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2023-06-18 01:07:31 | 2023-06-18 01:07:36 | 5.02 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2023-06-18 01:07:31 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2023-06-18 01:07:36 | 2023-06-18 01:07:37 | 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__20230614-182602/pypath_git/pypath/inputs/talklr.py", line 110, in talklr_annotations
uniprots = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3570, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:57:47 | |||
| ¶ | pypath.inputs.talklr.talklr_interactions | 2023-06-18 01:07:37 | 2023-06-18 01:07:37 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {} | 2023-06-18 01:07:37 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2023-06-18 01:07:37 | 2023-06-18 01:07:37 | 0.03 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2023-06-18 01:07:37 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2023-06-18 01:07:37 | 2023-06-18 09:12:21 | 29,084.18 | dict | {} | 0 | {'size': -2222} | 2023-06-18 01:07:37 | |
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2023-06-18 09:12:21 | 2023-06-18 09:12:21 | 0.11 | 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) | 23,110 | {'size': 25} | 2023-06-18 09:12:21 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2023-06-18 09:12:21 | 2023-06-18 09:12:21 | 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) | 1,823 | {'size': 3} | 2023-06-18 09:12:21 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2023-06-18 09:12:21 | 2023-06-18 09:12:21 | 0.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/tfcensus.py", line 72, in tfcensus_annotations
uniprots = mapping.map_names(ensg, 'ensembl', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3660, in map_names
return mapper.map_names(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2310, in map_names
return set.union(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2312, in <genexpr>
self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:57:54 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2023-06-18 09:12:21 | 2023-06-18 09:12:26 | 4.34 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2023-06-18 09:12:21 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2023-06-18 09:12:26 | 2023-06-18 09:12:50 | 23.93 | set | {ThreedcomplexContact(pdb='3lmx_1', uniprot_1='P00436', uniprot_2='P00437', chain_1='A', chain_2='M', n_residues=68.5, length_1=200, length_2=238, domain_s1=('49482',), domain_p1=('PF00775.16',), domain_s2=('49482',), domain_p2=('PF12391.3', 'PF00775.16'), ident=False, homo=True), ThreedcomplexConta...(truncated) | 259,809 | {} | 2023-06-18 09:12:26 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2023-06-18 09:12:51 | 2023-06-18 09:15:05 | 133.83 |
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__20230614-182602/pypath_git/pypath/inputs/threedcomplex.py", line 110, in threedcomplex_ddi
dom1 = intera.Domain(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/internals/intera.py", line 656, in __init__
entity.Entity(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 132, in __init__
self.set_label()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/core/entity.py", line 468, in set_label
self.label = mapping.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3681, in label
return mapper.label(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2641, in label
return self.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 20:58:23 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2023-06-18 09:15:05 | 2023-06-18 09:15:15 | 10.93 | dict | {'3lmx_1': {('P00436', 'P00437'): 1.0, ('P00437', 'P00437'): 6.5, ('P00436', 'P00436'): 2.5}, '1gyq_1': {('Q27890', 'Q27890'): 9.5}, '4mfg_1': {('Q183I2', 'Q183I2'): 14.5}, '3hwx_5': {('P17109', 'P17109'): 72.0}, '3hhq_7': {('P33317', 'P33317'): 29.5}, '4o8u_2': {('Q8TZE9', 'Q8TZE9'): 16.5}, '3aso_2...(truncated) | 81,193 | {} | 2023-06-18 09:15:05 | |
| ¶ | pypath.inputs.threedid.get_3did | 2023-06-18 09:15:16 | 2023-06-18 09:16:06 | 50.11 | tuple | ([], [None]) | 2 | {} | 2023-06-18 09:15:16 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2023-06-18 09:16:06 | 2023-06-18 09:16:08 | 2.76 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/threedid.py", line 59, in get_3did_ddi
u_pfam, pfam_u = pfam_input.pfam_uniprot(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/pfam.py", line 100, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-06-12 21:49:16 | |||
| ¶ | pypath.inputs.topdb.topdb_annotations | 2023-06-18 09:16:08 | 2023-06-18 13:46:26 | 16,217.36 | dict | {} | 0 | {'size': -1247} | 2023-06-18 09:16:08 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2023-06-18 13:46:26 | 2023-06-18 13:46:29 | 2.74 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2023-06-18 13:46:26 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.01 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;11290752;12601176', 'Fusion protein-pull down assay;Fluorescence probe labeling;Calciu...(truncated) | 359 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.trip.trip_process | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'HEK293', 'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.02 | list | [UnichemSource(number='1', label='chembl', name='ChEMBL', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) | 41 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.02 | dict | {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma', '22': 'pubc...(truncated) | 41 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.00 | set | {'</html>', '<html>', 'Error encountered when streaming data. Please try again later.', '</body>', '<body>', '<center><h1>502 Bad Gateway</h1></center>', 'Entry', '<hr><center>nginx</center>', '<head><title>502 Bad Gateway</title></head>'} | 9 | {'size': -207771} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.uniprot._cleanup | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.00 | NoneType | None | 0 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.uniprot._protein_datasheet |
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot._remove |
Not calling `pypath.inputs.uniprot._remove`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot._swissprot_param |
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.all_swissprots | 2023-06-18 13:46:29 | 2023-06-18 13:46:29 | 0.00 | set | {'</html>', '<html>', 'Error encountered when streaming data. Please try again later.', '</body>', '<body>', '<center><h1>502 Bad Gateway</h1></center>', 'Entry', '<hr><center>nginx</center>', '<head><title>502 Bad Gateway</title></head>'} | 9 | {'size': -20413} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.uniprot.all_trembls | 2023-06-18 13:46:29 | 2023-06-18 13:47:55 | 86.01 | set | {'A0A7S5EYJ0', 'F8WCF0', 'A0A1L2BM75', 'A0A8V8TMX0', 'A0A087WXC5', 'A0A0S2Z492', 'A0A5C2GF35', 'J3QS50', 'K7ENI0', 'F4YZV3', 'Q0VGM7', 'A0A223G181', 'I3NHZ9', 'A0A0N9QNI4', 'D3DQU2', 'E5RI53', 'O19797', 'A0A344AJN3', 'A0A3S6RGU0', 'H7C4Q1', 'F5H4S8', 'A0A5C2GLG2', 'L8E6W5', 'A0T4C3', 'H3BPW6', 'A0A7...(truncated) | 187,358 | {} | 2023-06-18 13:46:29 | |
| ¶ | pypath.inputs.uniprot.all_uniprots | 2023-06-18 13:47:55 | 2023-06-18 13:47:55 | 0.00 | set | {'</html>', '<html>', 'Error encountered when streaming data. Please try again later.', '</body>', '<body>', '<center><h1>502 Bad Gateway</h1></center>', 'Entry', '<hr><center>nginx</center>', '<head><title>502 Bad Gateway</title></head>'} | 9 | {'size': -207771} | 2023-06-18 13:47:55 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_db | 2023-06-18 13:47:55 | 2023-06-18 13:47:55 | 0.00 | set | {'</html>', '<html>', 'Error encountered when streaming data. Please try again later.', '</body>', '<body>', '<center><h1>502 Bad Gateway</h1></center>', 'Entry', '<hr><center>nginx</center>', '<head><title>502 Bad Gateway</title></head>'} | 9 | {'size': -207771} | 2023-06-18 13:47:55 | |
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2023-06-18 13:47:55 | 2023-06-18 13:47:55 | 0.68 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{'broke': True} | 2023-06-13 21:36:15 | |||
| ¶ | pypath.inputs.uniprot.init_db | 2023-06-18 13:47:55 | 2023-06-18 13:47:55 | 0.00 | NoneType | None | 0 | {} | 2023-06-18 13:47:55 | |
| ¶ | pypath.inputs.uniprot.is_swissprot |
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.is_trembl |
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.is_uniprot |
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2023-06-18 13:47:55 | 2023-06-18 13:48:22 | 26.99 | 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) | 14,420 | {} | 2023-06-18 13:47:55 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2023-06-18 13:48:22 | 2023-06-18 13:48:40 | 17.80 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Glycoprotein'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Transmembrane'), UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(k...(truncated) | 20,422 | {} | 2023-06-18 13:48:22 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2023-06-18 13:48:40 | 2023-06-18 13:48:59 | 18.29 | dict | {'A0A087X1C5': {UniprotLocation(location='Membrane', features=('Multi-pass membrane protein',)), UniprotLocation(location='Mitochondrion', features=None), UniprotLocation(location='Cytoplasm', features=None)}, 'A0A0B4J2F0': {UniprotLocation(location='Mitochondrion outer membrane', features=('Single-...(truncated) | 17,037 | {} | 2023-06-18 13:48:40 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2023-06-18 13:48:59 | 2023-06-18 13:48:59 | 0.09 | 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) | 27,305 | {} | 2023-06-18 13:48:59 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2023-06-18 13:48:59 | 2023-06-18 13:49:02 | 2.87 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'H8ZM71': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'Q9MV51': {'Momi fir', 'Abies firma'}, 'O81086': {'Grand fir', 'Abies grandis', 'Pinu...(truncated) | 555,077 | {} | 2023-06-18 13:48:59 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2023-06-18 13:49:02 | 2023-06-18 13:49:22 | 20.00 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Plasma', level='undefined'), UniprotTissue(tissue='Skeletal muscle', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Granulocytes', level='undefined'), UniprotTissue(tissue='Myelo...(truncated) | 10,047 | {} | 2023-06-18 13:49:02 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2023-06-18 13:49:22 | 2023-06-18 13:50:55 | 93.09 | dict | {'A0A087X1C5': {UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Cytoplasmic',...(truncated) | 5,237 | {} | 2023-06-18 13:49:22 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang._wang_process |
Not calling `pypath.inputs.wang._wang_process`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang.cui_interactions | 2023-06-18 13:50:55 | 2023-06-18 13:50:59 | 3.93 | list | [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) | 5,089 | {} | 2023-06-18 13:50:55 | |
| ¶ | pypath.inputs.wang.hsn_interactions | 2023-06-18 13:50:59 | 2023-06-18 13:51:01 | 1.45 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2023-06-18 13:50:59 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2023-06-18 13:51:01 | 2023-06-18 13:52:21 | 80.34 | dict | {'NA': {WangAnnotation(function='Phosphatase', location='Cytosol'), WangAnnotation(function='Ion', location='Cytosol'), WangAnnotation(function='DNA', location='Nucleus'), WangAnnotation(function='Lipid', location='Cytosol'), WangAnnotation(function='Adapter', location='Ribosomes'), WangAnnotation(f...(truncated) | 472 | {'size': -1072} | 2023-06-18 13:51:01 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2023-06-18 13:52:21 | 2023-06-18 13:52:21 | 0.34 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2023-06-18 13:52:21 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2023-06-18 13:52:21 | 2023-06-18 13:52:21 | 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__20230614-182602/pypath_git/pypath/inputs/wojtowicz2020.py", line 84, in wojtowicz2020_interactions
for rec in wojtowicz2020_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/wojtowicz2020.py", line 42, in wojtowicz2020_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 21:52:42 | |||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2023-06-18 13:52:21 | 2023-06-18 13:52:22 | 0.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/wojtowicz2020.py", line 42, in wojtowicz2020_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-06-12 21:52:42 | |||
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2023-06-18 13:52:22 | 2023-06-18 13:52:22 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/inputs/zhong2015.py", line 62, in zhong2015_annotations
uniprot = mapping.map_name0(rec[0], 'genesymbol', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 3601, in map_name0
return mapper.map_name0(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1809, in map_name0
names = self.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/share/common.py", line 2708, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1988, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 2520, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 1684, in which_table
reader = MapReader(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 263, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 293, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 455, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 654, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230614-182602/pypath_git/pypath/utils/mapping.py", line 851, in _read_mapping_uniprot_list
result.extend(list(res_c.fileobj)[1:])
ValueError: I/O operation on closed file.
|
{'broke': True} | 2023-06-13 21:39:52 |
The OmniPath Team • Saez Lab • 2023-06-18