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 2025-07-15 09:24:42 and 2025-07-15 14:19:46; pypath version: 0.16.20 (from git, installed by poetry; f85c82f )
| Modules collected: | 190 |
|---|---|
| Modules failed to import: | 5 |
| Functions collected: | 612 |
| Functions run without error: | 364 |
| Functions returned empty value: | 24 |
| Functions skipped due to lack of arguments: | 180 |
| Functions run with error: | 68 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2025-07-15 09:24:45 | 2025-07-15 09:24:46 | 0.41 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {'first': True} | 2025-07-15 09:24:45 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2025-07-15 09:24:46 | 2025-07-15 09:24:46 | 0.53 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {'first': True} | 2025-07-15 09:24:46 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2025-07-15 09:24:46 | 2025-07-15 09:25:55 | 68.47 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {'first': True} | 2025-07-15 09:24:46 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2025-07-15 09:25:55 | 2025-07-15 09:25:56 | 1.20 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {'first': True} | 2025-07-15 09:25:55 | |
| ¶ | pypath.inputs.adrecs._adrecs_base |
Not calling `pypath.inputs.adrecs._adrecs_base`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.adrecs._adrecs_drug_adr | 2025-07-15 09:25:56 | 2025-07-15 09:31:56 | 360.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/adrecs.py", line 176, in _adrecs_drug_adr
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 09:25:56 | |||
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2025-07-15 09:31:56 | 2025-07-15 09:32:30 | 33.89 | list | [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) | 13,855 | {'first': True} | 2025-07-15 09:31:56 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2025-07-15 09:32:30 | 2025-07-15 09:38:30 | 360.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/adrecs.py", line 176, in _adrecs_drug_adr
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 09:32:30 | |||
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2025-07-15 09:38:30 | 2025-07-15 09:41:32 | 182.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/common.py", line 114, in read_xls
book = openpyxl.load_workbook(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/openpyxl/reader/excel.py", line 346, in load_workbook
reader = ExcelReader(filename, read_only, keep_vba,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/openpyxl/reader/excel.py", line 123, in __init__
self.archive = _validate_archive(fn)
^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/openpyxl/reader/excel.py", line 77, in _validate_archive
file_format = os.path.splitext(filename)[-1].lower()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen posixpath>", line 118, in splitext
TypeError: expected str, bytes or os.PathLike object, not NoneType
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/adrecs.py", line 92, in adrecs_drug_identifiers
return _adrecs_base(
^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/adrecs.py", line 137, in _adrecs_base
contents = inputs_common.read_xls(path.outfile, cell_range = cell_range)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/common.py", line 124, in read_xls
raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: None
|
{'first': True} | 2025-07-15 09:38:30 | |||
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2025-07-15 09:41:32 | 2025-07-15 09:41:33 | 1.05 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='06.04.03.002', badd='BADD_A02408'), parent=AdrecsAdr(adr_class='06.04.03', badd='BADD_A02407')), AdrecsChildParent(child=AdrecsAdr(adr_class='18.04.01.002', badd='BADD_A01163'), parent=AdrecsAdr(adr_class='18.04.01', badd='BADD_A00994')), AdrecsChildPare...(truncated) | 13,828 | {'first': True} | 2025-07-15 09:41:32 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2025-07-15 09:41:33 | 2025-07-15 09:41:38 | 4.54 | dict | {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) | 4,243 | {'first': True} | 2025-07-15 09:41:33 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2025-07-15 09:41:38 | 2025-07-15 09:45:18 | 220.49 | dict | {'Q15848': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q96A54': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'Q86V24': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None)}, 'P35318': {Baccin2019Annotation(ma...(truncated) | 933 | {'first': True} | 2025-07-15 09:41:38 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2025-07-15 09:45:18 | 2025-07-15 09:45:19 | 0.43 | list | [Baccin2019Interaction(ligand='Q15848', receptor='Q96A54', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Baccin2019', 'Ramilowski2015'}, references={'12802337'}), Baccin2019Interaction(ligand='Q15848', receptor='Q86V24', correct='Correct', ligand_location='secre...(truncated) | 1,460 | {'first': True} | 2025-07-15 09:45:18 | |
| ¶ | pypath.inputs.biogps.biogps_datasets | 2025-07-15 09:45:19 | 2025-07-15 09:45:19 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {'first': True} | 2025-07-15 09:45:19 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2025-07-15 09:45:19 | 2025-07-15 09:45:51 | 32.71 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {'first': True} | 2025-07-15 09:45:19 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2025-07-15 09:45:52 | 2025-07-15 09:46:30 | 38.33 | 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) | 8,721 | {'first': True} | 2025-07-15 09:45:52 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2025-07-15 09:46:30 | 2025-07-15 09:46:32 | 1.59 | 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) | 7,446 | {'first': True} | 2025-07-15 09:46:30 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2025-07-15 09:46:32 | 2025-07-15 09:46:49 | 17.13 | 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) | 178,379 | {'first': True} | 2025-07-15 09:46:32 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2025-07-15 09:46:49 | 2025-07-15 09:46:50 | 0.33 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/biomart.py", line 241, in biomart_microarray_types
result = json.loads(c.result)
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/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
|
{'first': True} | 2025-07-15 09:46:49 | |||
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biomodels._get_biomodels | 2025-07-15 09:46:50 | 2025-07-15 09:46:50 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/biomodels.py", line 101, in _get_biomodels
loginurl = urls.urls['biomodels']['login'] % t
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'login'
|
{'first': True} | 2025-07-15 09:46:50 | |||
| ¶ | pypath.inputs.biomodels.download_single_model |
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.biomodels.get_biomodels | 2025-07-15 09:46:50 | 2025-07-15 09:46:50 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/biomodels.py", line 160, in get_biomodels
c0.perform()
pycurl.error: (3, 'URL rejected: Malformed input to a URL function')
|
{'first': True} | 2025-07-15 09:46:50 | |||
| ¶ | pypath.inputs.biomodels.get_biomodels_req | 2025-07-15 09:46:50 | 2025-07-15 09:46:50 | 0.45 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/biomodels.py", line 193, in get_biomodels_req
token = json.loads(r0.text)['token']
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'first': True} | 2025-07-15 09:46:50 | |||
| ¶ | pypath.inputs.biomodels.get_single_model |
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2025-07-15 09:46:50 | 2025-07-15 09:46:51 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/ca1.py", line 72, in ca1_interactions
for l in data['S1.txt'].decode('ascii').split('\n')[1:]:
^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'decode'
|
{'first': True} | 2025-07-15 09:46:50 | |||
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2025-07-15 09:46:51 | 2025-07-15 09:46:51 | 0.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancercellmap.py", line 51, in ccmap_interactions
c = curl.Curl(
^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 956, in __init__
self.process_file()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 1782, in process_file
self.extract_file()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 1813, in extract_file
self.extract()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 612, in extract
getattr(self, 'open_%s' % self.type)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 694, in open_zip
self.zipfile = zipfile.ZipFile(self.fileobj, 'r')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/zipfile.py", line 1313, in __init__
self._RealGetContents()
File "/usr/lib/python3.11/zipfile.py", line 1380, in _RealGetContents
raise BadZipFile("File is not a zip file")
zipfile.BadZipFile: File is not a zip file
|
{'first': True} | 2025-07-15 09:46:51 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2025-07-15 09:46:51 | 2025-07-15 09:46:51 | 0.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancerdrugsdb.py", line 203, in cancerdrugsdb_annotations
data = cancerdrugsdb_interactions()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancerdrugsdb.py", line 114, in cancerdrugsdb_interactions
data = cancerdrugsdb_download()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancerdrugsdb.py", line 57, in cancerdrugsdb_download
return list(csv.DictReader(c.result, delimiter = '\t'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 09:46:51 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2025-07-15 09:46:51 | 2025-07-15 09:46:51 | 0.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancerdrugsdb.py", line 57, in cancerdrugsdb_download
return list(csv.DictReader(c.result, delimiter = '\t'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 09:46:51 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2025-07-15 09:46:51 | 2025-07-15 09:46:51 | 0.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancerdrugsdb.py", line 114, in cancerdrugsdb_interactions
data = cancerdrugsdb_download()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cancerdrugsdb.py", line 57, in cancerdrugsdb_download
return list(csv.DictReader(c.result, delimiter = '\t'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/csv.py", line 86, in __init__
self.reader = reader(f, dialect, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 09:46:51 | |||
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2025-07-15 09:46:51 | 2025-07-15 09:46:54 | 2.93 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,248 | {'first': True} | 2025-07-15 09:46:51 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2025-07-15 09:46:54 | 2025-07-15 09:47:08 | 13.63 | dict | {'O14511': {CellcallAnnotation(role='ligand')}, 'Q15303': {CellcallAnnotation(role='receptor')}, 'O00587': {CellcallAnnotation(role='ligand')}, 'P46531': {CellcallAnnotation(role='receptor')}, 'P13236': {CellcallAnnotation(role='ligand')}, 'P51685': {CellcallAnnotation(role='receptor')}, 'P80098': {...(truncated) | 460 | {'first': True} | 2025-07-15 09:46:54 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2025-07-15 09:47:08 | 2025-07-15 09:47:08 | 0.04 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {'first': True} | 2025-07-15 09:47:08 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2025-07-15 09:47:08 | 2025-07-15 09:47:09 | 0.81 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {'first': True} | 2025-07-15 09:47:08 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2025-07-15 09:47:09 | 2025-07-15 09:47:09 | 0.11 | list | [CellcallInteraction(ligand_uniprot='O14511', receptor_uniprot='Q15303', core=True), CellcallInteraction(ligand_uniprot='O00587', receptor_uniprot='P46531', core=True), CellcallInteraction(ligand_uniprot='P13236', receptor_uniprot='P51685', core=True), CellcallInteraction(ligand_uniprot='P80098', re...(truncated) | 797 | {'first': True} | 2025-07-15 09:47:09 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2025-07-15 09:47:09 | 2025-07-15 09:47:10 | 0.67 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand'), Cellcellinteractions...(truncated) | 3,425 | {'first': True} | 2025-07-15 09:47:09 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2025-07-15 09:47:10 | 2025-07-15 09:47:10 | 0.00 | int | 9606 | 0 | {'first': True} | 2025-07-15 09:47:10 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_cofactors |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_complexes |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2025-07-15 09:47:10 | 2025-07-15 09:47:18 | 8.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cellchatdb.py", line 362, in cellchatdb_annotations
interactions = cellchatdb_interactions(organism = organism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cellchatdb.py", line 285, in cellchatdb_interactions
refs = sorted(pmid for pmid in refs if not pmid.startswith('23209'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cellchatdb.py", line 285, in <genexpr>
refs = sorted(pmid for pmid in refs if not pmid.startswith('23209'))
^^^^^^^^^^^^^^^
AttributeError: 'int' object has no attribute 'startswith'
|
{'first': True} | 2025-07-15 09:47:10 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2025-07-15 09:47:18 | 2025-07-15 09:47:25 | 6.89 | dict | {np.str_('ACTIVIN antagonist'): {'P19883'}, np.str_('ACTIVIN inhibition receptor'): {'Q13145'}, np.str_('ANGPT inhibition receptor 1'): {'P35590'}, np.str_('ANGPT inhibition receptor 2'): {'P23467'}, np.str_('BMP antagonist'): {'O00292', 'P12645', 'O60565', 'O75610', 'P41271', 'Q9H772', 'Q9H2X0', 'Q...(truncated) | 32 | {'first': True} | 2025-07-15 09:47:18 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2025-07-15 09:47:25 | 2025-07-15 09:47:32 | 7.48 | dict | {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) | 330 | {'first': True} | 2025-07-15 09:47:25 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2025-07-15 09:47:32 | 2025-07-15 09:47:38 | 6.26 | dict | {'interaction': interaction_name ... version TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... CellChatDB v1 TGFB1_ACVR1B_TGFBR2 TGFB1_ACVR1B_TGFBR2...(truncated) | 4 | {'first': True} | 2025-07-15 09:47:32 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2025-07-15 09:47:38 | 2025-07-15 09:47:46 | 7.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cellchatdb.py", line 285, in cellchatdb_interactions
refs = sorted(pmid for pmid in refs if not pmid.startswith('23209'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cellchatdb.py", line 285, in <genexpr>
refs = sorted(pmid for pmid in refs if not pmid.startswith('23209'))
^^^^^^^^^^^^^^^
AttributeError: 'int' object has no attribute 'startswith'
|
{'first': True} | 2025-07-15 09:47:38 | |||
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2025-07-15 09:47:46 | 2025-07-15 09:47:46 | 0.29 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {'first': True} | 2025-07-15 09:47:46 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2025-07-15 09:47:46 | 2025-07-15 09:47:46 | 0.17 | dict | {'P05112': {CellinkerAnnotation(role='ligand', location='Secreted', type='Cytokine-cytokine receptor interaction')}, 'P80370': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell...(truncated) | 1,919 | {'first': True} | 2025-07-15 09:47:46 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2025-07-15 09:47:46 | 2025-07-15 09:47:47 | 0.05 | dict | {Complex: COMPLEX:P05107_P11215: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, Complex: COMPLEX:O75581_Q9ULV1: {CellinkerAnnotation(role='receptor', locati...(truncated) | 134 | {'first': True} | 2025-07-15 09:47:46 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.00 | dict | {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) | 143 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.04 | set | {CellinkerInteraction(ligand='P05112', receptor='P80370', ligand_location='Secreted', receptor_location='Membrane', resources=None, pmids='10733486', type='Cytokine-cytokine receptor interaction'), CellinkerInteraction(ligand='P05362', receptor=Complex: COMPLEX:P05107_P11215, ligand_location='Membra...(truncated) | 3,810 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.05 | dict | {'P05112': {CellinkerAnnotation(role='ligand', location='Secreted', type='Cytokine-cytokine receptor interaction')}, 'P80370': {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='Cell...(truncated) | 1,785 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.13 | set | {CellinkerInteraction(ligand='5756', receptor='P03372', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='9048584', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='448457', receptor='P43116', ligand_location=None, receptor_location='Membrane', resou...(truncated) | 314 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.00 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_annotations |
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_get_entity |
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_hla |
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.19 | dict | {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) | 358 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2025-07-15 09:47:47 | 2025-07-15 09:47:47 | 0.02 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 358 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2025-07-15 09:47:47 | 2025-07-15 09:47:48 | 0.55 | list | [CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_a2b1_complex: COMPLEX:P05556_P17301, sources='CellPhoneDB', references='', interaction_type='ligand-ligand', type_a='ligand', type_b='ligand', is_ppi=True), CellphonedbInteraction(id_a='P12830', id_b=Complex integrin_aEb7_complex: COMPLEX:...(truncated) | 2,903 | {'first': True} | 2025-07-15 09:47:47 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2025-07-15 09:47:48 | 2025-07-15 09:47:48 | 0.02 | tuple | ({'O95393', 'A6NMZ7', 'O95399', 'Q92765', 'Q9UIW2', Complex Glycine_bySHMT1_and_SLC6A9: COMPLEX:P34896_P48067, 'P01215', 'Q8NFW1', 'O14511', 'P25942', Complex BetaKlotho_FGFR4: COMPLEX:P22455_Q86Z14, 'Q99731', 'O15520', 'Q6IA17', 'Q8N0W4', Complex integrin_a8b1_complex: COMPLEX:P05556_P53708, 'P0501...(truncated) | 2 | {'first': True} | 2025-07-15 09:47:48 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2025-07-15 09:47:48 | 2025-07-15 09:47:48 | 0.01 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,359 | {'first': True} | 2025-07-15 09:47:48 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2025-07-15 09:47:48 | 2025-07-15 09:47:48 | 0.47 | dict | {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='9883722')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) | 1,598 | {'first': True} | 2025-07-15 09:47:48 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2025-07-15 09:47:48 | 2025-07-15 09:47:48 | 0.16 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {'first': True} | 2025-07-15 09:47:48 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2025-07-15 09:47:48 | 2025-07-15 09:47:48 | 0.16 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {'first': True} | 2025-07-15 09:47:48 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2025-07-15 09:47:48 | 2025-07-15 09:47:49 | 0.26 | dict | {'P15391': {CelltypistAnnotation(cell_type='B cells', cell_subtype='B cells', cell_ontology='CL:0000236', marker_type='curated_marker', tissues=('Blood', 'Eye', 'Intestine', 'Kidney', 'Liver', 'Lung', 'Trachea'), datasets=('Braga et al. 2019', 'Martin et al. 2019', 'Miller et al. 2020', 'Popescu et ...(truncated) | 460 | {'first': True} | 2025-07-15 09:47:48 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2025-07-15 09:47:49 | 2025-07-15 09:48:28 | 39.24 | list | [Citation(allele='1261079', variation_id='1271228', nsv='', citation_source='PubMed', citation_id='25741868'), Citation(allele='2088618', variation_id='2028143', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='3136462', variation_id='2972682', nsv='', citation_source='Pub...(truncated) | 4,157,802 | {'first': True} | 2025-07-15 09:47:49 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2025-07-15 09:48:33 | 2025-07-15 09:55:19 | 406.14 | list | [Variant(allele='1943358', type='single nucleotide variant', variant='NM_152383.5(DIS3L2):c.353A>G (p.Glu118Gly)', entrez='129563', genesymbol='DIS3L2', clinical_significance='Uncertain significance', review_status='criteria provided, single submitter', rs='2469623790', phenotype_ids=('MONDO:MONDO:0...(truncated) | 7,131,811 | {'first': True} | 2025-07-15 09:48:33 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2025-07-15 11:13:29 | 2025-07-15 11:13:44 | 14.58 | list | [CollectriInteraction(tf='P01106', target='O14746', 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;...(truncated) | 64,990 | {'first': True} | 2025-07-15 11:13:29 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2025-07-15 11:13:44 | 2025-07-15 11:13:44 | 0.11 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {'first': True} | 2025-07-15 11:13:44 | |
| ¶ | pypath.inputs.compath._compath_mappings | 2025-07-15 11:13:44 | 2025-07-15 11:13:44 | 0.16 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {'first': True} | 2025-07-15 11:13:44 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2025-07-15 11:13:44 | 2025-07-15 11:13:44 | 0.01 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {'first': True} | 2025-07-15 11:13:44 | |
| ¶ | pypath.inputs.compleat.compleat_complexes | 2025-07-15 11:13:44 | 2025-07-15 11:13:46 | 1.54 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,695 | {'first': True} | 2025-07-15 11:13:44 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2025-07-15 11:13:46 | 2025-07-15 11:13:46 | 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 | {'first': True} | 2025-07-15 11:13:46 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2025-07-15 11:13:46 | 2025-07-15 11:15:33 | 107.27 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9': Complex Dynein-1 complex, variant 4: COMPLEX:O14576_P63167_P63172_Q14204_Q9NP97_Q9Y6G9, 'COMPLEX:Q86XT2_Q99816_Q9NZ...(truncated) | 2,210 | {'first': True} | 2025-07-15 11:13:46 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2025-07-15 11:15:33 | 2025-07-15 11:15:46 | 13.38 | list | [ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A024R0Y4', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='A0A0R4J2E4', id_b='A0A087WWR4', loc_a=(ComppiLocation(locati...(truncated) | 587,995 | {'first': True} | 2025-07-15 11:15:33 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2025-07-15 11:15:46 | 2025-07-15 11:16:00 | 13.45 | dict | {'A0A0R4J2E4': {ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='cytosol', score=0.8)}, 'A0A024R0Y4': {ComppiLocation(location='nucleus', score=0.8)}, 'A0A087WWR4': {ComppiLocation(location='nucleus', score=0.8)}, 'Q08379': {ComppiLocation(location='membrane', score=0.8), Comp...(truncated) | 22,799 | {'first': True} | 2025-07-15 11:15:46 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2025-07-15 11:16:00 | 2025-07-15 11:16:00 | 0.30 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {'first': True} | 2025-07-15 11:16:00 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2025-07-15 11:16:00 | 2025-07-15 11:16:00 | 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 | {'first': True} | 2025-07-15 11:16:00 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2025-07-15 11:16:00 | 2025-07-15 11:16:01 | 0.59 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {'first': True} | 2025-07-15 11:16:00 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2025-07-15 11:16:01 | 2025-07-15 11:16:01 | 0.00 | dict | {} | 0 | {'first': True} | 2025-07-15 11:16:01 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2025-07-15 11:16:01 | 2025-07-15 11:16:09 | 8.15 | dict | {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'Q9UP65': {Cpa...(truncated) | 855 | {'first': True} | 2025-07-15 11:16:01 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2025-07-15 11:16:09 | 2025-07-15 11:16:09 | 0.05 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='c-Met signaling pathway', cancer='Glioma', pathway_category='Others', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit tumor growth'), CpadPathwayCancer(pathway='MDM2-p53 pathway', cancer='Glioma', pathway_category='p53 signaling pathway', effe...(truncated) | 2 | {'first': True} | 2025-07-15 11:16:09 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2025-07-15 11:16:09 | 2025-07-15 11:16:09 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {'first': True} | 2025-07-15 11:16:09 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2025-07-15 11:16:09 | 2025-07-15 11:16:19 | 9.43 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 531,371 | {'first': True} | 2025-07-15 11:16:09 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2025-07-15 11:16:19 | 2025-07-15 11:16:21 | 2.12 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {'first': True} | 2025-07-15 11:16:19 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2025-07-15 11:16:21 | 2025-07-15 11:16:22 | 0.76 | dict | {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) | 1,449 | {'first': True} | 2025-07-15 11:16:21 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2025-07-15 11:16:22 | 2025-07-15 11:16:23 | 0.69 | dict | {'A1A5B4': {CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='MedB1', value...(truncated) | 1,410 | {'first': True} | 2025-07-15 11:16:22 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2025-07-15 11:16:23 | 2025-07-15 11:16:23 | 0.55 | dict | {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.11804, 'A8MVW0': None, 'A8MVW5': None, 'A8MWY0': None, 'A8TX70': None, 'O00116': None, 'O00206': 15.9843,...(truncated) | 47 | {'first': True} | 2025-07-15 11:16:23 | |
| ¶ | pypath.inputs.ctdbase._ctdbase_download |
Not calling `pypath.inputs.ctdbase._ctdbase_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase._map_keys |
Not calling `pypath.inputs.ctdbase._map_keys`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase._modify_dict |
Not calling `pypath.inputs.ctdbase._modify_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2025-07-15 11:16:23 | 2025-07-15 11:16:25 | 1.79 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P01374', score=0.5679445170294432, cytokine_genesymbol='LTA', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P01133', score=0.0056964250938285, cytokine_genesymbol='EGF', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='O95390', score=0.10751...(truncated) | 4,887 | {'first': True} | 2025-07-15 11:16:23 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2025-07-15 11:16:25 | 2025-07-15 11:16:25 | 0.03 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {'first': True} | 2025-07-15 11:16:25 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2025-07-15 11:16:25 | 2025-07-15 11:16:28 | 2.20 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {'first': True} | 2025-07-15 11:16:25 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2025-07-15 11:16:28 | 2025-07-15 11:16:29 | 1.36 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/dbptm.py", line 97, in dbptm_enzyme_substrate_old
for k, data in iteritems(extra):
^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
|
{'first': True} | 2025-07-15 11:16:28 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2025-07-15 11:16:29 | 2025-07-15 11:16:31 | 1.28 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {'first': True} | 2025-07-15 11:16:29 | |
| ¶ | pypath.inputs.ddinter._ensure_hashable |
Not calling `pypath.inputs.ddinter._ensure_hashable`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_drug_interactions |
Not calling `pypath.inputs.ddinter.ddinter_drug_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_identifiers |
Not calling `pypath.inputs.ddinter.ddinter_identifiers`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ddinter.ddinter_interactions | 2025-07-15 11:16:31 | 2025-07-15 11:16:33 | 1.93 |
Traceback (most recent call last):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/requests/models.py", line 974, in json
return complexjson.loads(self.text, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/ddinter.py", line 211, in ddinter_interactions
for i in range(1, ddinter_n_drugs()+1)
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/ddinter.py", line 68, in ddinter_n_drugs
return int(response.json()['recordsTotal'])
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/requests/models.py", line 978, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
|
{'first': True} | 2025-07-15 11:16:31 | |||
| ¶ | pypath.inputs.ddinter.ddinter_mappings | 2025-07-15 11:16:33 | 2025-07-15 11:16:35 | 2.16 |
Traceback (most recent call last):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/requests/models.py", line 974, in json
return complexjson.loads(self.text, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/ddinter.py", line 125, in ddinter_mappings
for idx in range(1, ddinter_n_drugs() + 1):
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/ddinter.py", line 68, in ddinter_n_drugs
return int(response.json()['recordsTotal'])
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/requests/models.py", line 978, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
|
{'first': True} | 2025-07-15 11:16:33 | |||
| ¶ | pypath.inputs.ddinter.ddinter_n_drugs | 2025-07-15 11:16:35 | 2025-07-15 11:16:36 | 1.10 |
Traceback (most recent call last):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/requests/models.py", line 974, in json
return complexjson.loads(self.text, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/ddinter.py", line 68, in ddinter_n_drugs
return int(response.json()['recordsTotal'])
^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/requests/models.py", line 978, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
|
{'first': True} | 2025-07-15 11:16:35 | |||
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2025-07-15 11:16:36 | 2025-07-15 11:16:36 | 0.45 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/deathdomain.py", line 43, in deathdomain_interactions
soup = bs4.BeautifulSoup(html, 'lxml')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{'first': True} | 2025-07-15 11:16:36 | |||
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2025-07-15 11:16:36 | 2025-07-15 11:16:37 | 0.13 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {'first': True} | 2025-07-15 11:16:36 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2025-07-15 11:16:37 | 2025-07-15 11:16:37 | 0.16 | list | [{'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1054, 'references': ['11201744'], 'substrate': 'P29597', 'start': None, 'end': None, 'typ': 'dephosphorylation'}, {'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1055, 'references': ['11201744'], 'substrate': 'P29597', 's...(truncated) | 537 | {'first': True} | 2025-07-15 11:16:37 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2025-07-15 11:16:37 | 2025-07-15 11:16:37 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {'first': True} | 2025-07-15 11:16:37 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2025-07-15 11:16:37 | 2025-07-15 11:16:39 | 2.65 | dict | {'O75469': {DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='Pharos'), DgidbAnnotation(category='DRUGGABLE GENOME', source='HingoraniCasas'), DgidbAnnotation(category='TRANSCRIPTION FACTOR COMPLEX', source='GO'), DgidbAnnotation(category='NUCLEAR HORMONE RECEPTOR', source='dGene'), Dgidb...(truncated) | 9,973 | {'first': True} | 2025-07-15 11:16:37 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2025-07-15 11:16:39 | 2025-07-15 11:16:47 | 7.28 | list | [DgidbInteraction(genesymbol='RAB40B', gene_concept_id='hgnc:18284', resource='TTD', type='NULL', drug_name='ADAPALENE', drug_concept_id='rxcui:60223', score='0.6250913242344582', approved='TRUE', anti_neoplastic='FALSE', immunotherapy='FALSE'), DgidbInteraction(genesymbol='ALCAM', gene_concept_id='...(truncated) | 84,175 | {'first': True} | 2025-07-15 11:16:39 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2025-07-15 11:16:47 | 2025-07-15 11:17:17 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/dgidb.py", line 132, in get_dgidb_old
soup = bs4.BeautifulSoup(html, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{'first': True} | 2025-07-15 11:16:47 | |||
| ¶ | pypath.inputs.dip.dip_interactions | 2025-07-15 11:17:17 | 2025-07-15 11:17:17 | 0.22 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {'first': True} | 2025-07-15 11:17:17 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.diseases._diseases_general |
Not calling `pypath.inputs.diseases._diseases_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2025-07-15 11:17:17 | 2025-07-15 11:17:17 | 0.31 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resource='TIGA', source_score=27, confidence=0.865), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:535', disease='Sleep disorder', resource='TIGA'...(truncated) | 30,470 | {'first': True} | 2025-07-15 11:17:17 | |
| ¶ | pypath.inputs.diseases.experiments_full | 2025-07-15 11:17:17 | 2025-07-15 11:17:19 | 1.64 | list | [DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:150', disease='Disease of mental health', resource='TIGA', source_score=18, confidence=0.717), DiseasesInteraction(gene_id='ENSP00000000233', genesymbol='ARF5', disease_id='DOID:1724', disease='Duodenal ulcer', resou...(truncated) | 345,254 | {'first': True} | 2025-07-15 11:17:17 | |
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2025-07-15 11:17:19 | 2025-07-15 11:17:19 | 0.14 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:1928', disease='Williams-Beuren syndrome', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ENSP00000001146', genesymbol='CYP26B1', disease_id='DOID:2340', disease='Cranio...(truncated) | 7,770 | {'first': True} | 2025-07-15 11:17:19 | |
| ¶ | pypath.inputs.diseases.knowledge_full | 2025-07-15 11:17:19 | 2025-07-15 11:17:20 | 0.49 | list | [DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050177', disease='Monogenic disease', resource='MedlinePlus', evidence_type='CURATED', confidence=5), DiseasesInteraction(gene_id='ABHD11-AS1', genesymbol='ABHD11-AS1', disease_id='DOID:0050736', disease='Autosomal...(truncated) | 98,579 | {'first': True} | 2025-07-15 11:17:19 | |
| ¶ | pypath.inputs.diseases.textmining_filtered | 2025-07-15 11:17:20 | 2025-07-15 11:17:21 | 1.39 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.245, confidence=3.623, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol...(truncated) | 288,901 | {'first': True} | 2025-07-15 11:17:20 | |
| ¶ | pypath.inputs.diseases.textmining_full | 2025-07-15 11:17:21 | 2025-07-15 11:18:12 | 51.28 | list | [DiseasesInteraction(gene_id='18S_rRNA', genesymbol='18S_rRNA', disease_id='DOID:9643', disease='Babesiosis', z_score=7.245, confidence=3.623, url='https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=18S_rRNA&type2=-26&id2=DOID:9643'), DiseasesInteraction(gene_id='18S_rRNA', genesymbol...(truncated) | 11,403,943 | {'first': True} | 2025-07-15 11:17:21 | |
| ¶ | pypath.inputs.domino.domino_ddi | 2025-07-15 11:18:12 | 2025-07-15 11:18:15 | 2.57 | list | [<pypath.internals.intera.DomainDomain object at 0x7fa3b5054790>, <pypath.internals.intera.DomainDomain object at 0x7fa3f46fd090>, <pypath.internals.intera.DomainDomain object at 0x7fa3ac76f6d0>, <pypath.internals.intera.DomainDomain object at 0x7fa3ac76e3d0>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {'first': True} | 2025-07-15 11:18:12 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2025-07-15 11:18:15 | 2025-07-15 11:18:16 | 1.15 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7fa2054a5990>, <pypath.internals.intera.DomainDomain object at 0x7fa2054a6d90>, <pypath.internals.intera.DomainDomain object at 0x7fa2054a64d0>, <pypath.internals.intera.DomainDomain object at 0x7fa2054a4410>, <pypath.internals.intera.Domain...(truncated) | 2 | {'first': True} | 2025-07-15 11:18:15 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2025-07-15 11:18:16 | 2025-07-15 11:18:17 | 0.36 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {'first': True} | 2025-07-15 11:18:16 | |
| ¶ | pypath.inputs.domino.get_domino | 2025-07-15 11:18:17 | 2025-07-15 11:18:17 | 0.34 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {'first': True} | 2025-07-15 11:18:17 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2025-07-15 11:18:17 | 2025-07-15 11:18:26 | 9.17 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {'first': True} | 2025-07-15 11:18:17 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-07-15 11:18:26 | 2025-07-15 11:18:40 | 14.17 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {'first': True} | 2025-07-15 11:18:26 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-07-15 11:18:40 | 2025-07-15 11:18:41 | 0.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
~~~~~~~~^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{'first': True} | 2025-07-15 11:18:40 | |||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-07-15 11:18:41 | 2025-07-15 11:18:41 | 0.33 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
~~~~~~~~^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{'first': True} | 2025-07-15 11:18:41 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-07-15 11:18:41 | 2025-07-15 11:18:43 | 1.92 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {'first': True} | 2025-07-15 11:18:41 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2025-07-15 11:18:43 | 2025-07-15 11:18:43 | 0.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/dorothea.py", line 146, in get_dorothea_old
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 11:18:43 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2025-07-15 11:18:43 | 2025-07-15 11:18:45 | 1.37 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {'first': True} | 2025-07-15 11:18:43 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2025-07-15 11:18:45 | 2025-07-15 11:18:59 | 14.08 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {'first': True} | 2025-07-15 11:18:45 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2025-07-15 11:18:59 | 2025-07-15 11:18:59 | 0.11 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
~~~~~~~~^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{'first': True} | 2025-07-15 11:18:59 | |||
| ¶ | pypath.inputs.drugbank._drugbank_credentials | 2025-07-15 11:18:59 | 2025-07-15 11:18:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/drugbank.py", line 49, in _drugbank_credentials
return credentials.credentials(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/credentials.py", line 115, in credentials
raise RuntimeError(msg)
RuntimeError: Failed to obtain credentials for resource `DrugBank`
|
{'first': True} | 2025-07-15 11:18:59 | |||
| ¶ | pypath.inputs.drugbank._drugbank_download |
Not calling `pypath.inputs.drugbank._drugbank_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_annotations | 2025-07-15 11:18:59 | 2025-07-15 11:18:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/drugbank.py", line 352, in drugbank_annotations
drugs = drugbank_drugs(
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
~~~^^^^^^^^^^^^^
KeyError: 'structure'
|
{'first': True} | 2025-07-15 11:18:59 | |||
| ¶ | pypath.inputs.drugbank.drugbank_drugs | 2025-07-15 11:18:59 | 2025-07-15 11:18:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
~~~^^^^^^^^^^^^^
KeyError: 'structure'
|
{'first': True} | 2025-07-15 11:18:59 | |||
| ¶ | pypath.inputs.drugbank.drugbank_interactions | 2025-07-15 11:18:59 | 2025-07-15 11:18:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/drugbank.py", line 198, in drugbank_interactions
for d in drugbank_drugs(user = user, passwd = passwd)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
~~~^^^^^^^^^^^^^
KeyError: 'structure'
|
{'first': True} | 2025-07-15 11:18:59 | |||
| ¶ | pypath.inputs.drugbank.drugbank_mapping |
Not calling `pypath.inputs.drugbank.drugbank_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_raw_interactions | 2025-07-15 11:18:59 | 2025-07-15 11:18:59 | 0.00 | list | [] | 0 | {'first': True} | 2025-07-15 11:18:59 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2025-07-15 11:18:59 | 2025-07-15 11:19:00 | 1.04 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {'first': True} | 2025-07-15 11:18:59 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2025-07-15 11:19:00 | 2025-07-15 11:19:01 | 1.17 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {'first': True} | 2025-07-15 11:19:00 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2025-07-15 11:19:01 | 2025-07-15 11:19:02 | 0.88 | dict | {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) | 353 | {'first': True} | 2025-07-15 11:19:01 | |
| ¶ | pypath.inputs.elm.elm_domains | 2025-07-15 11:19:02 | 2025-07-15 11:19:03 | 0.36 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {'first': True} | 2025-07-15 11:19:02 | |
| ¶ | pypath.inputs.elm.elm_instances | 2025-07-15 11:19:03 | 2025-07-15 11:20:51 | 108.92 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 4,277 | {'first': True} | 2025-07-15 11:19:03 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2025-07-15 11:20:51 | 2025-07-15 11:20:52 | 0.14 | 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) | 2,797 | {'first': True} | 2025-07-15 11:20:51 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2025-07-15 11:20:52 | 2025-07-15 11:21:04 | 12.48 | dict | {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=True)}, 'P30411': {EmbraceAnnotation(mainclass='receptor', neu...(truncated) | 844 | {'first': True} | 2025-07-15 11:20:52 | |
| ¶ | pypath.inputs.embrace.embrace_interactions | 2025-07-15 11:21:04 | 2025-07-15 11:21:04 | 0.14 | list | [EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(ligand='O43184', receptor='P05556'), EmbraceInteraction(ligand='O43184', receptor='P31431'), EmbraceInteraction(...(truncated) | 1,273 | {'first': True} | 2025-07-15 11:21:04 | |
| ¶ | pypath.inputs.embrace.embrace_raw | 2025-07-15 11:21:04 | 2025-07-15 11:21:04 | 0.12 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {'first': True} | 2025-07-15 11:21:04 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2025-07-15 11:21:04 | 2025-07-15 11:21:05 | 0.14 | list | [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol=None, N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0,...(truncated) | 1,832 | {'first': True} | 2025-07-15 11:21:04 | |
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2025-07-15 11:21:05 | 2025-07-15 11:21:05 | 0.42 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {'first': True} | 2025-07-15 11:21:05 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2025-07-15 11:21:05 | 2025-07-15 11:21:06 | 0.64 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 346 | {'first': True} | 2025-07-15 11:21:05 | |
| ¶ | pypath.inputs.eutils.esummary |
Not calling `pypath.inputs.eutils.esummary`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2025-07-15 11:21:06 | 2025-07-15 11:21:33 | 27.18 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {'first': True} | 2025-07-15 11:21:06 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2025-07-15 11:21:33 | 2025-07-15 11:21:33 | 0.03 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {'first': True} | 2025-07-15 11:21:33 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2025-07-15 11:21:33 | 2025-07-15 11:24:06 | 152.76 | list | [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) | 290,197 | {'first': True} | 2025-07-15 11:21:33 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2025-07-15 11:24:06 | 2025-07-15 11:24:06 | 0.06 | list | [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) | 354 | {'first': True} | 2025-07-15 11:24:06 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2025-07-15 11:24:06 | 2025-07-15 11:24:06 | 0.68 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,405 | {'first': True} | 2025-07-15 11:24:06 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2025-07-15 11:24:06 | 2025-07-15 11:25:19 | 72.55 | dict | {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0016020', 'GO:0005743', 'GO:0005739', 'GO:0045275'}, 'A0A023I7H2': {'GO:0016020', 'GO:0005743', 'GO:0005739'}, 'A0A023I7H5': {'GO:0016020', 'GO:0005743', 'GO:0005739', 'GO:0045259'}, 'A0A023I7J4': {'GO:0016020', 'GO:0005743', 'GO:0005739...(truncated) | 2 | {'first': True} | 2025-07-15 11:24:06 | |
| ¶ | pypath.inputs.go.get_goslim | 2025-07-15 11:25:19 | 2025-07-15 11:25:20 | 1.48 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 141 | {'first': True} | 2025-07-15 11:25:19 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-07-15 11:25:20 | 2025-07-15 11:31:25 | 364.37 | dict | {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016008': {('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 | {'first': True} | 2025-07-15 11:25:20 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2025-07-15 11:31:25 | 2025-07-15 11:31:25 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 190, in go_ancestors_goose
sql_path = os.path.join(common.DATA, 'goose_ancestors.sql')
^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2025-07-15 11:31:25 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2025-07-15 11:31:25 | 2025-07-15 11:31:30 | 4.71 | dict | {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016008': {('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 | {'first': True} | 2025-07-15 11:31:25 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-07-15 11:31:30 | 2025-07-15 11:31:32 | 2.19 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0016020', 'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H8': {'GO:0016020', 'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H9': {'GO:0016020', 'GO:0019814', 'GO:0005886', 'GO:...(truncated) | 3 | {'first': True} | 2025-07-15 11:31:30 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2025-07-15 11:31:32 | 2025-07-15 11:31:40 | 8.50 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0008486', reference='GO_REF:0000033', evidence_code='IBA', with_or_from='FB:FBgn0036111|MGI:MGI:1930957|MGI:MGI:2147931|PANTHER:PTN000290327|PomBase:SPAC13G6.14|SGD:S0000...(truncated) | 19,708 | {'first': True} | 2025-07-15 11:31:32 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2025-07-15 11:31:43 | 2025-07-15 11:31:44 | 1.16 | dict | {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0016020', 'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H8': {'GO:0016020', 'GO:0019814', 'GO:0005886', 'GO:0005576'}, 'A0A075B6H9': {'GO:0016020', 'GO:0019814', 'GO:0005886', 'GO:...(truncated) | 3 | {'first': True} | 2025-07-15 11:31:43 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2025-07-15 11:31:44 | 2025-07-15 11:31:44 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 833, in go_annotations_goose
sql_path = os.path.join(common.DATA, 'goose_annotations.sql')
^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2025-07-15 11:31:44 | |||
| ¶ | pypath.inputs.go.go_annotations_solr | 2025-07-15 11:31:44 | 2025-07-15 11:31:46 | 1.59 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 738, in go_annotations_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src/lxml/iterparse.pxi", line 78, in lxml.etree.iterparse.__init__
TypeError: expected str, bytes or os.PathLike object, not NoneType
|
{'first': True} | 2025-07-15 11:31:44 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2025-07-15 11:31:46 | 2025-07-15 11:31:48 | 1.93 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 61, in go_annotations_uniprot
for x in [x.split('\t') for x in data.split('\n')]
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
|
{'first': True} | 2025-07-15 11:31:46 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-07-15 11:31:48 | 2025-07-15 11:31:52 | 4.34 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016008', '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 | {'first': True} | 2025-07-15 11:31:48 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2025-07-15 11:31:52 | 2025-07-15 11:31:52 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 283, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 190, in go_ancestors_goose
sql_path = os.path.join(common.DATA, 'goose_ancestors.sql')
^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2025-07-15 11:31:52 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2025-07-15 11:31:52 | 2025-07-15 11:31:56 | 4.48 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016008', '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 | {'first': True} | 2025-07-15 11:31:52 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2025-07-15 11:31:56 | 2025-07-15 11:32:00 | 3.79 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {'first': True} | 2025-07-15 11:31:56 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2025-07-15 11:32:00 | 2025-07-15 11:32:00 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 564, in go_terms_goose
sql_path = os.path.join(common.DATA, 'goose_terms.sql')
^^^^^^^^^^^
AttributeError: module 'pypath.share.common' has no attribute 'DATA'
|
{'first': True} | 2025-07-15 11:32:00 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2025-07-15 11:32:00 | 2025-07-15 11:32:04 | 3.61 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {'first': True} | 2025-07-15 11:32:00 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2025-07-15 11:32:04 | 2025-07-15 11:32:05 | 0.72 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/go.py", line 436, in go_terms_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src/lxml/iterparse.pxi", line 78, in lxml.etree.iterparse.__init__
TypeError: expected str, bytes or os.PathLike object, not NoneType
|
{'first': True} | 2025-07-15 11:32:04 | |||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2025-07-15 11:32:05 | 2025-07-15 11:32:05 | 0.24 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 808 | {'first': True} | 2025-07-15 11:32:05 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2025-07-15 11:32:05 | 2025-07-15 11:32:06 | 1.49 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {'first': True} | 2025-07-15 11:32:05 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2025-07-15 11:32:06 | 2025-07-15 11:32:14 | 7.71 | tuple | ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) | 2 | {'first': True} | 2025-07-15 11:32:06 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2025-07-15 11:32:14 | 2025-07-15 11:32:14 | 0.19 | dict | {'Q8TDS4': {GutmgeneAnnotation(gut_microbiota='Clostridium butyricum', gut_microbiota_ncbi_id='1492', rank='species', strain='ATCC 19398', alteration='activation', throughput='low-throughput', associative_mode='causally', sample='HCT116, Caco-2, and HCT8', experimental_method='cell culture,in vitro ...(truncated) | 111 | {'first': True} | 2025-07-15 11:32:14 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2025-07-15 11:32:14 | 2025-07-15 11:32:14 | 0.01 | list | [GutmgeneRaw(index='123', pmid='31734354', gut_microbiota='Clostridium butyricum', gut_microbiota_ncbi_id='1492', rank='species', strain='ATCC 19398', gene='HCAR2', gene_id='338442', alteration='activation', throughput='low-throughput', associative_mode='causally', organism='human', sample='HCT116, ...(truncated) | 243 | {'first': True} | 2025-07-15 11:32:14 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2025-07-15 11:32:14 | 2025-07-15 11:32:14 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/havugimana.py", line 37, in get_havugimana
c = curl.Curl(url, large = True, silent = False)
^^^^
NameError: name 'curl' is not defined
|
{'first': True} | 2025-07-15 11:32:14 | |||
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2025-07-15 11:32:14 | 2025-07-15 11:32:14 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/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__20250715-092402/pypath_git/pypath/inputs/havugimana.py", line 37, in get_havugimana
c = curl.Curl(url, large = True, silent = False)
^^^^
NameError: name 'curl' is not defined
|
{'first': True} | 2025-07-15 11:32:14 | |||
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2025-07-15 11:32:14 | 2025-07-15 11:32:16 | 1.69 | dict | {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='Alpha-2-macroglobulin family')}, 'A8K2U0': {HGNCGeneGroupAnnotation(mainclass='Alpha-2...(truncated) | 15,593 | {'first': True} | 2025-07-15 11:32:14 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2025-07-15 11:32:16 | 2025-07-15 11:32:24 | 7.62 | list | [HippieInteraction(id_a='Q8IXW5', id_b='Q9NUG6', score=0.82, methods=None, references=('17643375', '24981860'), sources=None, organisms=None), HippieInteraction(id_a='Q13642', id_b='P04156', score=0.84, methods=None, references=('18482256', '28671123'), sources=None, organisms=None), HippieInteracti...(truncated) | 102,409 | {'first': True} | 2025-07-15 11:32:16 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2025-07-15 11:32:24 | 2025-07-15 11:33:39 | 75.47 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {'first': True} | 2025-07-15 11:32:24 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2025-07-15 11:33:39 | 2025-07-15 11:33:39 | 0.00 | dict | {'interactions': [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_rol...(truncated) | 2 | {'first': True} | 2025-07-15 11:33:39 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2025-07-15 11:33:39 | 2025-07-15 11:33:39 | 0.00 | dict | {'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P00491': {HPMRAnnotation(role='ligand', mainclass=None, subclass=None, subsubclass=None)}, 'P42702': {HPMRAnnotation(role='Receptor', mainclass='Cytokin...(truncated) | 1,141 | {'first': True} | 2025-07-15 11:33:39 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2025-07-15 11:33:39 | 2025-07-15 11:33:39 | 0.00 | dict | {} | 0 | {'first': True} | 2025-07-15 11:33:39 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2025-07-15 11:33:39 | 2025-07-15 11:33:39 | 0.00 | list | [HpmrInteraction(receptor='P40189', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P42702', partner_role='ligand', partner='P00491', references='15051883', unambiguous=True), HpmrInteraction(receptor='P26992', partner_role='ligand', partn...(truncated) | 634 | {'first': True} | 2025-07-15 11:33:39 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2025-07-15 11:33:39 | 2025-07-15 11:33:41 | 2.03 | dict | {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0000280'), HpoAnnotation(entrez_ge...(truncated) | 5,077 | {'first': True} | 2025-07-15 11:33:39 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2025-07-15 11:33:42 | 2025-07-15 11:33:44 | 2.56 | 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:617105', name='Epileptic encephalopathy, early infantil...(truncated) | 11,366 | {'first': True} | 2025-07-15 11:33:42 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2025-07-15 11:33:45 | 2025-07-15 11:33:46 | 1.69 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {'first': True} | 2025-07-15 11:33:45 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2025-07-15 11:33:46 | 2025-07-15 11:33:47 | 0.53 | 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) | 19,177 | {'first': True} | 2025-07-15 11:33:46 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2025-07-15 11:33:47 | 2025-07-15 11:33:50 | 3.43 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {'first': True} | 2025-07-15 11:33:47 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2025-07-15 11:33:50 | 2025-07-15 11:33:52 | 1.27 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {'first': True} | 2025-07-15 11:33:50 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2025-07-15 11:33:52 | 2025-07-15 11:33:53 | 1.25 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {'first': True} | 2025-07-15 11:33:52 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2025-07-15 11:33:53 | 2025-07-15 11:33:55 | 1.67 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {'first': True} | 2025-07-15 11:33:53 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2025-07-15 11:33:55 | 2025-07-15 11:34:25 | 30.24 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {'first': True} | 2025-07-15 11:33:55 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2025-07-15 11:34:25 | 2025-07-15 11:34:26 | 1.25 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='peroxisome', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,384 | {'first': True} | 2025-07-15 11:34:25 | |
| ¶ | pypath.inputs.humap.humap2_complexes | 2025-07-15 11:34:26 | 2025-07-15 11:34:28 | 1.92 | dict | {'COMPLEX:O95900_Q9BQS8': Complex: COMPLEX:O95900_Q9BQS8, 'COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9': Complex: COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9, 'COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6ZRY4_Q93062_Q96S66_Q9NZC3_Q9UF11_Q9Y6M7': Complex: COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6Z...(truncated) | 7,044 | {'first': True} | 2025-07-15 11:34:26 | |
| ¶ | pypath.inputs.humap.humap_complexes | 2025-07-15 11:34:28 | 2025-07-15 11:34:29 | 0.54 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/humap.py", line 35, in humap_complexes
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 11:34:28 | |||
| ¶ | pypath.inputs.humsavar._parse_desc |
Not calling `pypath.inputs.humsavar._parse_desc`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2025-07-15 11:34:29 | 2025-07-15 11:34:31 | 2.39 | dict | {'P04217': {UniprotVariant(genesymbol='A1BG', ftid='VAR_018369', aa_change='p.His52Arg', variant_category='LB/B', dbsnp='rs893184', disease=None, disease_symbol=None, disease_omim=None), UniprotVariant(genesymbol='A1BG', ftid='VAR_018370', aa_change='p.His395Arg', variant_category='LB/B', dbsnp='rs2...(truncated) | 13,122 | {'first': True} | 2025-07-15 11:34:29 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2025-07-15 11:34:31 | 2025-07-15 11:34:33 | 1.37 | list | [HuriInteraction(uniprot_a='Q8IY31', uniprot_b='Q9BQD3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='P49902', uniprot_b='P49902', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9BVJ6', uniprot_b='Q8NHQ1', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 5,652 | {'first': True} | 2025-07-15 11:34:31 | |
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2025-07-15 11:34:33 | 2025-07-15 11:34:36 | 3.18 | list | [HuriInteraction(uniprot_a='Q9H2A7', uniprot_b='Q6UY14', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q5SY16', uniprot_b='Q09666', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='Q8TAB5', uniprot_b='Q96F24', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 46,823 | {'first': True} | 2025-07-15 11:34:33 | |
| ¶ | pypath.inputs.huri.hi_iii_old | 2025-07-15 11:34:36 | 2025-07-15 11:34:36 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/huri.py", line 90, in hi_iii_old
url = urls.urls['hid']['hi-iii']
~~~~~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'hi-iii'
|
{'first': True} | 2025-07-15 11:34:36 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2025-07-15 11:34:36 | 2025-07-15 11:34:56 | 20.63 | list | [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) | 227,941 | {'first': True} | 2025-07-15 11:34:36 | |
| ¶ | pypath.inputs.huri.huri_interactions | 2025-07-15 11:34:56 | 2025-07-15 11:35:05 | 8.98 | list | [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) | 164,682 | {'first': True} | 2025-07-15 11:34:56 | |
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2025-07-15 11:35:05 | 2025-07-15 11:35:06 | 1.05 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {'first': True} | 2025-07-15 11:35:05 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2025-07-15 11:35:06 | 2025-07-15 11:35:08 | 1.07 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {'first': True} | 2025-07-15 11:35:06 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2025-07-15 11:35:08 | 2025-07-15 11:35:09 | 1.01 | list | [LitBmInteraction(uniprot_a='P23511', uniprot_b='Q13952'), LitBmInteraction(uniprot_a='P23511', uniprot_b='P25208'), LitBmInteraction(uniprot_a='P43351', uniprot_b='P43351'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q92843'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q07817'), LitBmInte...(truncated) | 13,535 | {'first': True} | 2025-07-15 11:35:08 | |
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2025-07-15 11:35:09 | 2025-07-15 11:35:09 | 0.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/huri.py", line 38, in rolland_hi_ii_14
xlsname = cell.cell_supplementary(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'close'
|
{'first': True} | 2025-07-15 11:35:09 | |||
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2025-07-15 11:35:09 | 2025-07-15 11:35:10 | 1.04 | list | [HuriInteraction(uniprot_a='A0A0S2Z436', uniprot_b='Q9BQQ3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='O94989', uniprot_b='Q53EZ4', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q8NHQ1', uniprot_b='Q9H7H0', isoform_a=1, isoform_b=1, score=None), HuriIntera...(truncated) | 2,880 | {'first': True} | 2025-07-15 11:35:09 | |
| ¶ | pypath.inputs.huri.yu2011_interactions | 2025-07-15 11:35:10 | 2025-07-15 11:35:11 | 1.30 | list | [HuriInteraction(uniprot_a='Q5VUM1', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P62166', uniprot_b='Q86UW9', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9NV12', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteractio...(truncated) | 7,331 | {'first': True} | 2025-07-15 11:35:10 | |
| ¶ | pypath.inputs.i3d.get_i3d | 2025-07-15 11:35:11 | 2025-07-15 11:35:20 | 8.55 | list | [{'A0A024RBG1': {'pfam': None, 'chain': 'B', 'seq': [[8, 148]]}, 'Q8NFP7': {'pfam': None, 'chain': 'A', 'seq': [[8, 146]]}, 'uniprots': ['A0A024RBG1', 'Q8NFP7'], 'source': 'I3D', 'pdb': ['5ltu'], 'references': []}, {'A0A075B5G3': {'pfam': None, 'chain': 'F', 'seq': [[1, 99]]}, 'Q8NBP7': {'pfam': Non...(truncated) | 22,184 | {'first': True} | 2025-07-15 11:35:11 | |
| ¶ | pypath.inputs.icellnet._icellnet_get_components |
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_entity |
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_references |
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_resources |
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2025-07-15 11:35:20 | 2025-07-15 11:35:20 | 0.85 | dict | {Complex: COMPLEX:P01033_P14780: {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None)}, 'P01033': {IcellnetAnnotation(role='ligand', family=None, subfamily=None, classification=None), IcellnetAnnotation(role='ligand', family='Cell adhesion', subfamily=None, classifica...(truncated) | 1,193 | {'first': True} | 2025-07-15 11:35:20 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2025-07-15 11:35:20 | 2025-07-15 11:35:21 | 0.04 | dict | {'COMPLEX:P01033_P14780': Complex: COMPLEX:P01033_P14780, 'COMPLEX:P01374_Q06643': Complex: COMPLEX:P01374_Q06643, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:P05106_P06756': Complex: COMPLEX:P05106_P06756, 'COMPLEX:P05556_P08648': Complex: COMPLEX:P05556_P08648, 'COMPLEX:P0847...(truncated) | 156 | {'first': True} | 2025-07-15 11:35:20 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2025-07-15 11:35:21 | 2025-07-15 11:35:21 | 0.03 | list | [IcellnetRecord(ligand=Complex: COMPLEX:P01033_P14780, receptor='Q07954', family=None, subfamily=None, classification=None, resources=None, references=['11279011']), IcellnetRecord(ligand=Complex: COMPLEX:P01374_Q06643, receptor='P36941', family='Cytokine', subfamily='TNF', classification=None, reso...(truncated) | 1,647 | {'first': True} | 2025-07-15 11:35:21 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2025-07-15 11:35:21 | 2025-07-15 11:35:21 | 0.55 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/imweb.py", line 72, in _get_imweb
hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'first': True} | 2025-07-15 11:35:21 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2025-07-15 11:35:21 | 2025-07-15 11:35:21 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/imweb.py", line 105, in get_imweb
c0.perform()
pycurl.error: (3, 'URL rejected: Malformed input to a URL function')
|
{'first': True} | 2025-07-15 11:35:21 | |||
| ¶ | pypath.inputs.imweb.get_inweb | 2025-07-15 11:35:21 | 2025-07-15 11:35:24 | 3.01 | DataFrame | Gene1 Gene2 Score Source 0 ANKFY1 RNF2 0.167000 InWeb_IM 1 MED4 SLK 0.148000 InWeb_IM 2 PCSK7 TBC1D22A 0.157078 InWeb3 3 EML1 FLNA 0.116073 InWeb3 4 PFKM SLC25A5 0.141000 InWeb_IM ... ... ... ...(truncated) | 883,356 | {'first': True} | 2025-07-15 11:35:21 | |
| ¶ | pypath.inputs.imweb.get_imweb_req | 2025-07-15 11:35:24 | 2025-07-15 11:35:24 | 0.13 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/imweb.py", line 138, in get_imweb_req
token = json.loads(r0.text)['token']
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{'first': True} | 2025-07-15 11:35:24 | |||
| ¶ | pypath.inputs.imweb.get_inweb | 2025-07-15 11:35:24 | 2025-07-15 11:35:26 | 2.03 | DataFrame | Gene1 Gene2 Score Source 0 ANKFY1 RNF2 0.167000 InWeb_IM 1 MED4 SLK 0.148000 InWeb_IM 2 PCSK7 TBC1D22A 0.157078 InWeb3 3 EML1 FLNA 0.116073 InWeb3 4 PFKM SLC25A5 0.141000 InWeb_IM ... ... ... ...(truncated) | 883,356 | {'first': True} | 2025-07-15 11:35:24 | |
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2025-07-15 11:35:26 | 2025-07-15 11:35:30 | 4.07 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {'first': True} | 2025-07-15 11:35:26 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2025-07-15 11:35:30 | 2025-07-15 11:35:31 | 0.64 | NoneType | None | 0 | {'first': True} | 2025-07-15 11:35:30 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2025-07-15 11:35:31 | 2025-07-15 11:35:31 | 0.40 | NoneType | None | 0 | {'first': True} | 2025-07-15 11:35:31 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2025-07-15 11:35:31 | 2025-07-15 11:37:12 | 100.27 | list | [IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'phage display'}, interaction_types={'direct interaction'}, mi_score=0.67, isoform_a=None, isoform_b=None), IntactInteraction(id_a='O43426', id_b='P49418', id_type_a='uniprot', i...(truncated) | 77,349 | {'first': True} | 2025-07-15 11:35:31 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2025-07-15 11:37:12 | 2025-07-15 11:37:12 | 0.51 | set | {'P23229', 'P20702', 'P18564', 'P05107', 'P38570', 'Q9UKX5', 'P26012', 'P05106', 'P08514', 'Q13349', 'P16144', 'P17301', 'P20701', 'P18084', 'Q13683', 'P05556', 'O75578', 'P26010', 'P56199', 'P26006', 'P06756', 'P11215', 'P53708', 'P08648', 'Q13797'} | 25 | {'first': True} | 2025-07-15 11:37:12 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2025-07-15 11:37:13 | 2025-07-15 11:37:14 | 1.40 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid receptor activity'), Interpro2GOAnnotation(go_term_id='GO:0008270', go_term_name='zinc ion binding'), Int...(truncated) | 14,743 | {'first': True} | 2025-07-15 11:37:13 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2025-07-15 11:37:14 | 2025-07-15 11:37:47 | 32.64 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/interpro.py", line 283, in interpro_annotations
for protein in entry['protein_subset']:
~~~~~^^^^^^^^^^^^^^^^^^
KeyError: 'protein_subset'
|
{'first': True} | 2025-07-15 11:37:14 | |||
| ¶ | pypath.inputs.interpro.interpro_entries | 2025-07-15 11:37:47 | 2025-07-15 11:37:59 | 12.48 | list | [InterproEntry(interpro_id='IPR000001', protein_count='20781', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 48,679 | {'first': True} | 2025-07-15 11:37:47 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2025-07-15 11:37:59 | 2025-07-15 11:37:59 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/intogen.py", line 51, in intogen_annotations
with settings.context(curl_connect_timeout = 100):
^^^^^^^^^^^^^^^^
AttributeError: module 'pypath.share.settings' has no attribute 'context'
|
{'first': True} | 2025-07-15 11:37:59 | |||
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2025-07-15 11:37:59 | 2025-07-15 11:37:59 | 0.07 | dict | {'IPI00534246': {'A0AQW4'}, 'IPI00538686': {'A0JPZ8'}, 'IPI00852271': {'A0JPZ8'}, 'IPI00570394': {'A0MDQ1'}, 'IPI00545643': {'A0MEB5'}, 'IPI00530730': {'A0MES8'}, 'IPI00524170': {'A0MEX7'}, 'IPI00535541': {'A0MFH4'}, 'IPI00528604': {'A0MFL4'}, 'IPI00523676': {'A1L4W5'}, 'IPI00541581': {'A1L4Y2'}, 'I...(truncated) | 86,754 | {'first': True} | 2025-07-15 11:37:59 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2025-07-15 11:37:59 | 2025-07-15 11:38:23 | 23.62 | list | [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['19955365']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetyl...(truncated) | 26,743 | {'first': True} | 2025-07-15 11:37:59 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2025-07-15 11:38:23 | 2025-07-15 11:38:24 | 0.67 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='growth factor'), ItalkAnnotation(mainclass='receptor', subclass='other')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | {'first': True} | 2025-07-15 11:38:23 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2025-07-15 11:38:24 | 2025-07-15 11:38:24 | 0.02 | list | [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) | 2,706 | {'first': True} | 2025-07-15 11:38:24 | |
| ¶ | pypath.inputs.italk.italk_raw | 2025-07-15 11:38:24 | 2025-07-15 11:38:24 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {'first': True} | 2025-07-15 11:38:24 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2025-07-15 11:38:24 | 2025-07-15 11:38:28 | 4.24 | list | [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) | 35,224 | {'first': True} | 2025-07-15 11:38:24 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2025-07-15 11:38:28 | 2025-07-15 11:38:28 | 0.15 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,224 | {'first': True} | 2025-07-15 11:38:28 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2025-07-15 11:38:28 | 2025-07-15 11:56:19 | 1,070.88 | list | [KeggInteraction(id_a='Q03113', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcriptional=False), KeggInteraction(id_a='O94763', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcription...(truncated) | 14,739 | {'first': True} | 2025-07-15 11:38:28 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2025-07-15 11:56:19 | 2025-07-15 11:56:43 | 23.61 | set | {KeggMedicusRawInteraction(id_a='C08150', id_b='85315', name_a='(MPA) Medroxyprogesterone acetate', name_b='PAQR8', effect='stimulation', itype='post_translational', pw_type='factor', type_a='perturbant', type_b='gene', network_id='N01357'), KeggMedicusRawInteraction(id_a='6655', id_b='3265', name_...(truncated) | 12,946 | {'first': True} | 2025-07-15 11:56:19 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2025-07-15 11:56:43 | 2025-07-15 11:56:44 | 1.27 | dict | {'COMPLEX:O60671_O60921_O75943_Q99638': Complex: COMPLEX:O60671_O60921_O75943_Q99638, 'COMPLEX:Q14457_Q6ZNE5_Q8NEB9': Complex: COMPLEX:Q14457_Q6ZNE5_Q8NEB9, 'COMPLEX:O00268_P15336': Complex: COMPLEX:O00268_P15336, 'COMPLEX:P06493_P14635': Complex: COMPLEX:P06493_P14635, 'COMPLEX:O43707_P18206_Q9Y4G6...(truncated) | 528 | {'first': True} | 2025-07-15 11:56:43 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2025-07-15 11:56:44 | 2025-07-15 11:56:44 | 0.37 | list | [KeggMedicusInteraction(id_a='Q07890', id_b='P01112', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='P61020', id_b='Q8NEB9', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) | 9,538 | {'first': True} | 2025-07-15 11:56:44 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2025-07-15 11:56:44 | 2025-07-15 11:56:56 | 12.04 | dict | {'O75608': {KeggPathway(pathway='Graft-versus-host disease'), KeggPathway(pathway='Alzheimer disease'), KeggPathway(pathway='Type I diabetes mellitus'), KeggPathway(pathway='Non-alcoholic fatty liver disease'), KeggPathway(pathway='Proteoglycans in cancer'), KeggPathway(pathway='Pathways of neurodeg...(truncated) | 2,672 | {'first': True} | 2025-07-15 11:56:44 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2025-07-15 11:56:56 | 2025-07-15 11:56:57 | 0.82 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kegg.py", line 212, in kegg_pathway_annotations_pathwaycommons
for row in c.result:
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 766, in iterfile
for line in fileobj:
File "/usr/lib/python3.11/gzip.py", line 314, in read1
return self._buffer.read1(size)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 499, in read
if not self._read_gzip_header():
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 468, in _read_gzip_header
last_mtime = _read_gzip_header(self._fp)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 428, in _read_gzip_header
raise BadGzipFile('Not a gzipped file (%r)' % magic)
gzip.BadGzipFile: Not a gzipped file (b'<!')
|
{'first': True} | 2025-07-15 11:56:56 | |||
| ¶ | pypath.inputs.kegg.kegg_pathways | 2025-07-15 11:56:57 | 2025-07-15 11:57:10 | 12.92 | tuple | ({'MAPK signaling pathway': {'O75608', 'Q12851', 'Q9UK32', 'Q96KG9', 'Q99558', 'Q9UBE8', 'O95257', 'Q12968', 'P52564', 'P10398', 'Q9HBH9', 'Q16644', 'Q9H1B7', 'P36896', 'P35813', 'Q9H2K8', 'P0DPQ6', 'P80192', 'Q03701', 'P32248', 'O95819', 'Q9Y3M2', 'O94763', 'P15976', 'Q96NL6', 'P01583', 'P62070', '...(truncated) | 2 | {'first': True} | 2025-07-15 11:56:57 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._generate_conv_functions | 2025-07-15 11:57:10 | 2025-07-15 11:57:10 | 0.00 | NoneType | None | 0 | {'first': True} | 2025-07-15 11:57:10 | |
| ¶ | pypath.inputs.kegg_api._generate_relation_functions | 2025-07-15 11:57:10 | 2025-07-15 11:57:10 | 0.00 | NoneType | None | 0 | {'first': True} | 2025-07-15 11:57:10 | |
| ¶ | pypath.inputs.kegg_api._kegg_conv |
Not calling `pypath.inputs.kegg_api._kegg_conv`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi |
Not calling `pypath.inputs.kegg_api._kegg_ddi`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_async |
Not calling `pypath.inputs.kegg_api._kegg_ddi_async`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_sync |
Not calling `pypath.inputs.kegg_api._kegg_ddi_sync`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general |
Not calling `pypath.inputs.kegg_api._kegg_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general_async |
Not calling `pypath.inputs.kegg_api._kegg_general_async`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_link |
Not calling `pypath.inputs.kegg_api._kegg_link`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_list |
Not calling `pypath.inputs.kegg_api._kegg_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_relations |
Not calling `pypath.inputs.kegg_api._kegg_relations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2025-07-15 11:57:10 | 2025-07-15 11:57:15 | 4.62 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kegg_api.py", line 127, in drug_to_drug
entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kegg_api.py", line 465, in <dictcomp>
self.proc_key(entry[0]): self.proc_value(entry[1])
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
return entry[0].split(':')[1]
~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
|
{'first': True} | 2025-07-15 11:57:10 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2025-07-15 11:57:15 | 2025-07-15 11:57:15 | 0.35 | dict | {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) | 503 | {'first': True} | 2025-07-15 11:57:15 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2025-07-15 11:57:15 | 2025-07-15 11:57:15 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/kirouac2010.py", line 87, in kirouac2010_interactions
tbl = embo.embopress_supplementary(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/embopress.py", line 102, in embopress_supplementary
inputs_common.read_xls(fname, sheet = sheet)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/common.py", line 68, in read_xls
raise FileNotFoundError(xls_file)
FileNotFoundError: /mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/cache/60cb3ecd06bbc7b62cecef5bc9bab30e-downloadSupplement
|
{'first': True} | 2025-07-15 11:57:15 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2025-07-15 11:57:15 | 2025-07-15 11:57:19 | 4.04 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {'first': True} | 2025-07-15 11:57:15 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2025-07-15 11:57:19 | 2025-07-15 11:57:22 | 2.56 | list | [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) | 2,765 | {'first': True} | 2025-07-15 11:57:19 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2025-07-15 11:57:22 | 2025-07-15 11:57:23 | 0.87 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {'first': True} | 2025-07-15 11:57:22 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2025-07-15 11:57:23 | 2025-07-15 11:57:23 | 0.41 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {'first': True} | 2025-07-15 11:57:23 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2025-07-15 11:57:23 | 2025-07-15 11:57:24 | 0.78 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {'first': True} | 2025-07-15 11:57:23 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2025-07-15 11:57:24 | 2025-07-15 11:57:36 | 11.57 | list | [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) | 593 | {'first': True} | 2025-07-15 11:57:24 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2025-07-15 11:57:36 | 2025-07-15 11:57:36 | 0.02 | 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 | {'first': True} | 2025-07-15 11:57:36 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2025-07-15 11:57:36 | 2025-07-15 11:57:36 | 0.02 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {'first': True} | 2025-07-15 11:57:36 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2025-07-15 11:57:36 | 2025-07-15 11:57:37 | 1.28 | dict | {'SciTegic09271913552D': LincsCompound(lincs=None, chembl=None, chebi=None, inchi='InChI=1S/C29H24N4O4S/c1-4-27(34)31-26-16-23(12-5-18(26)2)33-28(35)14-9-21-17-30-25-13-8-20(15-24(25)29(21)33)19-6-10-22(11-7-19)32-38(3,36)37/h4-17,32H,1H2,2-3H3,(H,31,34)', inchi_key='SFMJNHNUOVADRW-UHFFFAOYSA-N', sm...(truncated) | 371 | {'first': True} | 2025-07-15 11:57:36 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2025-07-15 11:57:37 | 2025-07-15 11:57:38 | 0.53 | list | [] | 0 | {'first': True} | 2025-07-15 11:57:37 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2025-07-15 11:57:38 | 2025-07-15 11:57:38 | 0.33 | list | [] | 0 | {'first': True} | 2025-07-15 11:57:38 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2025-07-15 11:57:38 | 2025-07-15 11:57:39 | 0.98 | list | [] | 0 | {'first': True} | 2025-07-15 11:57:38 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2025-07-15 11:57:39 | 2025-07-15 11:57:39 | 0.43 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism=9606, pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism=9606, pmid='22244333'), Lncd...(truncated) | 478 | {'first': True} | 2025-07-15 11:57:39 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2025-07-15 11:57:39 | 2025-07-15 11:57:40 | 0.47 | list | [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism=5888, pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism=9468, pmid='17175535'), LncrnadbInteraction(lncrna='G22', partner='SRP9', type='protein', o...(truncated) | 773 | {'first': True} | 2025-07-15 11:57:39 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2025-07-15 11:57:40 | 2025-07-15 11:58:17 | 36.76 | dict | {'P27824': {LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='melanosome', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=None, sc...(truncated) | 9,479 | {'first': True} | 2025-07-15 11:57:40 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2025-07-15 11:58:17 | 2025-07-15 11:58:17 | 0.38 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10632583', '11560943', '1502153')), LrdbAnnotation(role='receptor', ...(truncated) | 1,536 | {'first': True} | 2025-07-15 11:58:17 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2025-07-15 11:58:17 | 2025-07-15 11:58:17 | 0.03 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {'first': True} | 2025-07-15 11:58:17 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2025-07-15 11:58:17 | 2025-07-15 11:58:17 | 0.32 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {'first': True} | 2025-07-15 11:58:17 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2025-07-15 11:58:17 | 2025-07-15 11:58:18 | 0.99 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/matrisome.py", line 86, in __matrisome_annotations_2
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 11:58:17 | |||
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2025-07-15 11:58:18 | 2025-07-15 11:58:19 | 0.27 | dict | {'E9PPR9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H0YCP4': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'H7C5S3': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 2,501 | {'first': True} | 2025-07-15 11:58:18 | |
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2025-07-15 11:58:19 | 2025-07-15 11:58:19 | 0.50 | dict | {} | 0 | {'first': True} | 2025-07-15 11:58:19 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2025-07-15 11:58:19 | 2025-07-15 11:58:21 | 2.00 | set | {'P00748', 'P69905', 'Q9H112', 'P54753', 'P0C7T4', 'Q86Y30', 'Q12959', 'O14511', 'Q99731', 'O15240', 'O95995', 'P0DP57', 'Q76B58', 'Q5JQD4', 'P60852', 'Q9Y5Q6', 'A0A075B6K6', 'Q9H8L6', 'Q96BQ1', 'Q9UJA9', 'O94779', 'Q6UWP2', 'P01178', 'P29017', 'Q9UBU2', 'Q10588', 'P32455', 'Q9BSG5', 'Q13519', 'P310...(truncated) | 2,840 | {'first': True} | 2025-07-15 11:58:19 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2025-07-15 11:58:21 | 2025-07-15 11:58:21 | 0.12 | list | [MatrixdbInteraction(id_a='"chebi:""CHEBI:29105"""', id_b='uniprotkb:P05067', alt_ids_a='matrixdb:CAT_1', alt_ids_b='-', aliases_a='matrixdb:Zinc(short label)', aliases_b='"uniprotkb:""APP""(gene name)"', detection_method='"psi-mi:""MI:0004""(""affinity chromatography technology"")"', author='Bush A...(truncated) | 1,264 | {'first': True} | 2025-07-15 11:58:21 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2025-07-15 11:58:21 | 2025-07-15 11:58:21 | 0.07 | set | set() | 0 | {'first': True} | 2025-07-15 11:58:21 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2025-07-15 11:58:21 | 2025-07-15 11:58:21 | 0.06 | set | set() | 0 | {'first': True} | 2025-07-15 11:58:21 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2025-07-15 11:58:21 | 2025-07-15 11:58:22 | 1.09 | set | {'P20702', 'P62079', 'O95471', 'Q9NZ94', 'Q9UKX5', 'P25942', 'Q8TD84', 'Q9UQS6', 'P13612', 'Q9HDB5', 'P22105', 'Q13449', 'P25940', 'Q7Z3B1', 'P42771', 'Q8TAW8', 'Q68D78', 'Q4G160', 'Q96QR6', 'Q13797', 'Q6FIB4', 'Q6MZM7', 'P02751', 'Q6MZK0', 'Q02763', 'Q9BRX2', 'O00548', 'Q14773', 'O94856', 'P18827',...(truncated) | 112 | {'first': True} | 2025-07-15 11:58:21 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2025-07-15 11:58:22 | 2025-07-15 11:58:56 | 33.13 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,419 | {'first': True} | 2025-07-15 11:58:22 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2025-07-15 11:58:56 | 2025-07-15 11:58:56 | 0.13 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {'first': True} | 2025-07-15 11:58:56 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2025-07-15 11:58:56 | 2025-07-15 11:58:58 | 1.89 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {'first': True} | 2025-07-15 11:58:56 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2025-07-15 11:58:58 | 2025-07-15 11:58:58 | 0.78 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {'first': True} | 2025-07-15 11:58:58 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2025-07-15 11:58:58 | 2025-07-15 11:58:59 | 0.18 | list | [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) | 805 | {'first': True} | 2025-07-15 11:58:58 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.04 | tuple | ({'406881': {'MIRLET7A1', 'mirlet7a1'}, '406882': {'mirlet7a2', 'MIRLET7A2'}, '406883': {'mirlet7a3', 'MIRLET7A3'}, '406884': {'mirlet7b', 'MIRLET7B'}, '406885': {'mirlet7c', 'MIRLET7C'}, '406886': {'MIRLET7D', 'mirlet7d'}, '406887': {'MIRLET7E', 'mirlet7e'}, '406888': {'mirlet7f1', 'MIRLET7F1'}, '4...(truncated) | 2 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.06 | list | [('406881', '64742'), ('406882', '64743'), ('406883', '64744'), ('406884', '70782'), ('406884', '66458'), ('406884', '64745'), ('406885', '64746'), ('406885', '66459'), ('406885', '70783'), ('406885', '66460'), ('406886', '64747'), ('406886', '70784'), ('406886', '66461'), ('406886', '66462'), ('406...(truncated) | 4,244 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.02 | list | [('406881', 'MIRLET7A1'), ('406881', 'mirlet7a1'), ('406882', 'mirlet7a2'), ('406882', 'MIRLET7A2'), ('406883', 'mirlet7a3'), ('406883', 'MIRLET7A3'), ('406884', 'mirlet7b'), ('406884', 'MIRLET7B'), ('406885', 'mirlet7c'), ('406885', 'MIRLET7C'), ('406886', 'MIRLET7D'), ('406886', 'mirlet7d'), ('406...(truncated) | 9,158 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.06 | list | ['406881', '406882', '406883', '406884', '406884', '406884', '406885', '406885', '406885', '406885', '406886', '406886', '406886', '406886', '406887', '406887', '406887', '406888', '406889', '406948', '406948', '406950', '406952', '406953', '406953', '406979', '406979', '406980', '406981', '406982',...(truncated) | 4,244 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.02 | list | [('64685', 'let-7'), ('64687', 'mir-1'), ('64688', 'mir-2'), ('64706', 'mir-10'), ('64712', 'mir-10'), ('64742', 'MIRLET7A1'), ('64742', 'let-7'), ('80364', 'Mir3967'), ('64743', 'MIRLET7A2'), ('64743', 'let-7'), ('80363', 'Mir3966'), ('64744', 'MIRLET7A3'), ('64744', 'let-7'), ('80362', 'Mir101c'),...(truncated) | 5,300 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.06 | list | ['64742', '64743', '64744', '70782', '66458', '64745', '64746', '66459', '70783', '66460', '64747', '70784', '66461', '66462', '64748', '66463', '70785', '64749', '64750', '64751', '66482', '64752', '64753', '66491', '64754', '66494', '64755', '64756', '64757', '66498', '64758', '66499', '64759', '6...(truncated) | 4,244 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.08 | list | [('let-7', '100315026'), ('let-7', '100170412'), ('let-7', '406885'), ('let-7', '100315171'), ('let-7', '100170919'), ('let-7', '100316034'), ('let-7', '406887'), ('let-7', '100314974'), ('let-7', '100170931'), ('let-7', '100316036'), ('let-7', '100315502'), ('let-7', '100314497'), ('let-7', '100498...(truncated) | 4,379 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2025-07-15 11:58:59 | 2025-07-15 11:58:59 | 0.19 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2025-07-15 11:58:59 | 2025-07-15 11:59:00 | 0.40 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism=9606, target_organism=9606, pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organism=10090, target_or...(truncated) | 3,106 | {'first': True} | 2025-07-15 11:58:59 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2025-07-15 11:59:00 | 2025-07-15 12:05:15 | 375.11 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism=None, target_genesymbol='Cd320', target_entrez='54219', target_organism=None, target_site=None, method='Luciferase reporter assay//qRT-PCR//Western blot', category='Functional MTI', pmid='18158304', datase...(truncated) | 27,595 | {'first': True} | 2025-07-15 11:59:00 | |
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2025-07-15 12:05:15 | 2025-07-15 12:05:15 | 0.25 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {'first': True} | 2025-07-15 12:05:15 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2025-07-15 12:05:15 | 2025-07-15 12:05:27 | 11.47 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/msigdb.py", line 345, in msigdb_annotations
collection_data = msigdb_download_collections(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/msigdb.py", line 298, in msigdb_download_collections
msigdb_download(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/msigdb.py", line 237, in msigdb_download
for gset in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 12:05:15 | |||
| ¶ | pypath.inputs.msigdb.msigdb_download | 2025-07-15 12:05:27 | 2025-07-15 12:05:33 | 6.89 | dict | {'MT': {'MT-ND3', 'MT-ND1', 'MT-TD', 'MT-ATP8', 'MT-TM', 'MT-CO2', 'MT-ND6', 'MT-TN', 'MT-TE', 'MT-TW', 'MT-ND5', 'MT-TY', 'MT-ND4L', 'MT-TQ', 'MT-TL1', 'MT-TR', 'MT-TP', 'MT-CO1', 'MT-RNR1', 'MT-TG', 'MT-TK', 'MT-TS2', 'MT-ND4', 'MT-ATP6', 'MT-ND2', 'MT-TL2', 'MT-TF', 'MT-TI', 'MT-TV', 'MT-RNR2', '...(truncated) | 34,550 | {'first': True} | 2025-07-15 12:05:27 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2025-07-15 12:05:34 | 2025-07-15 12:05:36 | 2.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/msigdb.py", line 298, in msigdb_download_collections
msigdb_download(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/msigdb.py", line 237, in msigdb_download
for gset in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 12:05:34 | |||
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2025-07-15 12:05:36 | 2025-07-15 12:05:37 | 0.36 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {'first': True} | 2025-07-15 12:05:36 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2025-07-15 12:05:37 | 2025-07-15 12:05:37 | 0.15 | list | [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) | 2,171 | {'first': True} | 2025-07-15 12:05:37 | |
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2025-07-15 12:05:37 | 2025-07-15 12:05:37 | 0.11 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {'first': True} | 2025-07-15 12:05:37 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2025-07-15 12:05:37 | 2025-07-15 12:05:37 | 0.14 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {'first': True} | 2025-07-15 12:05:37 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2025-07-15 12:05:37 | 2025-07-15 12:06:07 | 30.27 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/netpath.py", line 43, in netpath_interactions
pwnames = netpath_names()
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/netpath.py", line 151, in netpath_names
soup = bs4.BeautifulSoup(html, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{'first': True} | 2025-07-15 12:05:37 | |||
| ¶ | pypath.inputs.netpath.netpath_names | 2025-07-15 12:06:07 | 2025-07-15 12:06:37 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/netpath.py", line 151, in netpath_names
soup = bs4.BeautifulSoup(html, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{'first': True} | 2025-07-15 12:06:07 | |||
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2025-07-15 12:06:37 | 2025-07-15 12:07:37 | 60.02 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/netpath.py", line 184, in netpath_pathway_annotations
pathway_ids = netpath_names()
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/netpath.py", line 151, in netpath_names
soup = bs4.BeautifulSoup(html, 'html.parser')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/bs4/__init__.py", line 442, in __init__
raise TypeError(
TypeError: Incoming markup is of an invalid type: None. Markup must be a string, a bytestring, or an open filehandle.
|
{'first': True} | 2025-07-15 12:06:37 | |||
| ¶ | pypath.inputs.offsides._sides_base |
Not calling `pypath.inputs.offsides._sides_base`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2025-07-15 12:07:37 | 2025-07-15 12:08:03 | 25.28 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {'first': True} | 2025-07-15 12:07:37 | |
| ¶ | pypath.inputs.oma._id_translate |
Not calling `pypath.inputs.oma._id_translate`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.oma.oma_orthologs | 2025-07-15 12:08:03 | 2025-07-15 12:09:52 | 109.07 | list | [OmaOrthology(a=OmaGene(id='PKD1_HUMAN', oma_group=1072295, hog='HOG:E0784712.1a', taxon=9606, chr='16', start=2089727, end=2135689, strand=-1, main_isoform=True), b=OmaGene(id='PKD1_MOUSE', oma_group=1072295, hog='HOG:E0784712.1a', taxon=10090, chr='17', start=24769237, end=24814513, strand=1, main...(truncated) | 22,374 | {'first': True} | 2025-07-15 12:08:03 | |
| ¶ | pypath.inputs.oma.oma_table | 2025-07-15 12:09:52 | 2025-07-15 12:10:01 | 8.81 | defaultdict | defaultdict(<class 'set'>, {'PKD1_HUMAN': {'PKD1_MOUSE'}, 'PG12B_HUMAN': {'Q8VC81'}, 'BMP8B_HUMAN': {'BMP8A_MOUSE'}, 'A0A1W2PPC1': {'A0A571BD03'}, 'HINFP_HUMAN': {'HINFP_MOUSE'}, 'FITM2_HUMAN': {'FITM2_MOUSE'}, 'RS8_HUMAN': {'RS8_MOUSE'}, 'INO80_HUMAN': {'INO80_MOUSE'}, 'H4_HUMAN': {'H4_MOUSE'}, 'Z5...(truncated) | 17,895 | {'first': True} | 2025-07-15 12:09:52 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2025-07-15 12:10:01 | 2025-07-15 12:10:01 | 0.42 | dict | {'ado': "Alzheimer's Disease Ontology (ADO)", 'afpo': 'African Population Ontology', 'agro': 'Agronomy Ontology', 'aism': 'Ontology for the Anatomy of the Insect SkeletoMuscular system', 'amphx': 'Amphioxus Development and Anatomy Ontology (AMPHX)', 'apo': 'Ascomycete Phenotype Ontology (APO)', 'apo...(truncated) | 268 | {'first': True} | 2025-07-15 12:10:01 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.opentargets._opentargets_general |
Not calling `pypath.inputs.opentargets._opentargets_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2025-07-15 12:10:01 | 2025-07-15 12:10:19 | 17.83 | list | [{'chembl_id': 'CHEMBL1200632', 'event': 'acute generalised exanthematous pustulosis', 'count': 17, 'llr': 34.164839700408265, 'critval': 13.880781728509543, 'meddraCode': '10048799'}, {'chembl_id': 'CHEMBL1200632', 'event': 'anal ulcer', 'count': 5, 'llr': 16.745304158079307, 'critval': 13.88078172...(truncated) | 112,928 | {'first': True} | 2025-07-15 12:10:01 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2025-07-15 12:10:19 | 2025-07-15 12:12:10 | 111.54 | list | [{'id': 'ENSG00000020219', 'tissues': [{'efo_code': 'UBERON_0012249', 'label': 'ectocervix', 'organs': ['reproductive organ', 'reproductive structure'], 'anatomical_systems': ['reproductive system'], 'rna': {'value': 2.0, 'zscore': -1, 'level': -1, 'unit': 'TPM'}, 'protein': {'reliability': False, '...(truncated) | 43,791 | {'first': True} | 2025-07-15 12:10:19 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2025-07-15 12:12:11 | 2025-07-15 12:13:15 | 64.73 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) | 2,146,271 | {'first': True} | 2025-07-15 12:12:11 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2025-07-15 12:13:15 | 2025-07-15 12:14:52 | 97.10 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001617', 'score': 0.05099149718673741, 'evidenceCount': 4}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001626', 'score': 0.00792543466157194, 'evidenceCount': 3}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000002330', 'score': 0.003...(truncated) | 6,960,486 | {'first': True} | 2025-07-15 12:13:15 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2025-07-15 12:14:52 | 2025-07-15 12:15:12 | 19.19 | dict | {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) | 88 | {'first': True} | 2025-07-15 12:14:52 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2025-07-15 12:15:12 | 2025-07-15 12:15:42 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/oreganno.py", line 72, in oreganno_interactions
for l in oreganno_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 12:15:12 | |||
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2025-07-15 12:15:42 | 2025-07-15 12:16:12 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 12:15:42 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2025-07-15 12:16:12 | 2025-07-15 12:16:15 | 3.21 | defaultdict | defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=True, cell_type='Acinar cells', organ='Pancreas', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=1.0, mouse_sensitivity=0.957143, human_specificity=0.000628931, mouse_specificit...(truncated) | 4,492 | {'first': True} | 2025-07-15 12:16:12 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2025-07-15 12:16:15 | 2025-07-15 12:16:15 | 0.04 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {'first': True} | 2025-07-15 12:16:15 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2025-07-15 12:16:15 | 2025-07-15 12:16:15 | 0.00 | list | [] | 0 | {'first': True} | 2025-07-15 12:16:15 | |
| ¶ | pypath.inputs.pathwaycommons._create_single_resource_method |
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2025-07-15 12:16:15 | 2025-07-15 12:16:28 | 13.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/pathwaycommons.py", line 120, in pathwaycommons_interactions
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{'first': True} | 2025-07-15 12:16:15 | |||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2025-07-15 12:16:28 | 2025-07-15 12:16:29 | 0.42 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {'first': True} | 2025-07-15 12:16:28 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2025-07-15 12:16:29 | 2025-07-15 12:16:29 | 0.06 | tuple | (None, None) | 2 | {'first': True} | 2025-07-15 12:16:29 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2025-07-15 12:16:29 | 2025-07-15 12:16:37 | 7.97 | 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) | 48,504 | {'first': True} | 2025-07-15 12:16:29 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2025-07-15 12:16:37 | 2025-07-15 12:16:43 | 5.67 | tuple | ({'P02185': {('1mlf', 'X-ray', 2.0), ('1naz', 'X-ray', 1.04), ('2mgf', 'X-ray', 1.8), ('1mbi', 'X-ray', 2.0), ('5uta', 'X-ray', 1.81), ('4lpi', 'X-ray', 1.36), ('5yzf', 'X-ray', 1.77), ('1dti', 'X-ray', 1.7), ('2spm', 'X-ray', 1.7), ('1mlm', 'X-ray', 1.8), ('5zzg', 'X-ray', 1.8), ('3m39', 'X-ray', 1...(truncated) | 2 | {'first': True} | 2025-07-15 12:16:37 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2025-07-15 12:16:43 | 2025-07-15 12:16:44 | 0.57 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {'first': True} | 2025-07-15 12:16:43 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2025-07-15 12:16:44 | 2025-07-15 12:28:04 | 680.89 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {'first': True} | 2025-07-15 12:16:44 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2025-07-15 12:28:04 | 2025-07-15 12:28:06 | 1.15 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {'first': True} | 2025-07-15 12:28:04 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2025-07-15 12:28:06 | 2025-07-15 12:28:10 | 4.14 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=9, end=152)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=9, end=154)}, '103m': {'PF00042': PfamDomain(chain='A', start=...(truncated) | 2 | {'first': True} | 2025-07-15 12:28:06 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2025-07-15 12:28:11 | 2025-07-15 12:35:48 | 457.49 | tuple | ({}, {}) | 2 | {'first': True} | 2025-07-15 12:28:11 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2025-07-15 12:35:48 | 2025-07-15 12:51:14 | 925.77 | tuple | ({}, {}) | 2 | {'first': True} | 2025-07-15 12:35:48 | |
| ¶ | pypath.inputs.pharos._create_query_functions | 2025-07-15 12:51:14 | 2025-07-15 12:51:14 | 0.00 | NoneType | None | 0 | {'first': True} | 2025-07-15 12:51:14 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2025-07-15 12:51:14 | 2025-07-15 13:14:17 | 1,383.42 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2025-07-15 12:51:14 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2025-07-15 13:14:18 | 2025-07-15 13:14:22 | 3.28 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2025-07-15 13:14:18 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2025-07-15 13:14:23 | 2025-07-15 13:14:26 | 3.27 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2025-07-15 13:14:23 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2025-07-15 13:14:27 | 2025-07-15 13:14:30 | 3.32 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2025-07-15 13:14:27 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2025-07-15 13:14:31 | 2025-07-15 13:14:34 | 3.28 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2025-07-15 13:14:31 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2025-07-15 13:14:35 | 2025-07-15 13:35:51 | 1,275.99 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {'first': True} | 2025-07-15 13:14:35 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2025-07-15 13:35:51 | 2025-07-15 13:35:54 | 3.18 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'first': True} | 2025-07-15 13:35:51 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2025-07-15 13:35:55 | 2025-07-15 13:35:55 | 0.32 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {'first': True} | 2025-07-15 13:35:55 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2025-07-15 13:35:55 | 2025-07-15 13:35:56 | 0.10 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/phosphatome.py", line 68, in phosphatome_annotations
tbl = inputs_common.read_xls(c.result['aag1796_Tables S1 to S23.xlsx'])
~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
|
{'first': True} | 2025-07-15 13:35:55 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2025-07-15 13:35:56 | 2025-07-15 13:35:58 | 2.21 | list | [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) | 2,426 | {'first': True} | 2025-07-15 13:35:56 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2025-07-15 13:35:58 | 2025-07-15 13:35:59 | 1.51 | list | [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) | 2,426 | {'first': True} | 2025-07-15 13:35:58 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2025-07-15 13:35:59 | 2025-07-15 13:35:59 | 0.10 | dict | {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) | 247 | {'first': True} | 2025-07-15 13:35:59 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2025-07-15 13:35:59 | 2025-07-15 13:36:01 | 1.23 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {'first': True} | 2025-07-15 13:35:59 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2025-07-15 13:36:01 | 2025-07-15 13:36:01 | 0.02 | list | [['PRKCB', 'PHF17'], ['CAMK4', 'SPR'], ['ACVR1', 'RPS6KA2'], ['PRKCA', 'CTTN'], ['CDK5', 'NFATC4'], ['MAPK1', 'PPARG'], ['CLK2', 'SAFB2'], ['MAPK14', 'KRT8'], ['MAPK3', 'CEBPA'], ['PLK1', 'WEE1'], ['BTK', 'ITK'], ['STK17A', 'SLC4A1AP'], ['GSK3A', 'SFRS1'], ['CDK5', 'ABI2'], ['MAP2K4', 'CTTN'], ['RPS...(truncated) | 1,821 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2025-07-15 13:36:01 | 2025-07-15 13:36:01 | 0.21 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2025-07-15 13:36:01 | 2025-07-15 13:36:01 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2025-07-15 13:36:01 | 2025-07-15 13:36:01 | 0.01 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P27361', 'P15408'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P28482', 'P08235'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P31749', 'P35240'], ['P45984', 'P...(truncated) | 9,094 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2025-07-15 13:36:01 | 2025-07-15 13:36:01 | 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 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2025-07-15 13:36:01 | 2025-07-15 13:36:01 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2025-07-15 13:36:01 | 2025-07-15 13:36:02 | 0.24 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 9,164 | {'first': True} | 2025-07-15 13:36:01 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2025-07-15 13:36:02 | 2025-07-15 13:36:02 | 0.01 | list | [['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['P...(truncated) | 4,374 | {'first': True} | 2025-07-15 13:36:02 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2025-07-15 13:36:02 | 2025-07-15 13:36:02 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'MS;AB', '24719451;15174125;23312004;21983960;15084291'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'MA;AB', '15342622'], ['P27361', 'P15408', 'human', 'human', 'WB;MS;MA;AB', '21712546;25547114;18452278'], ['...(truncated) | 2 | {'first': True} | 2025-07-15 13:36:02 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2025-07-15 13:36:02 | 2025-07-15 13:36:02 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'WB;MA;AB'...(truncated) | 4,790 | {'first': True} | 2025-07-15 13:36:02 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2025-07-15 13:36:02 | 2025-07-15 13:36:07 | 5.35 | 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')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) | 198,635 | {'first': True} | 2025-07-15 13:36:02 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2025-07-15 13:36:07 | 2025-07-15 13:36:24 | 16.57 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {'first': True} | 2025-07-15 13:36:07 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2025-07-15 13:36:24 | 2025-07-15 13:36:25 | 0.42 | 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 | {'first': True} | 2025-07-15 13:36:24 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2025-07-15 13:36:25 | 2025-07-15 13:38:22 | 116.79 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21148409', '21209006', '24876223', '28052875'}, 'isoforms': {1}, 'process': {''}, 'function': {'intracellular localization', 'protein stabilization', 'protein degradation', 'phosphorylation', 'ubiquitination'}...(truncated) | 3,621 | {'first': True} | 2025-07-15 13:36:25 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2025-07-15 13:38:22 | 2025-07-15 13:38:49 | 27.45 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {'first': True} | 2025-07-15 13:38:22 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2025-07-15 13:38:49 | 2025-07-15 13:38:50 | 0.47 | 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) | 394,059 | {'first': True} | 2025-07-15 13:38:49 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2025-07-15 13:38:50 | 2025-07-15 13:40:00 | 70.22 | dict | {'P35250': {ProgenyAnnotation(pathway='Trail', weight=-0.8006773132589663, p_value=0.6240861307828072), ProgenyAnnotation(pathway='VEGF', weight=-0.15684553639501156, p_value=0.8477560090795286), ProgenyAnnotation(pathway='p53', weight=-3.3513628049710005, p_value=0.000985568693599589), ProgenyAnnot...(truncated) | 18,582 | {'first': True} | 2025-07-15 13:38:50 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2025-07-15 13:40:00 | 2025-07-15 13:41:13 | 72.16 | DataFrame | gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {'first': True} | 2025-07-15 13:40:00 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2025-07-15 13:41:13 | 2025-07-15 13:41:17 | 4.73 | dict | {'normal': {'Adipose tissue:Adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detect...(truncated) | 2 | {'first': True} | 2025-07-15 13:41:13 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2025-07-15 13:41:19 | 2025-07-15 13:41:28 | 9.95 | dict | {'O43657': {ProtainatlasAnnotation(organ='Heart muscle', tissue='Heart muscle', cell_type='cardiomyocytes', level='Not detected', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnotation(o...(truncated) | 15,045 | {'first': True} | 2025-07-15 13:41:19 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_interactions | 2025-07-15 13:41:31 | 2025-07-15 13:41:31 | 0.35 | list | [ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interaction_type='', evidence=''), ProteinatlasInteraction(uniprot_a='', uniprot_b='', gene_a='', gene_b='', interac...(truncated) | 46,472 | {'first': True} | 2025-07-15 13:41:31 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2025-07-15 13:41:31 | 2025-07-15 13:41:32 | 0.34 | dict | {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) | 2,590 | {'first': True} | 2025-07-15 13:41:31 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2025-07-15 13:41:32 | 2025-07-15 13:41:32 | 0.52 | dict | {'O43657': {ProteinatlasSubcellularAnnotation(location='Cell Junctions', status='approved', reliability='Approved', main_location='Cell Junctions;Cytosol', additional_location='Nucleoli fibrillar center'), ProteinatlasSubcellularAnnotation(location='Nucleoli fibrillar center', status='additional', r...(truncated) | 13,336 | {'first': True} | 2025-07-15 13:41:32 | |
| ¶ | pypath.inputs.proteins.variants | 2025-07-15 13:41:32 | 2025-07-15 13:48:11 | 398.87 | 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) | 30,452 | {'first': True} | 2025-07-15 13:41:32 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2025-07-15 13:48:12 | 2025-07-15 13:48:14 | 1.97 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) | 2 | {'first': True} | 2025-07-15 13:48:12 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2025-07-15 13:48:14 | 2025-07-15 13:48:15 | 0.70 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'22304920', '24357804', '25728676', '24727247', '25545367'}, 'substrate': 'P15336', 'databases': {'PhosphoSite', 'REACH', 'SIGNOR', 'Sparser'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'23708658', '24727247'}, ...(truncated) | 22,139 | {'first': True} | 2025-07-15 13:48:14 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2025-07-15 13:48:15 | 2025-07-15 13:48:15 | 0.60 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {'first': True} | 2025-07-15 13:48:15 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2025-07-15 13:48:15 | 2025-07-15 13:48:24 | 8.44 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), Ramilo...(truncated) | 18,879 | {'first': True} | 2025-07-15 13:48:15 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2025-07-15 13:48:24 | 2025-07-15 13:48:24 | 0.00 | NoneType | None | 0 | {'first': True} | 2025-07-15 13:48:24 | |
| ¶ | pypath.inputs.rdata._rdata_data_frame_get_rownames |
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.rdata._rdata_list_get_names |
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._bp_collect_resources |
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._process_controls |
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_resources |
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_species |
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_compartment |
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_id |
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_res |
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_id |
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reaction |
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reactions | 2025-07-15 13:48:24 | 2025-07-15 13:48:41 | 17.62 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/reaction.py", line 981, in _reactome_reactions
for i in sp.find('bqbiol:haspart').find_all('rdf:li'):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'find_all'
|
{'first': True} | 2025-07-15 13:48:24 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2025-07-15 13:48:41 | 2025-07-15 13:48:43 | 1.80 | tuple | ({}, {}, {}) | 3 | {'first': True} | 2025-07-15 13:48:41 | |
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2025-07-15 13:48:43 | 2025-07-15 13:48:43 | 0.27 | NoneType | None | 0 | {'first': True} | 2025-07-15 13:48:43 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2025-07-15 13:48:43 | 2025-07-15 13:48:44 | 0.10 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {'first': True} | 2025-07-15 13:48:43 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2025-07-15 13:48:44 | 2025-07-15 13:48:44 | 0.31 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/pyreact.py", line 1296, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/pyreact.py", line 1172, in load_wikipathways
len(biopaxes.result),
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
|
{'first': True} | 2025-07-15 13:48:44 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2025-07-15 13:48:44 | 2025-07-15 13:48:50 | 6.50 | dict | {'BioPAX/Nicotine_pharmacodynamics_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/Alzheimer_disease_amyloid_secretase_pathway.owl': <ExFileObject name='/mnt/disk0/build/omnipath-b...(truncated) | 178 | {'first': True} | 2025-07-15 13:48:44 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2025-07-15 13:48:50 | 2025-07-15 13:48:53 | 2.53 | NoneType | None | 0 | {'first': True} | 2025-07-15 13:48:50 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2025-07-15 13:48:53 | 2025-07-15 13:49:17 | 24.36 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {'first': True} | 2025-07-15 13:48:53 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2025-07-15 13:49:17 | 2025-07-15 13:56:12 | 414.82 | 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 93 on 6/13/25, 9:16 PM using JSBML version 1....(truncated) | 2,803 | {'first': True} | 2025-07-15 13:49:17 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2025-07-15 13:56:34 | 2025-07-15 13:56:36 | 1.87 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/cache/9c...(truncated) | 2,803 | {'first': True} | 2025-07-15 13:56:34 | |
| ¶ | pypath.inputs.reactome._reactome_txt |
Not calling `pypath.inputs.reactome._reactome_txt`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reactome.pathway_hierarchy | 2025-07-15 13:56:36 | 2025-07-15 13:56:37 | 0.76 | list | [{'parent': 'R-BTA-109581', 'child': 'R-BTA-109606'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-169911'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-5357769'}, {'parent': 'R-BTA-109581', 'child': 'R-BTA-75153'}, {'parent': 'R-BTA-109582', 'child': 'R-BTA-140877'}, {'parent': 'R-BTA-109582', 'child'...(truncated) | 23,019 | {'first': True} | 2025-07-15 13:56:36 | |
| ¶ | pypath.inputs.reactome.reactome_raw |
Not calling `pypath.inputs.reactome.reactome_raw`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reactome_old._reactome_data |
Not calling `pypath.inputs.reactome_old._reactome_data`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reactome_old._reactome_data_gen |
Not calling `pypath.inputs.reactome_old._reactome_data_gen`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.reactome_old.reactome_chebis | 2025-07-15 13:56:37 | 2025-07-15 13:56:44 | 7.29 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{'first': True} | 2025-07-15 13:56:37 | |||
| ¶ | pypath.inputs.reactome_old.reactome_pathway_relations | 2025-07-15 13:56:44 | 2025-07-15 13:56:44 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{'first': True} | 2025-07-15 13:56:44 | |||
| ¶ | pypath.inputs.reactome_old.reactome_pathways | 2025-07-15 13:56:44 | 2025-07-15 13:56:45 | 0.99 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{'first': True} | 2025-07-15 13:56:44 | |||
| ¶ | pypath.inputs.reactome_old.reactome_uniprots | 2025-07-15 13:56:45 | 2025-07-15 13:57:03 | 17.58 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 904, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/reactome_old.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
^^^^^^
NameError: name 'fields' is not defined
|
{'first': True} | 2025-07-15 13:56:45 | |||
| ¶ | pypath.inputs.rhea.rhea_raw |
Not calling `pypath.inputs.rhea.rhea_raw`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2025-07-15 13:57:03 | 2025-07-15 13:57:04 | 1.66 | dict | {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='mouse'), ScconnectAnnota...(truncated) | 3,285 | {'first': True} | 2025-07-15 13:57:03 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2025-07-15 13:57:04 | 2025-07-15 13:57:04 | 0.02 | set | {Complex: COMPLEX:P29459_P29460, Complex: COMPLEX:P01562, Complex: COMPLEX:O15263, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:P0DML2_P0DML3, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:P01215_P01225, Complex: COMPLEX:P...(truncated) | 17 | {'first': True} | 2025-07-15 13:57:04 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2025-07-15 13:57:04 | 2025-07-15 14:00:16 | 191.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/scconnect.py", line 258, in scconnect_interactions
for ligand_target in itertools.product(ligands, targets):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/scconnect.py", line 197, in process_partner
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/scconnect.py", line 198, in <listcomp>
mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 3551, in map_name
return mapper.map_name(
^^^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2953, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 2193, in map_name
mapped_names = self.uniprot_cleanup(
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 2227, in uniprot_cleanup
uniprots = self.trembl_swissprot(
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 2868, in trembl_swissprot
genesymbols = self.map_name(
^^^^^^^^^^^^^^
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z76HPyxw-py3.11/lib/python3.11/site-packages/pypath_common/_misc.py", line 2953, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 1978, in map_name
mapped_names = self._map_name(
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 2510, in _map_name
tbl = self.which_table(
^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 1562, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 3208, in load_mapping
reader = MapReader(param = resource, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 258, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 288, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 450, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/utils/mapping.py", line 893, in read_mapping_uniprot
data = query.perform()
^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/uniprot.py", line 690, in perform
_id, *variables = zip(*self)
^^^^^^^^^^^^^^^
ValueError: not enough values to unpack (expected at least 1, got 0)
|
{'first': True} | 2025-07-15 13:57:04 | |||
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2025-07-15 14:00:16 | 2025-07-15 14:00:16 | 0.07 | dict | {'CID100005052': {SiderDrug(name='reserpine', atc='C02AA02')}, 'CID100005453': {SiderDrug(name='thiotepa', atc='L01AC01')}, 'CID109846180': {SiderDrug(name='eltrombopag', atc='B02BX05')}, 'CID100002676': {SiderDrug(name='cerivastatin', atc='C10AA06')}, 'CID100002148': {SiderDrug(name='p-aminohippura...(truncated) | 1,430 | {'first': True} | 2025-07-15 14:00:16 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2025-07-15 14:00:16 | 2025-07-15 14:00:16 | 0.19 | list | [SiderSideeffectMeddra(cid='C0034068', meddra_id='10037382', side_effect_name='Pulmonary eosinophilia'), SiderSideeffectMeddra(cid='C0022661', meddra_id='10038444', side_effect_name='Renal failure chronic'), SiderSideeffectMeddra(cid='C0919702', meddra_id='10050510', side_effect_name='Ventricular hy...(truncated) | 20,307 | {'first': True} | 2025-07-15 14:00:16 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2025-07-15 14:00:16 | 2025-07-15 14:00:30 | 14.09 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0010200', umls_concept_in_meddra='C0010200', side_effect='Cough', frequency='9%'), SiderSideeffetFrequency(umls_concept_on_label='C0030193', umls_concept_in_meddra='C0030193', side_effect='Pain', frequency='30%'), SiderSideeffetFreque...(truncated) | 968 | {'first': True} | 2025-07-15 14:00:16 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2025-07-15 14:00:30 | 2025-07-15 14:00:31 | 0.86 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0030554', umls_concept_in_meddra='C0030554', side_effect='Paraesthesia'), SiderSideeffect(umls_concept_on_label='C0917801', umls_concept_in_meddra='C0917801', side_effect='Insomnia'), SiderSideeffect(umls_concept_on_label='C0037199', umls_con...(truncated) | 1,430 | {'first': True} | 2025-07-15 14:00:30 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2025-07-15 14:00:31 | 2025-07-15 14:00:33 | 1.52 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathw...(truncated) | 2 | {'first': True} | 2025-07-15 14:00:31 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2025-07-15 14:00:33 | 2025-07-15 14:00:33 | 0.39 | dict | {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 785 | {'first': True} | 2025-07-15 14:00:33 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2025-07-15 14:00:33 | 2025-07-15 14:00:33 | 0.37 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {'first': True} | 2025-07-15 14:00:33 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2025-07-15 14:00:33 | 2025-07-15 14:00:34 | 1.01 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='Innate i...(truncated) | 839 | {'first': True} | 2025-07-15 14:00:33 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2025-07-15 14:00:34 | 2025-07-15 14:00:35 | 0.66 | 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) | 4,889 | {'first': True} | 2025-07-15 14:00:34 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2025-07-15 14:00:35 | 2025-07-15 14:00:37 | 2.25 | list | [{'typ': 'phosphorylation', 'resnum': 366, 'instance': 'GKKTKFASDDEHDEH', 'substrate': 'P05455', 'start': 359, 'end': 373, 'kinase': 'P68400', 'resaa': 'S', 'motif': 'GKKTKFASDDEHDEH', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'18257391'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) | 13,010 | {'first': True} | 2025-07-15 14:00:35 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2025-07-15 14:00:37 | 2025-07-15 14:00:38 | 0.54 | list | [SignorInteraction(source='P68400', target='P05455', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates', mechanism='phosphorylation', ncbi_tax_id='9606', pubmeds='18257391', direct=True, ptm_type='phosphorylation', ptm_residue='Ser366', ptm_...(truncated) | 94,689 | {'first': True} | 2025-07-15 14:00:37 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2025-07-15 14:00:38 | 2025-07-15 14:00:57 | 19.39 | dict | {'Q9UQQ2': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q6N021': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q969H0': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q8IXJ9': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P05412': {SignorPathway(pathway='Acute Myeloid Leukemi...(truncated) | 775 | {'first': True} | 2025-07-15 14:00:38 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2025-07-15 14:00:57 | 2025-07-15 14:00:57 | 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) | 91 | {'first': True} | 2025-07-15 14:00:57 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2025-07-15 14:00:58 | 2025-07-15 14:01:06 | 8.30 | dict | {'COMPLEX:P67775_Q15172_Q15257': Complex PP2A: COMPLEX:P67775_Q15172_Q15257, 'COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478': Complex AMPK: COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478, 'COMPLEX:P67870_P68400': Complex CK2: COMPLEX:P67870_P68400, 'COMPLEX:P05412_P15336': Compl...(truncated) | 154 | {'first': True} | 2025-07-15 14:00:58 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2025-07-15 14:01:06 | 2025-07-15 14:01:08 | 2.60 | list | [SpikeInteraction(entrez_a='554210', genesymbol_a='MIR429', entrez_b='55914', genesymbol_b='ERBB2IP', directed='1', pmids='20005803', integrity='2', effect='2', assay='', data_source='Published research', description='Luciferase activity assay', mechanism='N/A', regulation=True), SpikeInteraction(en...(truncated) | 8,903 | {'first': True} | 2025-07-15 14:01:06 | |
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2025-07-15 14:01:08 | 2025-07-15 14:01:59 | 50.87 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {'first': True} | 2025-07-15 14:01:08 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2025-07-15 14:01:59 | 2025-07-15 14:03:13 | 73.29 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {'first': True} | 2025-07-15 14:01:59 | |
| ¶ | pypath.inputs.string.string_effects | 2025-07-15 14:03:13 | 2025-07-15 14:03:13 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/string.py", line 64, in string_effects
_ = next(c.result)
^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not an iterator
|
{'first': True} | 2025-07-15 14:03:13 | |||
| ¶ | pypath.inputs.string.string_links_interactions | 2025-07-15 14:03:13 | 2025-07-15 14:03:37 | 24.72 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000262305', neighborhood_score=0, fusion=0, cooccurence=0, coexpression=0, experimental=663, database=0, textmining=866, combined_score=952, physical_combined_score=657), StringLinksInteraction(protein_a='ENSP00000000412', protein...(truncated) | 201,712 | {'first': True} | 2025-07-15 14:03:13 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2025-07-15 14:03:37 | 2025-07-15 14:03:39 | 1.15 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000349437', experimental=0, database=900, textmining=0, combined_score=900), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=960, database=0, textmining=291, combined_score=970),...(truncated) | 89,862 | {'first': True} | 2025-07-15 14:03:37 | |
| ¶ | pypath.inputs.string.string_species | 2025-07-15 14:03:39 | 2025-07-15 14:03:39 | 0.13 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 12,535 | {'first': True} | 2025-07-15 14:03:39 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2025-07-15 14:03:39 | 2025-07-15 14:03:41 | 2.45 | dict | {'A0AV02': (0.8363, 'Transporters', {'APC', 'SLC12', 'SLC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'APC', 'SLC', 'SLC5'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'TMEM30', 'Unknown_function'}), '...(truncated) | 2,844 | {'first': True} | 2025-07-15 14:03:39 | |
| ¶ | pypath.inputs.swisslipids._swisslipids |
Not calling `pypath.inputs.swisslipids._swisslipids`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2025-07-15 14:03:41 | 2025-07-15 14:03:44 | 2.75 | 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 | {'first': True} | 2025-07-15 14:03:41 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2025-07-15 14:03:44 | 2025-07-15 14:03:45 | 0.61 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='21054788', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False)}, 'Q16613': {Talklr...(truncated) | 1,344 | {'first': True} | 2025-07-15 14:03:44 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2025-07-15 14:03:45 | 2025-07-15 14:03:45 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {'first': True} | 2025-07-15 14:03:45 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2025-07-15 14:03:45 | 2025-07-15 14:03:45 | 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 | {'first': True} | 2025-07-15 14:03:45 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2025-07-15 14:03:45 | 2025-07-15 14:03:50 | 5.70 | dict | {'B1B1G6': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(family='Synaptosomal Vesicle Fusion Pore (SVF-Pore)', tcid='1.F.1.1.1')}, 'O00299'...(truncated) | 2,383 | {'first': True} | 2025-07-15 14:03:45 | |
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2025-07-15 14:03:50 | 2025-07-15 14:03:51 | 0.72 | 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) | 24,189 | {'first': True} | 2025-07-15 14:03:50 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2025-07-15 14:03:51 | 2025-07-15 14:03:51 | 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) | 2,062 | {'first': True} | 2025-07-15 14:03:51 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2025-07-15 14:03:51 | 2025-07-15 14:03:51 | 0.17 | dict | {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) | 1,871 | {'first': True} | 2025-07-15 14:03:51 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2025-07-15 14:03:51 | 2025-07-15 14:03:55 | 3.49 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {'first': True} | 2025-07-15 14:03:51 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2025-07-15 14:03:55 | 2025-07-15 14:04:17 | 21.71 | set | {ThreedcomplexContact(pdb='1dgr_1', uniprot_1='P50477', uniprot_2='P50477', chain_1='W', chain_2='V', n_residues=55.0, length_1=93, length_2=76, domain_s1=('51182_f2',), domain_p1=('PF00190.17',), domain_s2=('51182_f1',), domain_p2=('PF00190.17',), ident=False, homo=True), ThreedcomplexContact(pdb='...(truncated) | 258,754 | {'first': True} | 2025-07-15 14:03:55 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2025-07-15 14:04:18 | 2025-07-15 14:07:25 | 187.57 | list | [<pypath.internals.intera.DomainDomain object at 0x7fa359634690>, <pypath.internals.intera.DomainDomain object at 0x7fa359634390>, <pypath.internals.intera.DomainDomain object at 0x7fa359e97f90>, <pypath.internals.intera.DomainDomain object at 0x7fa359e97d90>, <pypath.internals.intera.DomainDomain o...(truncated) | 522,521 | {'first': True} | 2025-07-15 14:04:18 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2025-07-15 14:07:26 | 2025-07-15 14:07:36 | 10.34 | dict | {'1dgr_1': {('P50477', 'P50477'): 2.5}, '1nv3_2': {('P00636', 'P00636'): 24.0}, '1tth_1': {('P0A786', 'P0A7F3'): 16.0, ('P0A786', 'P0A786'): 21.5, ('P0A7F3', 'P0A7F3'): 20.0}, '4ekw_2': {('A8EVM5', 'A8EVM5'): 24.0}, '1bi9_2': {('Q63639', 'Q63639'): 12.0}, '1nlk_2': {('P15266', 'P15266'): 21.5}, '5f1...(truncated) | 80,848 | {'first': True} | 2025-07-15 14:07:26 | |
| ¶ | pypath.inputs.threedid.get_3did | 2025-07-15 14:07:36 | 2025-07-15 14:12:53 | 316.30 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/threedid.py", line 246, in get_3did
c = curl.Curl(urls.urls['3did_ddi']['url'], silent = False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 956, in __init__
self.process_file()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 1782, in process_file
self.extract_file()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 1813, in extract_file
self.extract()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 612, in extract
getattr(self, 'open_%s' % self.type)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 679, in open_gz
self.result = self.gzfile.read()
^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 301, in read
return self._buffer.read(size)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/_compression.py", line 118, in readall
while data := self.read(sys.maxsize):
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 507, in read
uncompress = self._decompressor.decompress(buf, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
zlib.error: Error -3 while decompressing data: invalid code lengths set
|
{'first': True} | 2025-07-15 14:07:36 | |||
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2025-07-15 14:12:53 | 2025-07-15 14:12:53 | 0.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 884, in test_input
value = fun(*_args, **_kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/inputs/threedid.py", line 44, in get_3did_ddi
c = curl.Curl(urls.urls['3did_ddi']['url'], silent = False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 956, in __init__
self.process_file()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 1782, in process_file
self.extract_file()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 1813, in extract_file
self.extract()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 612, in extract
getattr(self, 'open_%s' % self.type)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20250715-092402/pypath_git/pypath/share/curl.py", line 679, in open_gz
self.result = self.gzfile.read()
^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 301, in read
return self._buffer.read(size)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/_compression.py", line 118, in readall
while data := self.read(sys.maxsize):
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/gzip.py", line 507, in read
uncompress = self._decompressor.decompress(buf, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
zlib.error: Error -3 while decompressing data: invalid code lengths set
|
{'first': True} | 2025-07-15 14:12:53 | |||
| ¶ | pypath.inputs.topdb.topdb_annotations | 2025-07-15 14:12:53 | 2025-07-15 14:13:14 | 20.78 | dict | {} | 0 | {'first': True} | 2025-07-15 14:12:53 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2025-07-15 14:13:14 | 2025-07-15 14:13:14 | 0.00 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {'first': True} | 2025-07-15 14:13:14 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2025-07-15 14:13:14 | 2025-07-15 14:13:14 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;12601176;11983166', 'Calcium measurement;Patch clamp;Fusion protein-pull down assay;Fl...(truncated) | 359 | {'first': True} | 2025-07-15 14:13:14 | |
| ¶ | pypath.inputs.trip.trip_process | 2025-07-15 14:13:14 | 2025-07-15 14:13:14 | 0.00 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'HEK293', 'Rat vascular smooth muscle cell', 'Rat aortic vascular smooth muscle cell', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {'first': True} | 2025-07-15 14:13:14 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2025-07-15 14:13:14 | 2025-07-15 14:13:18 | 4.45 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {'first': True} | 2025-07-15 14:13:14 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2025-07-15 14:13:18 | 2025-07-15 14:13:18 | 0.01 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {'first': True} | 2025-07-15 14:13:18 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2025-07-15 14:13:18 | 2025-07-15 14:13:21 | 3.17 | list | [TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bak1', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bax', effect='Unknown', references=('22983126',)), TrrustInteraction(source_genesymbol='Aatf', target_genesymbol='Bbc3', ...(truncated) | 7,057 | {'first': True} | 2025-07-15 14:13:18 | |
| ¶ | pypath.inputs.twosides.twosides_interactions | 2025-07-15 14:13:21 | 2025-07-15 14:17:04 | 222.99 | list | [TwosidesInteraction(drug1_rxnorm='10355', drug1='Temazepam', drug2_rxnorm='136411', drug2='sildenafil', condition_meddra='10003239', condition='Arthralgia', prr='2.91667', pee_error='0.421275', mean_reporting_frequency='0.0448718'), TwosidesInteraction(drug1_rxnorm='1808', drug1='Bumetanide', drug2...(truncated) | 42,920,391 | {'first': True} | 2025-07-15 14:13:21 | |
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2025-07-15 14:17:04 | 2025-07-15 14:17:04 | 0.14 | 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='2024-12-11'), UnichemSource(number=2, label='DrugBank', name='drugbank', description='A database that com...(truncated) | 41 | {'first': True} | 2025-07-15 14:17:04 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2025-07-15 14:17:04 | 2025-07-15 14:17:04 | 0.01 | dict | {1: 'ChEMBL', 2: 'DrugBank', 3: 'PDBe', 4: 'Guide to Pharmacology', 5: 'PubChem: Drugs of the Future ', 6: 'KEGG Ligand', 7: 'ChEBI', 8: 'NIH Clinical Collection', 9: 'ZINC', 10: 'eMolecules', 12: 'Atlas', 14: 'FDA SRS', 15: 'SureChEMBL', 17: 'PharmGKB', 18: 'Human Metabolome Database', 20: 'Selleck...(truncated) | 41 | {'first': True} | 2025-07-15 14:17:04 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2025-07-15 14:17:04 | 2025-07-15 14:17:04 | 0.06 | set | {'Q6NUM3', 'A0A1B0GU55', 'B7Z2I1', 'A0AA34QVG5', 'Q8WW81', 'A6NKD7', 'A0A343E806', 'A0A087X1J2', 'A0A5C2GKT1', 'Q5QPE1', 'Q9HBE5', 'G8HT89', 'A0A343GRN3', 'M4WET6', 'A0A858LG45', 'O14794', 'Q9UFG1', 'A0A5C2FVH9', 'Q56P02', 'Q5Q1W2', 'J7F7B5', 'D3VVQ3', 'B2CB39', 'A0A6C0SGG7', 'H7C1G3', 'Q6NX49', 'H7...(truncated) | 205,205 | {'first': True} | 2025-07-15 14:17:04 | |
| ¶ | pypath.inputs.uniprot._protein_datasheet |
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot._swissprot_param |
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2025-07-15 14:17:05 | 2025-07-15 14:17:05 | 0.54 | list | [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ13', 'K7EN86'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZ66', 'K7EQ86'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZK0', 'A0A024QZP7'], ['A0A024Q...(truncated) | 72,358 | {'first': True} | 2025-07-15 14:17:05 | |
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.query_builder |
Not calling `pypath.inputs.uniprot.query_builder`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2025-07-15 14:17:05 | 2025-07-15 14:17:16 | 11.05 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M8', subfamily=None)}, 'A0AV02': {UniprotFamily(family='SLC12A transporter', subfamily=None)}, 'A0AV96': {UniprotFam...(truncated) | 14,485 | {'first': True} | 2025-07-15 14:17:05 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2025-07-15 14:17:16 | 2025-07-15 14:17:28 | 11.74 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Glycoprotein'), UniprotKeyword(keyword='Transmembrane'), UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='Iron'), Unip...(truncated) | 20,420 | {'first': True} | 2025-07-15 14:17:16 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations |
Not calling `pypath.inputs.uniprot.uniprot_locations`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2025-07-15 14:17:28 | 2025-07-15 14:17:28 | 0.08 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,837 | {'first': True} | 2025-07-15 14:17:28 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_query |
Not calling `pypath.inputs.uniprot.uniprot_query`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2025-07-15 14:17:28 | 2025-07-15 14:17:30 | 1.60 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'H8ZM71': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Pinus grandis', 'Grand fir', 'Abie...(truncated) | 558,858 | {'first': True} | 2025-07-15 14:17:28 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2025-07-15 14:17:30 | 2025-07-15 14:17:43 | 13.37 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Lymphocytes nor granulocytes', level='none'), UniprotTissue(ti...(truncated) | 10,169 | {'first': True} | 2025-07-15 14:17:30 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2025-07-15 14:17:44 | 2025-07-15 14:18:34 | 50.92 | dict | {'A0A087X1C5': {UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', ...(truncated) | 5,244 | {'first': True} | 2025-07-15 14:17:44 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db._cleanup | 2025-07-15 14:18:34 | 2025-07-15 14:18:34 | 0.00 | NoneType | None | 0 | {'first': True} | 2025-07-15 14:18:34 | |
| ¶ | pypath.inputs.uniprot_db._remove |
Not calling `pypath.inputs.uniprot_db._remove`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.all_swissprots | 2025-07-15 14:18:34 | 2025-07-15 14:18:34 | 0.01 | set | {'Q9HAB3', 'Q8TAU0', 'Q9UEW8', 'Q9BZL6', 'Q5RKV6', 'O95573', 'Q9HBE5', 'Q9BV19', 'Q96GR4', 'Q6X9E4', 'Q76B58', 'Q9UNA4', 'Q6ZW05', 'Q6NX49', 'Q9NZH5', 'O75164', 'Q8NH95', 'Q96KR6', 'Q8N972', 'Q8N815', 'Q14494', 'Q5T7M4', 'Q8WW12', 'Q9BSG0', 'Q8NGG7', 'Q3LI83', 'Q969J2', 'Q70J99', 'Q9C0C2', 'Q5QFB9',...(truncated) | 20,420 | {'first': True} | 2025-07-15 14:18:34 | |
| ¶ | pypath.inputs.uniprot_db.all_trembls | 2025-07-15 14:18:34 | 2025-07-15 14:19:41 | 66.37 | set | {'Q6NUM3', 'A0A1B0GU55', 'B7Z2I1', 'A0AA34QVG5', 'Q8WW81', 'A6NKD7', 'A0A343E806', 'A0A087X1J2', 'A0A5C2GKT1', 'Q5QPE1', 'G8HT89', 'A0A343GRN3', 'M4WET6', 'A0A858LG45', 'O14794', 'Q9UFG1', 'A0A5C2FVH9', 'Q56P02', 'Q5Q1W2', 'J7F7B5', 'D3VVQ3', 'B2CB39', 'A0A6C0SGG7', 'H7C1G3', 'H7C0F2', 'G0X8Q6', 'J3...(truncated) | 184,785 | {'first': True} | 2025-07-15 14:18:34 | |
| ¶ | pypath.inputs.uniprot_db.all_uniprots | 2025-07-15 14:19:41 | 2025-07-15 14:19:41 | 0.00 | set | {'Q6NUM3', 'A0A1B0GU55', 'B7Z2I1', 'A0AA34QVG5', 'Q8WW81', 'A6NKD7', 'A0A343E806', 'A0A087X1J2', 'A0A5C2GKT1', 'Q5QPE1', 'Q9HBE5', 'G8HT89', 'A0A343GRN3', 'M4WET6', 'A0A858LG45', 'O14794', 'Q9UFG1', 'A0A5C2FVH9', 'Q56P02', 'Q5Q1W2', 'J7F7B5', 'D3VVQ3', 'B2CB39', 'A0A6C0SGG7', 'H7C1G3', 'Q6NX49', 'H7...(truncated) | 205,205 | {'first': True} | 2025-07-15 14:19:41 | |
| ¶ | pypath.inputs.uniprot_db.get_db | 2025-07-15 14:19:41 | 2025-07-15 14:19:41 | 0.00 | set | {'Q6NUM3', 'A0A1B0GU55', 'B7Z2I1', 'A0AA34QVG5', 'Q8WW81', 'A6NKD7', 'A0A343E806', 'A0A087X1J2', 'A0A5C2GKT1', 'Q5QPE1', 'Q9HBE5', 'G8HT89', 'A0A343GRN3', 'M4WET6', 'A0A858LG45', 'O14794', 'Q9UFG1', 'A0A5C2FVH9', 'Q56P02', 'Q5Q1W2', 'J7F7B5', 'D3VVQ3', 'B2CB39', 'A0A6C0SGG7', 'H7C1G3', 'Q6NX49', 'H7...(truncated) | 205,205 | {'first': True} | 2025-07-15 14:19:41 | |
| ¶ | pypath.inputs.uniprot_db.init_db | 2025-07-15 14:19:41 | 2025-07-15 14:19:41 | 0.05 | NoneType | None | 0 | {'first': True} | 2025-07-15 14:19:41 | |
| ¶ | pypath.inputs.uniprot_db.is_swissprot |
Not calling `pypath.inputs.uniprot_db.is_swissprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_trembl |
Not calling `pypath.inputs.uniprot_db.is_trembl`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_db.is_uniprot |
Not calling `pypath.inputs.uniprot_db.is_uniprot`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.uniprot_idmapping.idtypes | 2025-07-15 14:19:41 | 2025-07-15 14:19:41 | 0.06 | set | {('PIR', 'UniProtKB'), ('UniProtKB_AC-ID', 'GuidetoPHARMACOLOGY'), ('Allergome', 'UniProtKB'), ('UniProtKB_AC-ID', 'STRING'), ('UniProtKB', 'GuidetoPHARMACOLOGY'), ('RefSeq_Protein', 'UniProtKB-Swiss-Prot'), ('UniProtKB-Swiss-Prot', 'Leproma'), ('WormBase_Protein', 'UniProtKB'), ('ZFIN', 'UniProtKB'...(truncated) | 481 | {'first': True} | 2025-07-15 14:19:41 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2025-07-15 14:19:41 | 2025-07-15 14:19:45 | 4.35 | list | [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) | 483 | {'first': True} | 2025-07-15 14:19:41 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2025-07-15 14:19:45 | 2025-07-15 14:19:46 | 0.14 | list | [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) | 495 | {'first': True} | 2025-07-15 14:19:45 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2025-07-15 14:19:46 | 2025-07-15 14:19:46 | 0.15 | dict | {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM')}, 'Q12864': {Zhong2015Ann...(truncated) | 466 | {'first': True} | 2025-07-15 14:19:46 |
The OmniPath Team • Saez Lab • 2025-07-15