Pypath inputs status report

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