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 2023-06-16 18:26:49 and 2023-06-16 21:26:37; pypath version: 0.15.4 (from git, installed by poetry; 7455e32 )

Modules collected: 169
Modules failed to import: 0
Functions collected: 568
Functions run without error: 357
Functions returned empty value: 22
Functions skipped due to lack of arguments: 165
Functions run with error: 46

Function Started Finished Elapsed (s) Result type Result repr Result size Error Change since last time Last succeeded
pypath.inputs.abs.abs_interactions 2023-06-16 18:26:51 2023-06-16 18:26:51 0.37 list [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) 650 {} 2023-06-16 18:26:51
pypath.inputs.acsn.acsn_interactions 2023-06-16 18:26:51 2023-06-16 18:26:51 0.51 list [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) 37,725 {} 2023-06-16 18:26:51
pypath.inputs.acsn.acsn_interactions_sif 2023-06-16 18:26:51 2023-06-16 18:26:52 0.36 list [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) 9,570 {} 2023-06-16 18:26:51
pypath.inputs.adhesome.adhesome_annotations 2023-06-16 18:26:52 2023-06-16 18:29:14 142.25 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 {} 2023-06-16 18:26:52
pypath.inputs.adhesome.adhesome_interactions 2023-06-16 18:29:14 2023-06-16 18:29:15 1.22 list [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) 6,542 {} 2023-06-16 18:29:14
pypath.inputs.almen2009.almen2009_annotations 2023-06-16 18:29:15 2023-06-16 18:29:17 1.96 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) 4,825 {} 2023-06-16 18:29:15
pypath.inputs.baccin2019.baccin2019_annotations 2023-06-16 18:29:17 2023-06-16 18:33:03 225.34 dict {'P01023': {Baccin2019Annotation(mainclass='ligand', subclass='other', location='secreted')}, 'Q07954': {Baccin2019Annotation(mainclass='receptor', subclass=None, location=None), Baccin2019Annotation(mainclass='receptor', subclass='growth_factor_receptor', location=None)}, 'P48960': {Baccin2019Annot...(truncated) 1,059 {} 2023-06-16 18:29:17
pypath.inputs.baccin2019.baccin2019_interactions 2023-06-16 18:33:03 2023-06-16 18:33:03 0.57 list [Baccin2019Interaction(ligand='P01023', receptor='Q07954', correct='Correct', ligand_location='secreted', ligand_category='other', resources={'Ramilowski2015', 'Baccin2019'}, references={'1702392', '12194978', '10652313'}), Baccin2019Interaction(ligand='P48960', receptor='P08174', correct='Correct',...(truncated) 1,720 {} 2023-06-16 18:33:03
pypath.inputs.biogps.biogps_datasets 2023-06-16 18:33:03 2023-06-16 18:33:03 0.00 list [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) 9 {} 2023-06-16 18:33:03
pypath.inputs.biogps.biogps_download 
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments.
 {} never
pypath.inputs.biogps.biogps_download_all 2023-06-16 18:33:03 2023-06-16 18:33:39 35.78 dict {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) 9 {} 2023-06-16 18:33:03
pypath.inputs.biogrid.biogrid_all_interactions 2023-06-16 18:33:40 2023-06-16 18:34:27 46.94 list [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855', experimental_system='Two-hybrid', experimental_system_type='physical', ltp=True, htp_score=None, multi_validated=True, tax_a='9606', tax_b='9606'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272', experimen...(truncated) 8,246 {} 2023-06-16 18:33:40
pypath.inputs.biogrid.biogrid_interactions 2023-06-16 18:34:27 2023-06-16 18:34:28 1.40 list [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) 7,004 {} 2023-06-16 18:34:27
pypath.inputs.biomart.biomart_homology 2023-06-16 18:34:28 2023-06-16 18:34:56 28.35 list [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) 178,164 {} 2023-06-16 18:34:28
pypath.inputs.biomart.biomart_microarray 
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments.
 {} never
pypath.inputs.biomart.biomart_microarray_types 2023-06-16 18:34:57 2023-06-16 18:34:57 0.22 list [{'description': None, 'vendor': 'PHALANX', 'type': 'OLIGO', 'format': 'EXPRESSION', 'array': 'OneArray', 'label': 'PHALANX OneArray'}, {'description': None, 'vendor': 'CODELINK', 'type': 'OLIGO', 'format': 'EXPRESSION', 'array': 'CODELINK', 'label': 'CODELINK CODELINK'}, {'vendor': 'ILLUMINA', 'des...(truncated) 35 {} 2023-06-16 18:34:57
pypath.inputs.biomart.biomart_query 
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments.
 {} never
pypath.inputs.biomodels._get_biomodels 2023-06-16 18:34:57 2023-06-16 18:34:57 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/biomodels.py", line 106, in _get_biomodels
    loginurl = urls.urls['biomodels']['login'] % t
KeyError: 'login'
{} 2023-06-12 18:37:15
pypath.inputs.biomodels.download_single_model 
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments.
 {} never
pypath.inputs.biomodels.get_biomodels 2023-06-16 18:34:57 2023-06-16 18:34:57 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/biomodels.py", line 165, in get_biomodels
    c0.perform()
pycurl.error: (3, '')
{} 2023-06-12 18:37:15
pypath.inputs.biomodels.get_biomodels_req 2023-06-16 18:34:57 2023-06-16 18:34:58 0.86 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/biomodels.py", line 198, in get_biomodels_req
    token = json.loads(r0.text)['token']
  File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{} 2023-06-12 18:37:15
pypath.inputs.biomodels.get_single_model 
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments.
 {} never
pypath.inputs.ca1.ca1_interactions 2023-06-16 18:34:58 2023-06-16 18:35:00 2.52 list [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) 1,788 {} 2023-06-16 18:34:58
pypath.inputs.cancercellmap.ccmap_interactions 2023-06-16 18:35:00 2023-06-16 18:35:02 1.81 list [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) 47,644 {} 2023-06-16 18:35:00
pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations 2023-06-16 18:35:02 2023-06-16 18:35:14 11.56 dict {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) 186 {} 2023-06-16 18:35:02
pypath.inputs.cancerdrugsdb.cancerdrugsdb_download 2023-06-16 18:35:14 2023-06-16 18:35:14 0.00 list [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) 297 {} 2023-06-16 18:35:14
pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions 2023-06-16 18:35:14 2023-06-16 18:35:14 0.02 list [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P51532', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) 2,268 {} 2023-06-16 18:35:14
pypath.inputs.cancersea.cancersea_annotations 2023-06-16 18:35:14 2023-06-16 18:35:16 2.35 dict {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Angiogenesis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) 1,247 {} 2023-06-16 18:35:14
pypath.inputs.cell.cell_supplementary 
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments.
 {} never
pypath.inputs.cellcall.cellcall_annotations 2023-06-16 18:35:16 2023-06-16 18:35:17 0.45 dict {'P52798': {CellcallAnnotation(role='ligand')}, 'P09619': {CellcallAnnotation(role='receptor')}, 'P01242': {CellcallAnnotation(role='ligand')}, 'P10912': {CellcallAnnotation(role='receptor')}, 'P35225': {CellcallAnnotation(role='ligand')}, 'Q14627': {CellcallAnnotation(role='receptor')}, 'P20827': {...(truncated) 460 {} 2023-06-16 18:35:16
pypath.inputs.cellcall.cellcall_download 2023-06-16 18:35:17 2023-06-16 18:35:17 0.04 list [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) 19,144 {} 2023-06-16 18:35:17
pypath.inputs.cellcall.cellcall_download_all 2023-06-16 18:35:17 2023-06-16 18:35:18 0.97 list [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) 38,645 {} 2023-06-16 18:35:17
pypath.inputs.cellcall.cellcall_interactions 2023-06-16 18:35:18 2023-06-16 18:35:18 0.11 list [CellcallInteraction(ligand_uniprot='P52798', receptor_uniprot='P09619', core=True), CellcallInteraction(ligand_uniprot='P01242', receptor_uniprot='P10912', core=True), CellcallInteraction(ligand_uniprot='P35225', receptor_uniprot='Q14627', core=True), CellcallInteraction(ligand_uniprot='P20827', re...(truncated) 797 {} 2023-06-16 18:35:18
pypath.inputs.cellcellinteractions.cellcellinteractions_annotations 2023-06-16 18:35:18 2023-06-16 18:35:19 0.75 dict {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor'), Cellcellinteractio...(truncated) 3,425 {} 2023-06-16 18:35:18
pypath.inputs.cellchatdb._cellchatdb_organism 2023-06-16 18:35:19 2023-06-16 18:35:19 0.00 int 9606 0 {} 2023-06-16 18:35:19
pypath.inputs.cellchatdb._cellchatdb_process_cofactors 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments.
 {} never
pypath.inputs.cellchatdb._cellchatdb_process_complexes 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments.
 {} never
pypath.inputs.cellchatdb.cellchatdb_annotations 2023-06-16 18:35:19 2023-06-16 18:35:27 8.15 dict {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P19883': {CellChatDBAnnotation(role='antagonist', pathway='ACTIVIN', cat...(truncated) 1,067 {} 2023-06-16 18:35:19
pypath.inputs.cellchatdb.cellchatdb_cofactors 2023-06-16 18:35:27 2023-06-16 18:35:32 5.33 dict {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O75610', 'P41271', 'Q9H772', 'Q9H2X0', 'P12645', 'Q13253', 'O00292', 'O60565'}, 'BMP inhibition receptor': {'Q13145'...(truncated) 31 {} 2023-06-16 18:35:27
pypath.inputs.cellchatdb.cellchatdb_complexes 2023-06-16 18:35:32 2023-06-16 18:35:39 6.33 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) 153 {} 2023-06-16 18:35:32
pypath.inputs.cellchatdb.cellchatdb_download 2023-06-16 18:35:39 2023-06-16 18:35:44 5.49 dict {'interaction': interaction_name ... rownames TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 TGFB1_ACVR1B_TGF...(truncated) 4 {} 2023-06-16 18:35:39
pypath.inputs.cellchatdb.cellchatdb_interactions 2023-06-16 18:35:44 2023-06-16 18:35:50 5.57 list [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) 11,113 {} 2023-06-16 18:35:44
pypath.inputs.cellinker._cellinker_interactions_raw 2023-06-16 18:35:50 2023-06-16 18:35:50 0.31 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2023-06-16 18:35:50
pypath.inputs.cellinker._cellinker_uniprots 
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments.
 {} never
pypath.inputs.cellinker.cellinker_annotations 2023-06-16 18:35:50 2023-06-16 18:35:50 0.18 dict {'P01298': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'P50391': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, 'P02751': {CellinkerAnnotation(role='ligand', location='ECM',...(truncated) 1,921 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_complex_annotations 2023-06-16 18:35:50 2023-06-16 18:35:50 0.05 dict {Complex: COMPLEX:P13612_P26010: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction')}, Complex: COMPLEX:P05106_P06756: {CellinkerAnnotation(role='receptor', location='Membrane', t...(truncated) 134 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_complexes 2023-06-16 18:35:50 2023-06-16 18:35:50 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 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_complexes_raw 2023-06-16 18:35:50 2023-06-16 18:35:50 0.00 list [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) 145 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_lr_interactions 2023-06-16 18:35:50 2023-06-16 18:35:50 0.05 set {CellinkerInteraction(ligand='P01298', receptor='P50391', ligand_location='Secreted', receptor_location='Membrane', resources='HPMR;Guide2Pharma', pmids='7493937;7592911;8643460;16807358', type='Secreted protein to receptor interaction'), CellinkerInteraction(ligand='P02751', receptor=Complex: COMPL...(truncated) 3,812 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_lr_interactions_raw 2023-06-16 18:35:50 2023-06-16 18:35:50 0.01 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_protein_annotations 2023-06-16 18:35:50 2023-06-16 18:35:50 0.06 dict {'P01298': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'P50391': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, 'P02751': {CellinkerAnnotation(role='ligand', location='ECM',...(truncated) 1,787 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_smol_interactions 2023-06-16 18:35:50 2023-06-16 18:35:51 0.13 set {CellinkerInteraction(ligand='73755067', receptor='Q9Y2T6', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='17765871;20136841;23396314', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5280360', receptor='P35408', ligand_location=None, receptor_lo...(truncated) 314 {} 2023-06-16 18:35:50
pypath.inputs.cellinker.cellinker_smol_interactions_raw 2023-06-16 18:35:51 2023-06-16 18:35:51 0.00 list [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) 341 {} 2023-06-16 18:35:51
pypath.inputs.cellinker.components_to_complex 
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_annotations 
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_get_entity 
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_hla 
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments.
 {} never
pypath.inputs.cellphonedb.cellphonedb_complex_annotations 2023-06-16 18:35:51 2023-06-16 18:35:51 0.24 dict {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) 359 {} 2023-06-16 18:35:51
pypath.inputs.cellphonedb.cellphonedb_complexes 2023-06-16 18:35:51 2023-06-16 18:35:51 0.01 dict {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) 359 {} 2023-06-16 18:35:51
pypath.inputs.cellphonedb.cellphonedb_interactions 2023-06-16 18:35:51 2023-06-16 18:35:51 0.55 list [CellphonedbInteraction(id_a=Complex 12oxoLeukotrieneB4_byPTGR1: COMPLEX:Q14914, id_b='Q15722', sources='CellPhoneDB', references='', interaction_type='ligand-receptor', type_a='ligand', type_b='receptor'), CellphonedbInteraction(id_a=Complex 12oxoLeukotrieneB4_byPTGR1: COMPLEX:Q14914, id_b='Q9NPC1'...(truncated) 2,915 {} 2023-06-16 18:35:51
pypath.inputs.cellphonedb.cellphonedb_ligands_receptors 2023-06-16 18:35:51 2023-06-16 18:35:51 0.03 tuple ({'P01160', 'P10092', 'P28906', 'O75888', Complex BMP9_BMP15: COMPLEX:O95972_Q9UK05, Complex integrin_a1b1_complex: COMPLEX:P05556_P56199, 'Q5T4F7', 'O94933', 'P15018', Complex AldosteroneCorticosterone_byCYP11B2: COMPLEX:P19099, 'Q9Y4D2', 'P01298', 'Q9Y5W5', 'P16410', 'P19440', 'P78509', 'P09341', ...(truncated) 2 {} 2023-06-16 18:35:51
pypath.inputs.cellphonedb.cellphonedb_protein_annotations 2023-06-16 18:35:51 2023-06-16 18:35:51 0.02 dict {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) 1,354 {} 2023-06-16 18:35:51
pypath.inputs.celltalkdb.celltalkdb_annotations 2023-06-16 18:35:51 2023-06-16 18:36:07 15.67 dict {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='9883722')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) 1,598 {} 2023-06-16 18:35:51
pypath.inputs.celltalkdb.celltalkdb_download 2023-06-16 18:36:07 2023-06-16 18:36:07 0.00 list [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) 3,398 {} 2023-06-16 18:36:07
pypath.inputs.celltalkdb.celltalkdb_interactions 2023-06-16 18:36:07 2023-06-16 18:36:07 0.01 list [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) 3,398 {} 2023-06-16 18:36:07
pypath.inputs.celltypist.celltypist_annotations 2023-06-16 18:36:07 2023-06-16 18:36:07 0.26 dict {'P11836': {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) 459 {} 2023-06-16 18:36:07
pypath.inputs.chembl.chembl_activities 
Not calling `pypath.inputs.chembl.chembl_activities`, not enough arguments.
 {} never
pypath.inputs.chembl.chembl_documents 2023-06-16 18:36:07 2023-06-16 18:37:28 80.36 dict {'CHEMBL1139451': 14695813, 'CHEMBL1148466': 14695814, 'CHEMBL1139452': 14695824, 'CHEMBL1139453': 14695825, 'CHEMBL1139454': 14695826, 'CHEMBL1139455': 14695827, 'CHEMBL1139456': 14695815, 'CHEMBL1139457': 14695828, 'CHEMBL1139458': 14695816, 'CHEMBL1148467': 14695833, 'CHEMBL1139459': 14695834, 'C...(truncated) 80,293 {} 2023-06-16 18:36:07
pypath.inputs.chembl.chembl_drug_indications 2023-06-16 18:37:28 2023-06-16 18:38:33 64.83 list [ChemblIndication(efo_id='EFO:0000404', efo_term='diffuse scleroderma', max_phase=2.0, mesh_heading='Scleroderma, Diffuse', mesh_id='D045743', molecule_chembl='CHEMBL1201823'), ChemblIndication(efo_id='EFO:0000685', efo_term='rheumatoid arthritis', max_phase=4.0, mesh_heading='Arthritis, Rheumatoid'...(truncated) 51,582 {} 2023-06-16 18:37:28
pypath.inputs.chembl.chembl_mechanisms 2023-06-16 18:38:33 2023-06-16 18:38:43 10.19 list [ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_action='Carbonic anhydrase VII inhibitor', chembl='CHEMBL19', target_chembl='CHEMBL2326'), ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_acti...(truncated) 7,098 {} 2023-06-16 18:38:33
pypath.inputs.chembl.chembl_targets 2023-06-16 18:38:43 2023-06-16 18:40:48 124.79 list [ChemblTarget(accession='O43451', target_chembl_id='CHEMBL2074'), ChemblTarget(accession='O60706', target_chembl_id='CHEMBL1971'), ChemblTarget(accession='O76074', target_chembl_id='CHEMBL1827'), ChemblTarget(accession='O95180', target_chembl_id='CHEMBL1859'), ChemblTarget(accession='O96760', target...(truncated) 15,398 {} 2023-06-16 18:38:43
pypath.inputs.clinvar.clinvar_citations 2023-06-16 18:40:48 2023-06-16 18:41:15 27.74 list [Citation(allele='237814', variation_id='236258', nsv='', citation_source='PubMed', citation_id='27094817'), Citation(allele='852233', variation_id='860301', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='516443', variation_id='534086', nsv='', citation_source='PubMed', ...(truncated) 2,715,961 {} 2023-06-16 18:40:48
pypath.inputs.clinvar.clinvar_raw 2023-06-16 18:41:19 2023-06-16 18:43:01 102.13 list [Variant(allele='2295783', type='single nucleotide variant', variant='NM_001387850.1(FILIP1L):c.2158G>A (p.Asp720Asn)', entrez='11259', genesymbol='FILIP1L', clinical_significance='Uncertain significance', review_status='criteria provided, single submitter', rs='-1', phenotype_ids=('MeSH:D030342', '...(truncated) 4,464,832 {} 2023-06-16 18:41:19
pypath.inputs.collectri.collectri_interactions 2023-06-16 18:52:41 2023-06-16 18:52:43 2.32 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) 64,969 {} 2023-06-16 18:52:41
pypath.inputs.collectri.collectri_raw 2023-06-16 18:52:43 2023-06-16 18:52:44 0.09 list [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) 43,416 {} 2023-06-16 18:52:43
pypath.inputs.compleat.compleat_complexes 2023-06-16 18:52:44 2023-06-16 18:52:46 2.63 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) 9,692 {'size': -1} 2023-06-16 18:52:44
pypath.inputs.compleat.compleat_raw 2023-06-16 18:52:46 2023-06-16 18:52:46 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 {} 2023-06-16 18:52:46
pypath.inputs.complexportal.complexportal_complexes 2023-06-16 18:52:46 2023-06-16 18:54:02 75.41 dict {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:Q86XT2_Q99816_Q9NZ09_Q9UK41': Complex ESCRT-I complex, VPS37D-UBAP1 variant: COMPLEX:Q86XT2_Q99816_Q9NZ09_Q9UK41, 'COMPLEX:Q86XE3_Q8NE86_Q9BPX6_Q9H4I9': Comple...(truncated) 1,620 {} 2023-06-16 18:52:46
pypath.inputs.comppi.comppi_interaction_locations 2023-06-16 18:54:02 2023-06-16 18:54:17 15.05 list [ComppiInteraction(id_a='Q8TES7', id_b='O75478', 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='Q8TES7', id_b='O75478', loc_a=(ComppiLocation(location='cytosol', sc...(truncated) 589,097 {} 2023-06-16 18:54:02
pypath.inputs.comppi.comppi_locations 2023-06-16 18:54:17 2023-06-16 18:54:33 16.46 dict {'Q8TES7': {ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='membrane', score=0.96), ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation...(truncated) 18,254 {} 2023-06-16 18:54:17
pypath.inputs.connectomedb.connectomedb_annotations 2023-06-16 18:54:33 2023-06-16 18:54:34 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 {} 2023-06-16 18:54:33
pypath.inputs.connectomedb.connectomedb_interactions 2023-06-16 18:54:34 2023-06-16 18:54:34 0.02 list [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) 2,293 {} 2023-06-16 18:54:34
pypath.inputs.corum.corum_complexes 2023-06-16 18:54:34 2023-06-16 18:54:34 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 {} 2023-06-16 18:54:34
pypath.inputs.cosmic.cancer_gene_census_annotations 2023-06-16 18:54:34 2023-06-16 18:54:37 2.24 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cosmic.py", line 137, in cancer_gene_census_annotations
    data = csv.DictReader(c.fileobj, delimiter = ',')
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 18:55:36
pypath.inputs.cpad.cpad_annotations 2023-06-16 18:54:37 2023-06-16 18:54:43 6.55 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')}, 'MIMAT0000431'...(truncated) 1,037 {'size': -1} 2023-06-16 18:54:37
pypath.inputs.cpad.cpad_pathway_cancer 2023-06-16 18:54:43 2023-06-16 18:54:43 0.09 tuple ({'Glioma': {CpadPathwayCancer(pathway='ERK signaling pathway', cancer='Glioma', pathway_category='MAPK signaling pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='induce apoptosis'), CpadPathwayCancer(pathway='STAT3 signaling pathway', cancer='Glioma', pathway_category='Jak-STAT si...(truncated) 2 {} 2023-06-16 18:54:43
pypath.inputs.cpad.get_cpad 2023-06-16 18:54:43 2023-06-16 18:54:43 0.04 list [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) 4,709 {} 2023-06-16 18:54:43
pypath.inputs.cpdb.cpdb_interactions 2023-06-16 18:54:43 2023-06-16 18:54:50 6.37 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 531,371 {} 2023-06-16 18:54:43
pypath.inputs.cpdb.cpdb_interactions_ltp 2023-06-16 18:54:50 2023-06-16 18:54:53 2.95 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 482,222 {} 2023-06-16 18:54:50
pypath.inputs.credentials.credentials 
Not calling `pypath.inputs.credentials.credentials`, not enough arguments.
 {} never
pypath.inputs.cspa.cspa_annotations 2023-06-16 18:54:54 2023-06-16 18:54:55 0.86 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) 1,446 {} 2023-06-16 18:54:54
pypath.inputs.cspa.cspa_cell_type_annotations 2023-06-16 18:54:55 2023-06-16 18:54:55 0.81 dict {'A1A5B4': {CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='ZL55', value=18.74705), CspaCellType(cell_type='MedB1', valu...(truncated) 1,407 {} 2023-06-16 18:54:55
pypath.inputs.cspa.cspa_cell_types 2023-06-16 18:54:55 2023-06-16 18:54:56 0.71 dict {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'P0DN37': None, 'A0A0B4J2A2': 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 {} 2023-06-16 18:54:55
pypath.inputs.ctdbase._ctdbase_download 
Not calling `pypath.inputs.ctdbase._ctdbase_download`, not enough arguments.
 {} never
pypath.inputs.ctdbase._map_keys 
Not calling `pypath.inputs.ctdbase._map_keys`, not enough arguments.
 {} never
pypath.inputs.ctdbase._modify_dict 
Not calling `pypath.inputs.ctdbase._modify_dict`, not enough arguments.
 {} never
pypath.inputs.ctdbase.ctdbase_relations 
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments.
 {} never
pypath.inputs.ctdbase.ctdbase_vocabulary 
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments.
 {} never
pypath.inputs.cytosig.cytosig_annotations 2023-06-16 18:54:56 2023-06-16 18:54:58 2.31 dict {'Q9NPC4': {CytosigAnnotation(cytokine='P01137', score=-0.0123877715497178, cytokine_genesymbol='TGFB1', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P23560', score=0.0, cytokine_genesymbol='BDNF', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P14210', score=-0.033923853042669...(truncated) 4,889 {} 2023-06-16 18:54:56
pypath.inputs.cytosig.cytosig_df 2023-06-16 18:54:59 2023-06-16 18:54:59 0.04 DataFrame Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) 4,881 {} 2023-06-16 18:54:59
pypath.inputs.dbptm.dbptm_enzyme_substrate 2023-06-16 18:54:59 2023-06-16 18:55:01 1.94 list [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) 223,135 {} 2023-06-16 18:54:59
pypath.inputs.dbptm.dbptm_enzyme_substrate_old 2023-06-16 18:55:01 2023-06-16 18:55:03 1.77 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/dbptm.py", line 102, in dbptm_enzyme_substrate_old
    for k, data in iteritems(extra):
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/future/utils/__init__.py", line 314, in iteritems
    func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
{} 2023-06-12 18:56:01
pypath.inputs.dbptm.dbptm_interactions 2023-06-16 18:55:03 2023-06-16 18:55:05 1.78 list [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) 2,071 {} 2023-06-16 18:55:03
pypath.inputs.deathdomain.deathdomain_interactions 2023-06-16 18:55:05 2023-06-16 18:55:06 0.92 list [] 0 {} 2023-06-16 18:55:05
pypath.inputs.deathdomain.deathdomain_interactions_rescued 2023-06-16 18:55:06 2023-06-16 18:55:06 0.18 list [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) 184 {} 2023-06-16 18:55:06
pypath.inputs.depod.depod_enzyme_substrate 2023-06-16 18:55:06 2023-06-16 18:55:06 0.07 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 {} 2023-06-16 18:55:06
pypath.inputs.depod.depod_interactions 2023-06-16 18:55:06 2023-06-16 18:55:06 0.01 list [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) 832 {} 2023-06-16 18:55:06
pypath.inputs.dgidb.dgidb_annotations 2023-06-16 18:55:06 2023-06-16 18:55:08 2.14 dict {'Q9BXS1': {DgidbAnnotation(category='ENZYME')}, 'Q9BZH6': {DgidbAnnotation(category='TRANSCRIPTION FACTOR')}, 'Q96Q89': {DgidbAnnotation(category='ENZYME')}, 'Q99470': {DgidbAnnotation(category='DRUGGABLE GENOME')}, 'Q9H211': {DgidbAnnotation(category='KINASE')}, 'O95069': {DgidbAnnotation(category...(truncated) 10,494 {} 2023-06-16 18:55:06
pypath.inputs.dgidb.dgidb_interactions 2023-06-16 18:55:08 2023-06-16 18:55:14 5.29 list [DgidbInteraction(genesymbol='ABL1', entrez='25', resource='GuideToPharmacology', type='inhibitor', drug_name='ZAK INHIBITOR 6P', drug_chembl=None, score=None, pmid=None), DgidbInteraction(genesymbol='HSP90AB1', entrez='3326', resource='DTC', type=None, drug_name='RADANAMYCIN', drug_chembl='chembl:C...(truncated) 85,022 {} 2023-06-16 18:55:08
pypath.inputs.dgidb.get_dgidb_old 2023-06-16 18:55:14 2023-06-16 18:56:18 64.36 set {'Q5W0U4', 'Q96RI1', 'Q5GFL6', 'P01298', 'P35568', 'Q9BXM7', 'P31785', 'Q9H4G1', 'P16591', 'Q9NQX3', 'Q6VMQ6', 'O60814', 'Q99715', 'P04156', 'P01229', 'P11166', 'Q9Y267', 'O00574', 'P49720', 'O15391', 'P26006', 'Q4JDL3', 'P00374', 'P59541', 'Q8NGA4', 'Q9NP62', 'Q6R327', 'Q9UNE7', 'P02746', 'P23219',...(truncated) 5,907 {} 2023-06-16 18:55:14
pypath.inputs.dip.dip_interactions 2023-06-16 18:56:18 2023-06-16 18:56:18 0.26 list [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) 2,283 {} 2023-06-16 18:56:18
pypath.inputs.dip.dip_login 
Not calling `pypath.inputs.dip.dip_login`, not enough arguments.
 {} never
pypath.inputs.disgenet.wrapper 
Not calling `pypath.inputs.disgenet.wrapper`, not enough arguments.
 {} never
pypath.inputs.disgenet.wrapper 
Not calling `pypath.inputs.disgenet.wrapper`, not enough arguments.
 {} never
pypath.inputs.disgenet.wrapper 
Not calling `pypath.inputs.disgenet.wrapper`, not enough arguments.
 {} never
pypath.inputs.domino.domino_ddi 2023-06-16 18:56:18 2023-06-16 18:56:23 4.48 list [<pypath.internals.intera.DomainDomain object at 0x7f8ee4687ee0>, <pypath.internals.intera.DomainDomain object at 0x7f8ee46861a0>, <pypath.internals.intera.DomainDomain object at 0x7f8ee4686200>, <pypath.internals.intera.DomainDomain object at 0x7f8ee4687580>, <pypath.internals.intera.DomainDomain o...(truncated) 1,294 {} 2023-06-16 18:56:18
pypath.inputs.domino.domino_enzsub 2023-06-16 18:56:23 2023-06-16 18:56:24 0.97 dict {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f8ee46872b0>, <pypath.internals.intera.DomainDomain object at 0x7f8ee4686aa0>, <pypath.internals.intera.DomainDomain object at 0x7f8ee4686b30>, <pypath.internals.intera.DomainDomain object at 0x7f8ee46854b0>, <pypath.internals.intera.Domain...(truncated) 2 {} 2023-06-16 18:56:23
pypath.inputs.domino.domino_interactions 2023-06-16 18:56:24 2023-06-16 18:56:24 0.39 list [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) 6,687 {} 2023-06-16 18:56:24
pypath.inputs.domino.get_domino 2023-06-16 18:56:24 2023-06-16 18:56:25 0.37 list [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) 14,539 {} 2023-06-16 18:56:24
pypath.inputs.dorothea._process_resources 
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments.
 {} never
pypath.inputs.dorothea.dorothea_full_raw 2023-06-16 18:56:25 2023-06-16 18:56:33 8.40 DataFrame tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) 1,019,220 {} 2023-06-16 18:56:25
pypath.inputs.dorothea.dorothea_interactions 2023-06-16 18:56:33 2023-06-16 18:56:47 13.94 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2023-06-16 18:56:33
pypath.inputs.dorothea.dorothea_old_csv 2023-06-16 18:56:47 2023-06-16 18:56:48 0.55 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2023-06-12 18:58:05
pypath.inputs.dorothea.dorothea_old_csv 2023-06-16 18:56:48 2023-06-16 18:56:48 0.27 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2023-06-12 18:58:05
pypath.inputs.dorothea.dorothea_rda_raw 2023-06-16 18:56:48 2023-06-16 18:56:50 1.80 DataFrame tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) 454,504 {} 2023-06-16 18:56:48
pypath.inputs.dorothea.get_dorothea_old 2023-06-16 18:56:50 2023-06-16 18:56:50 0.34 list [['AHR', 'CYP1A1', '0', 'A', True, False, True, False, 'HTRIdb,trrust_signed', '', 'hocomoco_v11', '', 'HTRIdb,trrust_signed,hocomoco_v11'], ['AHR', 'CYP1A2', '0', 'A', True, False, False, False, 'HTRIdb,trrust_signed', '', '', '', 'HTRIdb,trrust_signed'], ['AHR', 'CYP1B1', '0', 'A', True, False, Tr...(truncated) 14,260 {} 2023-06-16 18:56:50
pypath.inputs.dorothea.dorothea_rda_raw 2023-06-16 18:56:50 2023-06-16 18:56:51 1.22 DataFrame tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) 454,504 {} 2023-06-16 18:56:50
pypath.inputs.dorothea.dorothea_interactions 2023-06-16 18:56:51 2023-06-16 18:57:06 14.20 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2023-06-16 18:56:51
pypath.inputs.dorothea.dorothea_old_csv 2023-06-16 18:57:06 2023-06-16 18:57:06 0.10 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2023-06-12 18:58:05
pypath.inputs.drugbank._drugbank_credentials 2023-06-16 18:57:06 2023-06-16 18:57:06 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/drugbank.py", line 55, in _drugbank_credentials
    return credentials.credentials(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/credentials.py", line 120, in credentials
    raise RuntimeError(msg)
RuntimeError: Failed to obtain credentials for resource `DrugBank`
{} 2023-06-12 18:58:05
pypath.inputs.drugbank._drugbank_download 
Not calling `pypath.inputs.drugbank._drugbank_download`, not enough arguments.
 {} never
pypath.inputs.drugbank.drugbank_annotations 2023-06-16 18:57:06 2023-06-16 18:57:06 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/drugbank.py", line 358, in drugbank_annotations
    drugs = drugbank_drugs(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/drugbank.py", line 309, in drugbank_drugs
    for dbid, struct in raw['structure'].items():
KeyError: 'structure'
{} 2023-06-12 18:58:05
pypath.inputs.drugbank.drugbank_drugs 2023-06-16 18:57:06 2023-06-16 18:57:06 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/drugbank.py", line 309, in drugbank_drugs
    for dbid, struct in raw['structure'].items():
KeyError: 'structure'
{} 2023-06-12 18:58:05
pypath.inputs.drugbank.drugbank_interactions 2023-06-16 18:57:06 2023-06-16 18:57:06 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/drugbank.py", line 204, in drugbank_interactions
    for d in drugbank_drugs(user = user, passwd = passwd)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/drugbank.py", line 309, in drugbank_drugs
    for dbid, struct in raw['structure'].items():
KeyError: 'structure'
{} 2023-06-12 18:58:05
pypath.inputs.drugbank.drugbank_mapping 
Not calling `pypath.inputs.drugbank.drugbank_mapping`, not enough arguments.
 {} never
pypath.inputs.drugbank.drugbank_raw_interactions 2023-06-16 18:57:06 2023-06-16 18:57:06 0.00 list [] 0 {} 2023-06-16 18:57:06
pypath.inputs.drugcentral.drugcentral_drugs 2023-06-16 18:57:06 2023-06-16 18:57:07 1.11 list [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) 4,099 {} 2023-06-16 18:57:06
pypath.inputs.drugcentral.drugcentral_interactions 2023-06-16 18:57:07 2023-06-16 18:57:08 1.22 list [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) 23,115 {} 2023-06-16 18:57:07
pypath.inputs.drugcentral.drugcentral_mapping 
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments.
 {} never
pypath.inputs.ebi.ebi_rest 
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments.
 {} never
pypath.inputs.elm.elm_classes 2023-06-16 18:57:08 2023-06-16 18:57:26 18.42 dict {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) 321 {} 2023-06-16 18:57:08
pypath.inputs.elm.elm_domains 2023-06-16 18:57:26 2023-06-16 18:57:27 0.57 dict {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) 604 {} 2023-06-16 18:57:26
pypath.inputs.elm.elm_instances 2023-06-16 18:57:27 2023-06-16 18:59:25 118.11 list [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) 3,977 {} 2023-06-16 18:57:27
pypath.inputs.elm.elm_interactions 2023-06-16 18:59:25 2023-06-16 19:00:38 73.08 list [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) 2,442 {} 2023-06-16 18:59:25
pypath.inputs.embopress.embopress_supplementary 
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments.
 {} never
pypath.inputs.embrace._embrace_id_translation 
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments.
 {} never
pypath.inputs.embrace.embrace_annotations 2023-06-16 19:00:38 2023-06-16 19:00:38 0.07 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 163, in embrace_annotations
    for rec in embrace_translated(organism = organism):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 87, in embrace_translated
    raw = embrace_raw()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:02:19
pypath.inputs.embrace.embrace_interactions 2023-06-16 19:00:38 2023-06-16 19:00:38 0.08 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 129, in embrace_interactions
    for rec in embrace_translated(organism = organism)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 87, in embrace_translated
    raw = embrace_raw()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:02:19
pypath.inputs.embrace.embrace_raw 2023-06-16 19:00:38 2023-06-16 19:00:38 0.07 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:02:19
pypath.inputs.embrace.embrace_translated 2023-06-16 19:00:38 2023-06-16 19:00:39 0.06 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 87, in embrace_translated
    raw = embrace_raw()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embrace.py", line 42, in embrace_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:02:20
pypath.inputs.encode.encode_tf_mirna_interactions 2023-06-16 19:00:39 2023-06-16 19:00:39 0.46 list [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) 1,237 {} 2023-06-16 19:00:39
pypath.inputs.ensembl.ensembl_organisms 2023-06-16 19:00:39 2023-06-16 19:00:40 0.59 list [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) 314 {} 2023-06-16 19:00:39
pypath.inputs.exocarta._get_exocarta_vesiclepedia 2023-06-16 19:00:40 2023-06-16 19:00:49 8.97 list [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) 32,085 {} 2023-06-16 19:00:40
pypath.inputs.exocarta.get_exocarta 2023-06-16 19:00:49 2023-06-16 19:00:49 0.03 list [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) 32,085 {} 2023-06-16 19:00:49
pypath.inputs.exocarta.get_vesiclepedia 2023-06-16 19:00:49 2023-06-16 19:01:42 53.65 list [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) 290,197 {} 2023-06-16 19:00:49
pypath.inputs.genecards.genecards_datasheet 
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments.
 {} never
pypath.inputs.genecards.genecards_soup 
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments.
 {} never
pypath.inputs.genecards.genecards_summaries 
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments.
 {} never
pypath.inputs.go.get_go_desc 
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments.
 {} never
pypath.inputs.go.get_go_quick 2023-06-16 19:01:42 2023-06-16 19:03:24 101.53 dict {'terms': {'C': defaultdict(<class 'set'>, {'A0A023I7F4': {'GO:0005743', 'GO:0070469', 'GO:0045275', 'GO:0016020', 'GO:0005739'}, 'A0A023I7H2': {'GO:0016020', 'GO:0005739', 'GO:0005743', 'GO:0070469'}, 'A0A023I7H5': {'GO:0016020', 'GO:0005743', 'GO:0045263', 'GO:0005739'}, 'A0A023I7J4': {'GO:0016020...(truncated) 2 {'fixed': True} 2023-06-16 19:01:42
pypath.inputs.go.get_goslim 2023-06-16 19:03:24 2023-06-16 19:03:25 0.88 list ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) 141 {} 2023-06-16 19:03:24
pypath.inputs.go.go_ancestors_quickgo 2023-06-16 19:03:25 2023-06-16 19:14:57 692.79 dict {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016014': {('GO:0098797', 'is_a'), ...(truncated) 3 {} 2023-06-16 19:03:25
pypath.inputs.go.go_ancestors_goose 2023-06-16 19:14:58 2023-06-16 19:14:58 0.05 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 211, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2023-06-12 19:18:26
pypath.inputs.go.go_ancestors_quickgo 2023-06-16 19:14:58 2023-06-16 19:15:02 4.39 dict {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016011': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016014': {('GO:0098797', 'is_a'), ...(truncated) 3 {} 2023-06-16 19:14:58
pypath.inputs.go.go_annotations_goa 2023-06-16 19:15:02 2023-06-16 19:15:07 4.68 dict {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005634', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005615', 'G...(truncated) 3 {} 2023-06-16 19:15:02
pypath.inputs.go.go_annotations_all 2023-06-16 19:15:07 2023-06-16 19:15:13 5.83 dict {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0003723', reference='GO_REF:0000043', evidence_code='IEA', with_or_from='UniProtKB-KW:KW-0694', aspect='F', db_object_name='Diphosphoinositol polyphosphate phosphohydrola...(truncated) 19,625 {} 2023-06-16 19:15:07
pypath.inputs.go.go_annotations_goa 2023-06-16 19:15:15 2023-06-16 19:15:16 1.07 dict {'C': {'A0A024RBG1': {'GO:0005829', 'GO:0005634', 'GO:0005737'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005615', 'GO:0005886', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005615', 'G...(truncated) 3 {} 2023-06-16 19:15:15
pypath.inputs.go.go_annotations_goose 2023-06-16 19:15:16 2023-06-16 19:15:16 0.04 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 858, in go_annotations_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2023-06-12 19:18:48
pypath.inputs.go.go_annotations_solr 2023-06-16 19:15:16 2023-06-16 19:15:17 1.45 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 744, in go_annotations_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:18:51
pypath.inputs.go.go_annotations_uniprot 2023-06-16 19:15:17 2023-06-16 19:15:18 0.35 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 67, in go_annotations_uniprot
    for x in [x.split('\t') for x in data.split('\n')]
AttributeError: 'NoneType' object has no attribute 'split'
{} 2023-06-12 19:18:52
pypath.inputs.go.go_descendants_quickgo 2023-06-16 19:15:18 2023-06-16 19:15:22 4.18 dict {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) 3 {} 2023-06-16 19:15:18
pypath.inputs.go.go_descendants_goose 2023-06-16 19:15:22 2023-06-16 19:15:22 0.03 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 289, in go_descendants_goose
    anc = go_ancestors_goose(aspects = aspects)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 211, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2023-06-12 19:18:57
pypath.inputs.go.go_descendants_quickgo 2023-06-16 19:15:22 2023-06-16 19:15:26 4.37 dict {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016009', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016011', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) 3 {} 2023-06-16 19:15:22
pypath.inputs.go.go_descendants_to_ancestors 
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments.
 {} never
pypath.inputs.go.go_terms_quickgo 2023-06-16 19:15:26 2023-06-16 19:15:30 3.34 dict {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) 3 {} 2023-06-16 19:15:26
pypath.inputs.go.go_terms_goose 2023-06-16 19:15:30 2023-06-16 19:15:30 0.03 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 584, in go_terms_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2023-06-12 19:19:08
pypath.inputs.go.go_terms_quickgo 2023-06-16 19:15:30 2023-06-16 19:15:33 3.55 dict {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) 3 {} 2023-06-16 19:15:30
pypath.inputs.go.go_terms_solr 2023-06-16 19:15:33 2023-06-16 19:15:34 0.60 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/go.py", line 442, in go_terms_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:19:15
pypath.inputs.gpcrdb.gpcrdb_annotations 2023-06-16 19:15:34 2023-06-16 19:15:34 0.29 dict {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) 424 {} 2023-06-16 19:15:34
pypath.inputs.graphviz.graphviz_attrs 2023-06-16 19:15:34 2023-06-16 19:15:35 1.29 tuple ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) 3 {} 2023-06-16 19:15:34
pypath.inputs.guide2pharma.guide2pharma_complexes 
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments.
 {} never
pypath.inputs.guide2pharma.guide2pharma_download 2023-06-16 19:15:35 2023-06-16 19:15:38 2.91 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 {} 2023-06-16 19:15:35
pypath.inputs.guide2pharma.guide2pharma_interactions 
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments.
 {} never
pypath.inputs.havugimana.get_havugimana 2023-06-16 19:15:38 2023-06-16 19:15:38 0.07 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/havugimana.py", line 44, in get_havugimana
    path = cell_input.cell_supplementary(supp_url, article_url)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:19:20
pypath.inputs.havugimana.havugimana_complexes 2023-06-16 19:15:38 2023-06-16 19:15:39 0.06 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/havugimana.py", line 59, in havugimana_complexes
    for rec in get_havugimana():
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/havugimana.py", line 44, in get_havugimana
    path = cell_input.cell_supplementary(supp_url, article_url)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:19:20
pypath.inputs.hgnc.hgnc_genegroups 2023-06-16 19:15:39 2023-06-16 19:15:42 3.24 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) 15,145 {'size': 1} 2023-06-16 19:15:39
pypath.inputs.hippie.hippie_interactions 2023-06-16 19:15:42 2023-06-16 19:16:02 20.02 list [HippieInteraction(id_a='P02751', id_b='P02751', score=0.9, methods=None, references=('17914904', '18042364', '18160478', '19826086', '19931242', '20541508', '23750785'), sources=None, organisms=None), HippieInteraction(id_a='Q8WVE6', id_b='O60637', score=0.82, methods=None, references=('28514442', ...(truncated) 102,282 {} 2023-06-16 19:15:42
pypath.inputs.homologene.get_homologene 2023-06-16 19:16:02 2023-06-16 19:16:02 0.04 list ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) 275,237 {} 2023-06-16 19:16:02
pypath.inputs.homologene.homologene_dict 
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments.
 {} never
pypath.inputs.homologene.homologene_uniprot_dict 
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments.
 {} never
pypath.inputs.hpmr.get_hpmr 2023-06-16 19:16:02 2023-06-16 19:16:02 0.00 dict {'interactions': [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462...(truncated) 3 {} 2023-06-16 19:16:02
pypath.inputs.hpmr.hpmr_annotations 2023-06-16 19:16:02 2023-06-16 19:16:02 0.00 dict {'P26992': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='CICYTR (Cytokine Type 1 receptors)', subsubclass=None)}, 'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P42...(truncated) 1,141 {} 2023-06-16 19:16:02
pypath.inputs.hpmr.hpmr_complexes 2023-06-16 19:16:02 2023-06-16 19:16:02 0.00 dict {} 0 {} 2023-06-16 19:16:02
pypath.inputs.hpmr.hpmr_interactions 2023-06-16 19:16:02 2023-06-16 19:16:02 0.00 list [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462', 'Ligand', 'P26...(truncated) 619 {} 2023-06-16 19:16:02
pypath.inputs.hpo.hpo_annotations 2023-06-16 19:16:02 2023-06-16 19:16:05 2.91 defaultdict defaultdict(<class 'set'>, {'P11245': {HPOAnnotations(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939'), HPOAnnotations(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007')}, 'P49588': {HPOAnnotations(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0008...(truncated) 4,858 {} 2023-06-16 19:16:02
pypath.inputs.hpo.hpo_diseases 2023-06-16 19:16:05 2023-06-16 19:16:08 2.38 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='ORPHA:96147', name='Kleefstra syndrome due to 9q34 microdele...(truncated) 10,644 {} 2023-06-16 19:16:05
pypath.inputs.hpo.hpo_ontology 2023-06-16 19:16:08 2023-06-16 19:16:10 1.74 dict {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) 5 {} 2023-06-16 19:16:08
pypath.inputs.hpo.hpo_terms 2023-06-16 19:16:10 2023-06-16 19:16:10 0.56 dict {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) 17,610 {} 2023-06-16 19:16:10
pypath.inputs.hprd.get_hprd 2023-06-16 19:16:10 2023-06-16 19:16:14 3.63 list [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) 86,981 {} 2023-06-16 19:16:10
pypath.inputs.hprd.hprd_enzyme_substrate 2023-06-16 19:16:14 2023-06-16 19:16:16 1.85 list [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) 4,671 {} 2023-06-16 19:16:14
pypath.inputs.hprd.hprd_interactions 2023-06-16 19:16:16 2023-06-16 19:16:18 1.51 list [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) 4,671 {} 2023-06-16 19:16:16
pypath.inputs.hprd.hprd_interactions_htp 2023-06-16 19:16:18 2023-06-16 19:16:19 1.39 list [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) 39,241 {} 2023-06-16 19:16:18
pypath.inputs.htri.htri_interactions 2023-06-16 19:16:19 2023-06-16 19:16:22 2.84 list [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) 18,630 {} 2023-06-16 19:16:19
pypath.inputs.humancellmap.humancellmap_annotations 2023-06-16 19:16:22 2023-06-16 19:16:23 1.18 dict {'Q9NRG9': {HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) 4,371 {} 2023-06-16 19:16:22
pypath.inputs.humap.humap2_complexes 2023-06-16 19:16:23 2023-06-16 19:16:25 1.56 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) 6,944 {} 2023-06-16 19:16:23
pypath.inputs.humap.humap_complexes 2023-06-16 19:16:25 2023-06-16 19:16:26 0.91 dict {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) 4,508 {} 2023-06-16 19:16:25
pypath.inputs.huri._huri_interactions 
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments.
 {} never
pypath.inputs.huri.hi_i_interactions 2023-06-16 19:16:26 2023-06-16 19:16:27 1.38 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) 5,630 {} 2023-06-16 19:16:26
pypath.inputs.huri.hi_ii_interactions 2023-06-16 19:16:27 2023-06-16 19:16:32 5.31 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) 46,709 {} 2023-06-16 19:16:27
pypath.inputs.huri.hi_iii_old 2023-06-16 19:16:32 2023-06-16 19:16:32 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/huri.py", line 95, in hi_iii_old
    url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
{} 2023-06-12 19:20:23
pypath.inputs.huri.hi_union_interactions 2023-06-16 19:16:32 2023-06-16 19:16:51 18.37 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) 229,721 {} 2023-06-16 19:16:32
pypath.inputs.huri.huri_interactions 2023-06-16 19:16:51 2023-06-16 19:17:28 37.58 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) 166,657 {} 2023-06-16 19:16:51
pypath.inputs.huri.lit_bm_13_interactions 2023-06-16 19:17:28 2023-06-16 19:17:29 0.87 list [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) 11,045 {} 2023-06-16 19:17:28
pypath.inputs.huri.lit_bm_17_interactions 2023-06-16 19:17:29 2023-06-16 19:17:30 1.32 list [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) 48,796 {} 2023-06-16 19:17:29
pypath.inputs.huri.lit_bm_interactions 2023-06-16 19:17:30 2023-06-16 19:17:33 2.89 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
    size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
{} 2023-06-12 19:20:59
pypath.inputs.huri.rolland_hi_ii_14 2023-06-16 19:17:33 2023-06-16 19:17:33 0.13 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/huri.py", line 43, in rolland_hi_ii_14
    xlsname = cell.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:21:14
pypath.inputs.huri.vidal_hi_iii_old 
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments.
 {} never
pypath.inputs.huri.yang2016_interactions 2023-06-16 19:17:33 2023-06-16 19:17:35 1.18 list [HuriInteraction(uniprot_a='P07196', 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), HuriInteractio...(truncated) 2,823 {} 2023-06-16 19:17:33
pypath.inputs.huri.yu2011_interactions 2023-06-16 19:17:35 2023-06-16 19:17:36 1.86 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) 7,326 {} 2023-06-16 19:17:35
pypath.inputs.i3d.get_i3d 2023-06-16 19:17:36 2023-06-16 19:17:45 8.71 list [{'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P02647': {'pfam': None, 'chain': 'A', 'seq': [[68, 265]]}, 'uniprots': ['A0A024RAV5', 'P02647'], 'source': 'I3D', 'pdb': ['2mse'], 'references': []}, {'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P10398': {'pfam': N...(truncated) 15,984 {} 2023-06-16 19:17:36
pypath.inputs.icellnet._icellnet_get_components 
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_entity 
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_references 
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_resources 
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments.
 {} never
pypath.inputs.icellnet.icellnet_annotations 2023-06-16 19:17:45 2023-06-16 19:17:46 0.31 dict {'Q13443': {IcellnetAnnotation(role='ligand', family='ECM', subfamily=None, classification=('Ecm',))}, Complex: COMPLEX:P05556_P56199: {IcellnetAnnotation(role='receptor', family=None, subfamily=None, classification=('Semaphorin',)), IcellnetAnnotation(role='receptor', family='ECM', subfamily=None, ...(truncated) 853 {} 2023-06-16 19:17:45
pypath.inputs.icellnet.icellnet_complexes 2023-06-16 19:17:46 2023-06-16 19:17:46 0.03 dict {'COMPLEX:P05556_P56199': Complex: COMPLEX:P05556_P56199, 'COMPLEX:P05556_P26006': Complex: COMPLEX:P05556_P26006, 'COMPLEX:P05556_P23229': Complex: COMPLEX:P05556_P23229, 'COMPLEX:P05556_P06756': Complex: COMPLEX:P05556_P06756, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:Q0477...(truncated) 131 {} 2023-06-16 19:17:46
pypath.inputs.icellnet.icellnet_interactions 2023-06-16 19:17:46 2023-06-16 19:17:46 0.03 list [IcellnetRecord(ligand='Q13443', receptor=Complex: COMPLEX:P05556_P56199, family='ECM', subfamily=None, classification=['Ecm'], resources=None, references=['15361064']), IcellnetRecord(ligand='Q13443', receptor=Complex: COMPLEX:P05556_P26006, family='ECM', subfamily=None, classification=['Ecm'], res...(truncated) 1,023 {} 2023-06-16 19:17:46
pypath.inputs.ielm.get_ielm 
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments.
 {} never
pypath.inputs.ielm.get_ielm_huge 
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments.
 {} never
pypath.inputs.imweb._get_imweb 2023-06-16 19:17:46 2023-06-16 19:17:47 1.84 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/imweb.py", line 77, in _get_imweb
    hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
  File "/usr/lib/python3.10/json/__init__.py", line 339, in loads
    raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not NoneType
{} 2023-06-12 19:21:27
pypath.inputs.imweb.get_imweb 2023-06-16 19:17:47 2023-06-16 19:17:47 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/imweb.py", line 110, in get_imweb
    c0.perform()
pycurl.error: (3, '')
{} 2023-06-12 19:21:29
pypath.inputs.imweb.get_imweb_req 2023-06-16 19:17:47 2023-06-16 19:17:48 0.64 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/imweb.py", line 143, in get_imweb_req
    token = json.loads(r0.text)['token']
  File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
{} 2023-06-12 19:21:29
pypath.inputs.innatedb.innatedb_interactions 2023-06-16 19:17:48 2023-06-16 19:17:50 1.54 list [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) 19,036 {} 2023-06-16 19:17:48
pypath.inputs.instruct.get_instruct 2023-06-16 19:17:50 2023-06-16 19:17:51 1.43 NoneType None 0 {} 2023-06-16 19:17:50
pypath.inputs.instruct.get_instruct_offsets 2023-06-16 19:17:51 2023-06-16 19:17:52 0.42 NoneType None 0 {} 2023-06-16 19:17:51
pypath.inputs.intact._try_isoform 
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments.
 {} never
pypath.inputs.intact.intact_interactions 2023-06-16 19:17:52 2023-06-16 19:19:06 74.54 list [IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, interaction_types={'direct interaction'}, mi_score=0.77, isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', i...(truncated) 71,496 {} 2023-06-16 19:17:52
pypath.inputs.integrins.get_integrins 2023-06-16 19:19:06 2023-06-16 19:19:07 1.00 set {'Q13797', 'P17301', 'P20702', 'Q13683', 'P26006', 'P26010', 'O75578', 'P56199', 'P23229', 'P08648', 'P53708', 'P11215', 'Q9UKX5', 'P05107', 'P26012', 'P08514', 'P16144', 'Q13349', 'P18564', 'P20701', 'P05106', 'P18084', 'P38570', 'P05556', 'P06756'} 25 {} 2023-06-16 19:19:06
pypath.inputs.interpro.interpro2go_annotations 2023-06-16 19:19:07 2023-06-16 19:19:09 1.81 defaultdict defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid receptor activity'), Interpro2GOAnnotation(go_term_id='GO:0003677', go_term_name='DNA binding'), Interpro2GOAnnotation(go_term_id='GO:0005634', go_term_name='nucleus'), Interpro2GOA...(truncated) 14,657 {} 2023-06-16 19:19:07
pypath.inputs.interpro.interpro_annotations 2023-06-16 19:19:09 2023-06-16 19:20:09 60.21 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/interpro.py", line 274, in interpro_annotations
    totalrec = int(res['count'])
TypeError: 'NoneType' object is not subscriptable
{} 2023-06-12 19:22:37
pypath.inputs.interpro.interpro_entries 2023-06-16 19:20:09 2023-06-16 19:20:30 20.84 list [InterproEntry(interpro_id='IPR000001', protein_count='18450', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) 38,816 {} 2023-06-16 19:20:09
pypath.inputs.interpro.interpro_xrefs 
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments.
 {} never
pypath.inputs.intogen.intogen_annotations 2023-06-16 19:20:30 2023-06-16 19:20:31 1.01 dict {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) 483 {} 2023-06-16 19:20:30
pypath.inputs.ipi._ipi_uniprot_pairs 
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments.
 {} never
pypath.inputs.ipi.ipi_uniprot 2023-06-16 19:20:31 2023-06-16 19:20:32 0.31 dict {'IPI00807623': {'A0A183'}, 'IPI00396341': {'A0AUZ9'}, 'IPI00884975': {'A0AUZ9'}, 'IPI00884987': {'A0AUZ9'}, 'IPI00885003': {'A0AUZ9'}, 'IPI00855723': {'A0AV02'}, 'IPI00867607': {'A0AV02'}, 'IPI00793608': {'A0AV02'}, 'IPI00867726': {'A0AV02'}, 'IPI00867740': {'A0AV02'}, 'IPI00169342': {'A0AV96'}, 'I...(truncated) 51,106 {} 2023-06-16 19:20:31
pypath.inputs.iptmnet.iptmnet_interactions 2023-06-16 19:20:32 2023-06-16 19:24:17 225.05 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) 17,081 {} 2023-06-16 19:20:32
pypath.inputs.italk.italk_annotations 2023-06-16 19:24:17 2023-06-16 19:24:18 0.82 dict {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='other'), ItalkAnnotation(mainclass='receptor', subclass='growth factor')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) 1,414 {} 2023-06-16 19:24:17
pypath.inputs.italk.italk_interactions 2023-06-16 19:24:18 2023-06-16 19:24:18 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 {} 2023-06-16 19:24:18
pypath.inputs.italk.italk_raw 2023-06-16 19:24:18 2023-06-16 19:24:18 0.01 DataFrame Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) 2,649 {} 2023-06-16 19:24:18
pypath.inputs.kea.kea_enzyme_substrate 2023-06-16 19:24:18 2023-06-16 19:24:20 2.53 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) 35,252 {} 2023-06-16 19:24:18
pypath.inputs.kea.kea_interactions 2023-06-16 19:24:20 2023-06-16 19:24:20 0.17 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) 35,252 {} 2023-06-16 19:24:20
pypath.inputs.kegg.kegg_dbget 
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments.
 {} never
pypath.inputs.kegg.kegg_interactions 2023-06-16 19:24:20 2023-06-16 19:28:24 244.07 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) 14,571 {} 2023-06-16 19:24:20
pypath.inputs.kegg.kegg_medicus 2023-06-16 19:28:24 2023-06-16 19:28:42 17.76 set {KeggMedicusRawInteraction(id_a='7390', id_b='7389', name_a='UROS', name_b='UROD', effect='enzyme_enzyme', itype='post_translational', pw_type='reference', type_a='gene', type_b='gene', network_id='N00601'), KeggMedicusRawInteraction(id_a='112', id_b='C00575', name_a='ADCY6', name_b="3',5'-Cyclic AM...(truncated) 12,578 {} 2023-06-16 19:28:24
pypath.inputs.kegg.kegg_medicus_complexes 2023-06-16 19:28:42 2023-06-16 19:28:43 0.43 dict {'COMPLEX:O43684_O60566_Q9UI95': Complex: COMPLEX:O43684_O60566_Q9UI95, 'COMPLEX:O14640_O75474': Complex: COMPLEX:O14640_O75474, 'COMPLEX:P49768_Q92542_Q96BI3_Q9NZ42': Complex: COMPLEX:P49768_Q92542_Q96BI3_Q9NZ42, 'COMPLEX:O00399_O75935_P61163_Q13561_Q14203_Q9BTE1_Q9NZ32_Q9UJW0': Complex: COMPLEX:O0...(truncated) 501 {} 2023-06-16 19:28:42
pypath.inputs.kegg.kegg_medicus_interactions 2023-06-16 19:28:43 2023-06-16 19:28:43 0.39 list [KeggMedicusInteraction(id_a='P10746', id_b='P06132', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='enzyme_enzyme'), KeggMedicusInteraction(id_a='P62993', id_b='Q07890', entity_type_a='protein', entity_type_b='protein', interaction_type='post_transl...(truncated) 9,363 {} 2023-06-16 19:28:43
pypath.inputs.kegg.kegg_pathway_annotations 2023-06-16 19:28:43 2023-06-16 19:28:48 4.66 dict {'P36897': {KeggPathway(pathway='Th17 cell differentiation'), KeggPathway(pathway='Pancreatic cancer'), KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Hippo signaling pathway'), KeggPathway(pathway='Adherens junction'), KeggPathway(pathway='FoxO signaling pathway'), KeggPathway(...(truncated) 2,585 {} 2023-06-16 19:28:43
pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons 2023-06-16 19:28:48 2023-06-16 19:28:48 0.41 dict {'A8K7J7': {KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPath...(truncated) 813 {} 2023-06-16 19:28:48
pypath.inputs.kegg.kegg_pathways 2023-06-16 19:28:48 2023-06-16 19:28:52 4.26 tuple ({'MAPK signaling pathway': {'P36897', 'O95257', 'Q9HD43', 'Q96NL6', 'Q15628', 'Q9BQ95', 'P08571', 'Q9UKG9', 'Q8IVH8', 'O00622', 'P14778', 'Q03112', 'Q16584', 'P09603', 'O95382', 'O14733', 'Q9Y2U5', 'O75688', 'P01100', 'P22736', 'Q8IW41', 'P31152', 'P45983', 'P17612', 'P46734', 'P15056', 'P19438', '...(truncated) 2 {} 2023-06-16 19:28:48
pypath.inputs.kegg_api. 
Not calling `pypath.inputs.kegg_api.`, not enough arguments.
 {} never
pypath.inputs.kegg_api._generate_conv_functions 2023-06-16 19:28:53 2023-06-16 19:28:53 0.00 NoneType None 0 {} 2023-06-16 19:28:53
pypath.inputs.kegg_api._generate_relation_functions 2023-06-16 19:28:53 2023-06-16 19:28:53 0.00 NoneType None 0 {} 2023-06-16 19:28:53
pypath.inputs.kegg_api._kegg_conv 
Not calling `pypath.inputs.kegg_api._kegg_conv`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_ddi 
Not calling `pypath.inputs.kegg_api._kegg_ddi`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_ddi_async 
Not calling `pypath.inputs.kegg_api._kegg_ddi_async`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_ddi_sync 
Not calling `pypath.inputs.kegg_api._kegg_ddi_sync`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_general 
Not calling `pypath.inputs.kegg_api._kegg_general`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_general_async 
Not calling `pypath.inputs.kegg_api._kegg_general_async`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_link 
Not calling `pypath.inputs.kegg_api._kegg_link`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_list 
Not calling `pypath.inputs.kegg_api._kegg_list`, not enough arguments.
 {} never
pypath.inputs.kegg_api._kegg_relations 
Not calling `pypath.inputs.kegg_api._kegg_relations`, not enough arguments.
 {} never
pypath.inputs.kegg_api.disease_to_drug 
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments.
 {} never
pypath.inputs.kegg_api.disease_to_gene 
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments.
 {} never
pypath.inputs.kegg_api.disease_to_pathway 
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments.
 {} never
pypath.inputs.kegg_api.drug_to_disease 
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments.
 {} never
pypath.inputs.kegg_api.drug_to_drug 2023-06-16 19:28:53 2023-06-16 19:28:53 0.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/kegg_api.py", line 133, in drug_to_drug
    entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
TypeError: Can't instantiate abstract class _Drug with abstract methods __init__, load
{} 2023-06-12 19:35:59
pypath.inputs.kegg_api.drug_to_gene 
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments.
 {} never
pypath.inputs.kegg_api.drug_to_pathway 
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments.
 {} never
pypath.inputs.kegg_api.gene_to_disease 
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments.
 {} never
pypath.inputs.kegg_api.gene_to_drug 
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments.
 {} never
pypath.inputs.kegg_api.gene_to_pathway 
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments.
 {} never
pypath.inputs.kegg_api.kegg_drug_to_chebi 
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments.
 {} never
pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid 
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments.
 {} never
pypath.inputs.kegg_api.kegg_gene_to_uniprot 
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments.
 {} never
pypath.inputs.kegg_api.pathway_to_disease 
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments.
 {} never
pypath.inputs.kegg_api.pathway_to_drug 
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments.
 {} never
pypath.inputs.kegg_api.pathway_to_gene 
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments.
 {} never
pypath.inputs.kinasedotcom.kinasedotcom_annotations 2023-06-16 19:28:53 2023-06-16 19:28:53 0.38 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) 504 {} 2023-06-16 19:28:53
pypath.inputs.kirouac2010.kirouac2010_interactions 2023-06-16 19:28:53 2023-06-16 19:28:56 3.41 list [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) 267 {} 2023-06-16 19:28:53
pypath.inputs.lambert2018.lambert2018_annotations 2023-06-16 19:28:56 2023-06-16 19:28:56 0.09 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/lambert2018.py", line 104, in lambert2018_annotations
    for r in lambert2018_s1_raw():
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/lambert2018.py", line 44, in lambert2018_s1_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:36:00
pypath.inputs.lambert2018.lambert2018_s1_raw 2023-06-16 19:28:56 2023-06-16 19:28:56 0.08 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/lambert2018.py", line 44, in lambert2018_s1_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 19:36:00
pypath.inputs.laudanna.laudanna_directions 2023-06-16 19:28:56 2023-06-16 19:28:57 0.79 list [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) 77,555 {} 2023-06-16 19:28:56
pypath.inputs.laudanna.laudanna_effects 2023-06-16 19:28:57 2023-06-16 19:28:58 0.31 list [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) 63,438 {} 2023-06-16 19:28:57
pypath.inputs.li2012.get_li2012 2023-06-16 19:28:58 2023-06-16 19:29:06 8.12 list [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) 583 {} 2023-06-16 19:28:58
pypath.inputs.li2012.li2012_dmi 2023-06-16 19:29:06 2023-06-16 19:29:06 0.21 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/li2012.py", line 133, in li2012_dmi
    se = seq.swissprot_seq(isoforms = True)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/seq.py", line 55, in swissprot_seq
    data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
{} 2023-06-12 19:36:10
pypath.inputs.li2012.li2012_enzyme_substrate 2023-06-16 19:29:06 2023-06-16 19:29:06 0.03 list [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) 349 {} 2023-06-16 19:29:06
pypath.inputs.li2012.li2012_interactions 2023-06-16 19:29:06 2023-06-16 19:29:06 0.03 list [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) 503 {} 2023-06-16 19:29:06
pypath.inputs.lincs.lincs_compounds 2023-06-16 19:29:06 2023-06-16 19:29:10 3.63 dict {'10001': LincsCompound(lincs='LSM-1001', chembl='CHEMBL14762', chebi='CHEBI:354.22', inchi='InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1', inchi_key='BTIHMVBBUGXLCJ-OAHLLOKOSA-N', smil...(truncated) 1,320 {} 2023-06-16 19:29:06
pypath.inputs.lmpid.lmpid_dmi 2023-06-16 19:29:10 2023-06-16 19:29:10 0.63 list [] 0 {} 2023-06-16 19:29:10
pypath.inputs.lmpid.lmpid_interactions 2023-06-16 19:29:10 2023-06-16 19:29:11 0.75 list [] 0 {} 2023-06-16 19:29:10
pypath.inputs.lmpid.load_lmpid 2023-06-16 19:29:11 2023-06-16 19:29:11 0.38 list [] 0 {} 2023-06-16 19:29:11
pypath.inputs.lncdisease.lncdisease_interactions 2023-06-16 19:29:11 2023-06-16 19:29:12 0.20 list [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism='human', pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism='human', pmid='22244333')...(truncated) 478 {} 2023-06-16 19:29:11
pypath.inputs.lncrnadb.lncrnadb_interactions 2023-06-16 19:29:12 2023-06-16 19:29:12 0.34 list [] 0 {} 2023-06-16 19:29:12
pypath.inputs.locate.locate_localizations 2023-06-16 19:29:12 2023-06-16 19:29:51 39.10 dict {'P27824': {LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='melanosome', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='lysosomes', cls='typeI', pm...(truncated) 9,496 {} 2023-06-16 19:29:12
pypath.inputs.lrdb.lrdb_annotations 2023-06-16 19:29:51 2023-06-16 19:29:52 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=('10747918', '1374383', '14596620', '1718973')), LrdbAnnotation(role='...(truncated) 1,536 {} 2023-06-16 19:29:51
pypath.inputs.lrdb.lrdb_interactions 2023-06-16 19:29:52 2023-06-16 19:29:52 0.03 list [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) 3,251 {} 2023-06-16 19:29:52
pypath.inputs.macrophage._trim_gname 
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments.
 {} never
pypath.inputs.macrophage.macrophage_interactions 2023-06-16 19:29:52 2023-06-16 19:29:52 0.30 list [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) 4,516 {} 2023-06-16 19:29:52
pypath.inputs.matrisome.__matrisome_annotations_2 2023-06-16 19:29:52 2023-06-16 19:29:53 1.12 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/matrisome.py", line 91, in __matrisome_annotations_2
    _ = next(c.result)
TypeError: 'NoneType' object is not an iterator
{} 2023-06-12 19:36:56
pypath.inputs.matrisome.matrisome_annotations 2023-06-16 19:29:53 2023-06-16 19:29:53 0.28 dict {'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) 1,067 {} 2023-06-16 19:29:53
pypath.inputs.matrixdb._matrixdb_protein_list 
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments.
 {} never
pypath.inputs.matrixdb.matrixdb_annotations 2023-06-16 19:29:53 2023-06-16 19:29:57 3.20 dict {'P01614': {MatrixdbAnnotation(mainclass='membrane'), MatrixdbAnnotation(mainclass='secreted')}, 'Q7Z4L0': {MatrixdbAnnotation(mainclass='membrane')}, 'P49326': {MatrixdbAnnotation(mainclass='membrane')}, 'Q96AQ2': {MatrixdbAnnotation(mainclass='membrane')}, 'P04264': {MatrixdbAnnotation(mainclass='...(truncated) 10,094 {} 2023-06-16 19:29:53
pypath.inputs.matrixdb.matrixdb_ecm_proteins 2023-06-16 19:29:57 2023-06-16 19:29:57 0.00 set {'O95460', 'Q16363', 'Q5GFL6', 'Q9NS15', 'P21754', 'Q96PB8', 'P78509', 'Q02388', 'P55081', 'Q7Z5L7', 'O00300', 'P02818', 'P55082', 'Q99715', 'P98160', 'Q9BXS0', 'A6NCI4', 'Q6UXI7', 'Q9Y6F9', 'Q6AZY7', 'Q6UXH1', 'Q9BSG5', 'Q13753', 'Q9NQ30', 'Q68BL7', 'A1KZ92', 'Q8N6G6', 'Q5JSJ4', 'O43155', 'Q075Z2',...(truncated) 483 {} 2023-06-16 19:29:57
pypath.inputs.matrixdb.matrixdb_interactions 2023-06-16 19:29:57 2023-06-16 19:29:57 0.13 list [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) 425 {} 2023-06-16 19:29:57
pypath.inputs.matrixdb.matrixdb_membrane_proteins 2023-06-16 19:29:57 2023-06-16 19:29:59 2.05 set {'P01614', 'Q7Z4L0', 'P49326', 'Q96AQ2', 'P04264', 'P31785', 'O95139', 'O14609', 'Q8NHS1', 'Q9NQX3', 'O14653', 'P01611', 'Q8N6M3', 'A1L0T0', 'P04156', 'Q9BTX7', 'O75129', 'P11166', 'O00574', 'O00461', 'P26006', 'P59541', 'Q9BSA4', 'Q8IZL8', 'Q4ZG55', 'Q8NGA4', 'Q6P9B9', 'P23219', 'Q9BZD4', 'A0A0J9YX...(truncated) 8,238 {} 2023-06-16 19:29:57
pypath.inputs.matrixdb.matrixdb_secreted_proteins 2023-06-16 19:29:59 2023-06-16 19:29:59 0.35 set {'P01160', 'P01614', 'O75888', 'P78536', 'Q6EIG7', 'P23297', 'P13995', 'P04211', 'Q5GFL6', 'P01298', 'P12645', 'P04264', 'A0A0B4J1V2', 'Q9H4G1', 'A0A0B4J1Z2', 'Q2M2E5', 'P01611', 'Q969D9', 'P20827', 'A0A075B6S2', 'Q8N690', 'Q9H0U6', 'O60814', 'Q8N6C8', 'Q7Z6Z7', 'Q99715', 'P01229', 'O43242', 'Q9HCJ2...(truncated) 2,922 {} 2023-06-16 19:29:59
pypath.inputs.mcam.mcam_cell_adhesion_molecules 2023-06-16 19:29:59 2023-06-16 19:30:00 1.02 set {'P28906', 'Q04900', 'P20702', 'Q13740', 'Q13895', 'Q6MZF4', 'P56856', 'Q9HDB5', 'Q96GP6', 'P18827', 'Q8TEW0', 'Q13835', 'Q92896', 'P35443', 'P43121', 'Q6NW40', 'P07359', 'Q49MI3', 'P02751', 'Q05084', 'Q9BXN2', 'Q9BYD3', 'P42771', 'Q6MZM7', 'P50895', 'P22105', 'Q9NPY3', 'Q14956', 'P53708', 'P11215',...(truncated) 103 {} 2023-06-16 19:29:59
pypath.inputs.membranome.membranome_annotations 2023-06-16 19:30:00 2023-06-16 19:30:26 26.31 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) 2,384 {} 2023-06-16 19:30:00
pypath.inputs.mimp.get_kinase_class 2023-06-16 19:30:26 2023-06-16 19:30:27 0.16 dict {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) 4 {} 2023-06-16 19:30:26
pypath.inputs.mimp.mimp_enzyme_substrate 2023-06-16 19:30:27 2023-06-16 19:30:31 4.08 list [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) 17,030 {} 2023-06-16 19:30:27
pypath.inputs.mimp.mimp_interactions 2023-06-16 19:30:31 2023-06-16 19:30:31 0.54 list [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) 17,030 {} 2023-06-16 19:30:31
pypath.inputs.mir2disease.mir2disease_interactions 2023-06-16 19:30:31 2023-06-16 19:30:31 0.20 list [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) 805 {} 2023-06-16 19:30:31
pypath.inputs.mirbase.get_mirbase_aliases 2023-06-16 19:30:31 2023-06-16 19:30:32 0.06 tuple ({'MIMAT0000062': {'hsa-let-7a', 'hsa-let-7a-5p'}, 'MIMAT0000063': {'hsa-let-7b', 'hsa-let-7b-5p'}, 'MIMAT0000064': {'hsa-let-7c-5p', 'hsa-let-7c'}, 'MIMAT0000065': {'hsa-let-7d', 'hsa-let-7d-5p'}, 'MIMAT0000066': {'hsa-let-7e', 'hsa-let-7e-5p'}, 'MIMAT0000067': {'hsa-let-7f-5p', 'hsa-let-7f'}, 'MIM...(truncated) 2 {} 2023-06-16 19:30:31
pypath.inputs.mirbase.mirbase_ids 2023-06-16 19:30:32 2023-06-16 19:30:32 0.08 list [('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000068', 'MI...(truncated) 3,027 {} 2023-06-16 19:30:32
pypath.inputs.mirbase.mirbase_mature 2023-06-16 19:30:32 2023-06-16 19:30:32 0.06 list [('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000064', 'hsa-let-7c-5p'), ('MIMAT0000064', 'hsa-let-7c'), ('MIMAT0000065', 'hsa-let-7d'), ('MIMAT0000065', 'hsa-let-7d-5p'), ('MIMAT0000066', 'hsa-let-7e'),...(truncated) 3,487 {} 2023-06-16 19:30:32
pypath.inputs.mirbase.mirbase_mature_all 2023-06-16 19:30:32 2023-06-16 19:30:32 0.08 list ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) 3,027 {} 2023-06-16 19:30:32
pypath.inputs.mirbase.mirbase_precursor 2023-06-16 19:30:32 2023-06-16 19:30:32 0.06 list [('MI0000060', 'hsa-let-7a-1L'), ('MI0000060', 'hsa-let-7a-1'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) 2,173 {} 2023-06-16 19:30:32
pypath.inputs.mirbase.mirbase_precursor_all 2023-06-16 19:30:32 2023-06-16 19:30:32 0.08 list ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000068', 'MI0000067', 'MI0000069', 'MI0000070', 'MI0000115', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) 3,027 {} 2023-06-16 19:30:32
pypath.inputs.mirbase.mirbase_precursor_to_mature 2023-06-16 19:30:32 2023-06-16 19:30:32 0.14 list [('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMAT0000062'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT...(truncated) 3,361 {} 2023-06-16 19:30:32
pypath.inputs.mirdeathdb.mirdeathdb_interactions 2023-06-16 19:30:32 2023-06-16 19:30:32 0.20 list [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) 462 {} 2023-06-16 19:30:32
pypath.inputs.mirecords.mirecords_interactions 2023-06-16 19:30:32 2023-06-16 19:30:33 0.40 list [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism='Homo sapiens', target_organism='Homo sapiens', pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organ...(truncated) 3,106 {} 2023-06-16 19:30:32
pypath.inputs.mirtarbase._mirtarbase_interactions 
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments.
 {} never
pypath.inputs.mirtarbase.mirtarbase_interactions 2023-06-16 19:30:33 2023-06-16 19:31:39 66.13 list [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism='Mus musculus', target_genesymbol='Cd320', target_entrez='54219', target_organism='Mus musculus', target_site='AGAGACTGGGGTCCTCAGACACTCCC', method='Luciferase reporter assay//qRT-PCR//Western blot', catego...(truncated) 21,560 {} 2023-06-16 19:30:33
pypath.inputs.mitab.mitab_field_list 
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_field_uniprot 
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments.
 {} never
pypath.inputs.mppi.mppi_interactions 2023-06-16 19:31:39 2023-06-16 19:31:39 0.56 list [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) 777 {} 2023-06-16 19:31:39
pypath.inputs.msigdb.msigdb_annotations 2023-06-16 19:31:39 2023-06-16 19:32:36 56.68 dict {'Q96BD6': {MsigdbAnnotation(collection='mirna_targets_mirdb', geneset='MIR12133'), MsigdbAnnotation(collection='immunesigdb', geneset='KAECH_NAIVE_VS_MEMORY_CD8_TCELL_UP'), MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='SUNG_METASTASIS_STROMA_UP'), MsigdbAnnotation(colle...(truncated) 20,100 {} 2023-06-16 19:31:39
pypath.inputs.msigdb.msigdb_download 2023-06-16 19:32:38 2023-06-16 19:32:52 13.86 dict {'chr1p11': {'FCGR1BP', 'RPL22P6', 'MTIF2P1', 'NOTCH2NLR', 'PFN1P2', 'RNVU1-4', 'EMBP1', 'NBPF26', 'PPIAL4A', 'PDE4DIPP2', 'SRGAP2C', 'LINC00623', 'PDE4DIPP4', 'RNVU1-19', 'H2BP1', 'H3P4', 'NBPF8', 'LINC01691', 'LINC02798', 'FAM72B', 'SRGAP2-AS1'}, 'chr1p12': {'HSD3B2', 'RNA5SP56', 'ENSG00000226172'...(truncated) 33,591 {} 2023-06-16 19:32:38
pypath.inputs.msigdb.msigdb_download_collections 2023-06-16 19:32:52 2023-06-16 19:32:53 0.49 dict {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'PTX3', 'TNFAIP8', 'NFAT5', 'IER5', 'B4GALT5', 'IL12B', 'TNF', 'BIRC2', 'ICOSLG', 'NR4A3', 'ZFP36', 'CXCL11', 'CEBPD', 'RELA', 'PANX1', 'SOCS3', 'TRIP10', 'BCL2A1', 'SAT1', 'EGR3', 'CCL20', 'CCNL1', 'TNFAIP2', 'IL15RA', 'ZBTB10', 'PLAU', ...(truncated) 18 {} 2023-06-16 19:32:52
pypath.inputs.ncrdeathdb.ncrdeathdb_interactions 2023-06-16 19:32:53 2023-06-16 19:32:53 0.35 list [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) 7,305 {} 2023-06-16 19:32:53
pypath.inputs.negatome.negatome_interactions 2023-06-16 19:32:53 2023-06-16 19:33:23 30.00 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/negatome.py", line 54, in negatome_interactions
    for l in f:
TypeError: 'NoneType' object is not iterable
{} 2023-06-12 19:39:07
pypath.inputs.netbiol._netbiol_interactions 
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments.
 {} never
pypath.inputs.netbiol.arn_interactions 2023-06-16 19:33:23 2023-06-16 19:33:23 0.13 list [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) 95 {} 2023-06-16 19:33:23
pypath.inputs.netbiol.nrf2ome_interactions 2023-06-16 19:33:23 2023-06-16 19:33:23 0.13 list [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) 109 {} 2023-06-16 19:33:23
pypath.inputs.netpath.netpath_interactions 2023-06-16 19:33:23 2023-06-16 19:33:26 2.40 list [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) 7,555 {} 2023-06-16 19:33:23
pypath.inputs.netpath.netpath_names 2023-06-16 19:33:26 2023-06-16 19:33:26 0.01 dict {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) 35 {} 2023-06-16 19:33:26
pypath.inputs.netpath.netpath_pathway_annotations 2023-06-16 19:33:26 2023-06-16 19:33:44 18.05 dict {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Notch'), NetpathPa...(truncated) 1,870 {} 2023-06-16 19:33:26
pypath.inputs.oma.oma_orthologs 
Not calling `pypath.inputs.oma.oma_orthologs`, not enough arguments.
 {} never
pypath.inputs.ontology.listof_ontologies 2023-06-16 19:33:44 2023-06-16 19:33:45 0.97 dict {'rs': 'Rat Strain Ontology', 'sbo': 'Systems Biology Ontology', 'scdo': 'Sickle Cell Disease Ontology', 'sdgio': 'Sustainable Development Goals Interface Ontology', 'sepio': 'Scientific Evidence and Provenance Information Ontology', 'sibo': 'Social Insect Behavior Ontology', 'spd': 'Spider Ontology...(truncated) 280 {} 2023-06-16 19:33:44
pypath.inputs.ontology.ontology 
Not calling `pypath.inputs.ontology.ontology`, not enough arguments.
 {} never
pypath.inputs.opm.opm_annotations 2023-06-16 19:33:45 2023-06-16 19:34:06 20.70 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) 87 {} 2023-06-16 19:33:45
pypath.inputs.oreganno.oreganno_interactions 2023-06-16 19:34:06 2023-06-16 19:36:12 126.09 list [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) 5,903 {} 2023-06-16 19:34:06
pypath.inputs.oreganno.oreganno_raw 2023-06-16 19:36:12 2023-06-16 19:36:24 12.05 list [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) 5,688,970 {} 2023-06-16 19:36:12
pypath.inputs.panglaodb.panglaodb_annotations 2023-06-16 19:36:24 2023-06-16 19:36:25 1.56 defaultdict defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=False, cell_type='Enterocytes', organ='GI tract', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=0.0, mouse_sensitivity=0.00331126, human_specificity=0.00439422, mouse_specifici...(truncated) 4,792 {} 2023-06-16 19:36:24
pypath.inputs.panglaodb.panglaodb_raw 2023-06-16 19:36:25 2023-06-16 19:36:25 0.04 list [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) 8,286 {} 2023-06-16 19:36:25
pypath.inputs.pathophenodb.disease_pathogen_interactions 2023-06-16 19:36:25 2023-06-16 19:36:25 0.00 list [] 0 {} 2023-06-16 19:36:25
pypath.inputs.pathwaycommons._create_single_resource_method 
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons.pathwaycommons_interactions 2023-06-16 19:36:25 2023-06-16 19:36:40 14.75 list [PathwayCommonsInteraction(id_a='A1CF', interaction_type='in-complex-with', id_b='APOBEC1', resource='Reactome'), PathwayCommonsInteraction(id_a='A1CF', interaction_type='in-complex-with', id_b='APOBEC2', resource='Reactome'), PathwayCommonsInteraction(id_a='A1CF', interaction_type='in-complex-with'...(truncated) 1,261,865 {} 2023-06-16 19:36:25
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pazar.pazar_interactions 2023-06-16 19:36:41 2023-06-16 19:36:41 0.24 list [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) 16,386 {} 2023-06-16 19:36:41
pypath.inputs.pdb.pdb_chains 2023-06-16 19:36:41 2023-06-16 19:36:50 8.25 tuple ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) 2 {} 2023-06-16 19:36:41
pypath.inputs.pdb.pdb_complexes 2023-06-16 19:36:52 2023-06-16 19:37:00 8.08 dict {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963, 'COMPLEX:P00669': Complex: COMPLEX:P00669, 'COMPLEX:P07378': Complex: COMPLEX:P07378, 'COMPLEX:P01837_P01869': Complex: COMPLEX...(truncated) 42,870 {} 2023-06-16 19:36:52
pypath.inputs.pdb.pdb_uniprot 2023-06-16 19:37:00 2023-06-16 19:37:33 32.95 tuple ({'P02185': {('2mgf', 'X-ray', 1.8), ('2w6x', 'X-ray', 1.73), ('3e4n', 'X-ray', 1.21), ('5utd', 'X-ray', 1.78), ('5vnu', 'X-ray', 1.58), ('4qau', 'X-ray', 1.6), ('1irc', 'X-ray', 2.17), ('1f63', 'X-ray', 1.8), ('1mbn', 'X-ray', 2.0), ('5ych', 'X-ray', 1.35), ('6d45', 'X-ray', 1.78), ('1naz', 'X-ray'...(truncated) 2 {} 2023-06-16 19:37:00
pypath.inputs.pdzbase.pdzbase_interactions 2023-06-16 19:37:33 2023-06-16 19:37:34 0.92 list [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) 339 {} 2023-06-16 19:37:33
pypath.inputs.pepcyber.pepcyber_details 
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments.
 {} never
pypath.inputs.pepcyber.pepcyber_interactions 2023-06-16 19:37:34 2023-06-16 19:49:05 690.58 list [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) 5,590 {} 2023-06-16 19:37:34
pypath.inputs.pfam._pfam_uniprot 
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments.
 {} never
pypath.inputs.pfam.pfam_names 2023-06-16 19:49:05 2023-06-16 19:49:06 1.14 tuple ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) 2 {} 2023-06-16 19:49:05
pypath.inputs.pfam.pfam_pdb 2023-06-16 19:49:06 2023-06-16 19:49:10 3.86 tuple ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': PfamDomain(chain='A', star...(truncated) 2 {} 2023-06-16 19:49:06
pypath.inputs.pfam.pfam_regions 2023-06-16 19:49:10 2023-06-16 19:54:31 320.07 tuple ({}, {}) 2 {} 2023-06-16 19:49:10
pypath.inputs.pfam.pfam_uniprot 2023-06-16 19:54:31 2023-06-16 19:54:32 1.02 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/pfam.py", line 100, in pfam_uniprot
    data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
{} 2023-06-12 19:59:27
pypath.inputs.pharos._create_query_functions 2023-06-16 19:54:32 2023-06-16 19:54:32 0.00 NoneType None 0 {} 2023-06-16 19:54:32
pypath.inputs.pharos.pharos_diseases 2023-06-16 19:54:32 2023-06-16 19:55:35 63.47 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2023-06-16 19:54:32
pypath.inputs.pharos.pharos_expression 2023-06-16 19:55:36 2023-06-16 19:55:40 3.66 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2023-06-16 19:55:36
pypath.inputs.pharos.pharos_general 
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments.
 {} never
pypath.inputs.pharos.pharos_gtex 2023-06-16 19:55:41 2023-06-16 19:55:44 3.30 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2023-06-16 19:55:41
pypath.inputs.pharos.pharos_ligands 2023-06-16 19:55:46 2023-06-16 19:55:50 4.13 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2023-06-16 19:55:46
pypath.inputs.pharos.pharos_orthologs 2023-06-16 19:55:51 2023-06-16 19:55:54 3.25 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2023-06-16 19:55:51
pypath.inputs.pharos.pharos_targets 2023-06-16 19:55:55 2023-06-16 19:56:30 34.33 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) 20,412 {} 2023-06-16 19:55:55
pypath.inputs.pharos.pharos_xrefs 2023-06-16 19:56:30 2023-06-16 19:56:33 3.58 list [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) 20,412 {} 2023-06-16 19:56:30
pypath.inputs.phobius.phobius_annotations 2023-06-16 19:56:34 2023-06-16 19:56:35 0.35 dict {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) 20,350 {} 2023-06-16 19:56:34
pypath.inputs.phosphatome.phosphatome_annotations 2023-06-16 19:56:35 2023-06-16 19:56:39 4.32 dict {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) 264 {} 2023-06-16 19:56:35
pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate 2023-06-16 19:56:39 2023-06-16 19:56:41 1.46 list [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) 2,426 {} 2023-06-16 19:56:39
pypath.inputs.phosphoelm.phosphoelm_interactions 2023-06-16 19:56:41 2023-06-16 19:56:41 0.52 list [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) 2,426 {} 2023-06-16 19:56:41
pypath.inputs.phosphoelm.phosphoelm_kinases 2023-06-16 19:56:41 2023-06-16 19:56:41 0.14 dict {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) 247 {} 2023-06-16 19:56:41
pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate 2023-06-16 19:56:41 2023-06-16 19:56:43 1.79 list [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) 4,417 {} 2023-06-16 19:56:41
pypath.inputs.phosphonetworks.phosphonetworks_interactions 2023-06-16 19:56:43 2023-06-16 19:56:43 0.02 list [['CAMKK1', 'CLK1'], ['PRKAA2', 'EEF1D'], ['NUAK1', 'CASP6'], ['BUB1', 'NCL'], ['CLK1', 'TRIM28'], ['TTK', 'RBBP5'], ['PRKACA', 'RNUXA'], ['CLK2', 'KHDRBS1'], ['DYRK2', 'HSF1'], ['PRKCA', 'CASR'], ['PIM2', 'ZYX'], ['DYRK2', 'HIRIP3'], ['CDK4', 'NUP133'], ['AKT1', 'ZHX1'], ['RPS6KA4', 'PPP1R13L'], ['...(truncated) 1,821 {} 2023-06-16 19:56:43
pypath.inputs.phosphopoint.phosphopoint_directions 2023-06-16 19:56:43 2023-06-16 19:56:43 0.23 list [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) 9,269 {} 2023-06-16 19:56:43
pypath.inputs.phosphopoint.phosphopoint_interactions 2023-06-16 19:56:43 2023-06-16 19:56:43 0.01 list [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) 9,269 {} 2023-06-16 19:56:43
pypath.inputs.phosphosite._phosphosite_filter_organism 
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments.
 {} never
pypath.inputs.phosphosite.phosphosite_directions 2023-06-16 19:56:43 2023-06-16 19:56:43 0.04 list [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P45984', 'P46937'], ['P06493', 'Q9GZV5'], ['P11309', 'P52907'], ['O14757', 'Q...(truncated) 8,971 {} 2023-06-16 19:56:43
pypath.inputs.phosphosite.phosphosite_enzyme_substrate 2023-06-16 19:56:43 2023-06-16 19:56:44 0.34 list [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) 13,459 {} 2023-06-16 19:56:43
pypath.inputs.phosphosite.phosphosite_interactions 2023-06-16 19:56:44 2023-06-16 19:56:44 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) 2 {} 2023-06-16 19:56:44
pypath.inputs.phosphosite.phosphosite_interactions_all 2023-06-16 19:56:44 2023-06-16 19:56:44 0.01 list [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) 9,041 {} 2023-06-16 19:56:44
pypath.inputs.phosphosite.phosphosite_interactions_curated 2023-06-16 19:56:44 2023-06-16 19:56:44 0.00 list [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) 4,309 {} 2023-06-16 19:56:44
pypath.inputs.phosphosite.phosphosite_interactions_new 2023-06-16 19:56:44 2023-06-16 19:56:44 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) 2 {} 2023-06-16 19:56:44
pypath.inputs.phosphosite.phosphosite_interactions_noref 2023-06-16 19:56:44 2023-06-16 19:56:44 0.00 list [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'AB;WB;MA'...(truncated) 4,732 {} 2023-06-16 19:56:44
pypath.inputs.phosphosite.phosphosite_ptm_orthology 2023-06-16 19:56:44 2023-06-16 19:56:49 5.41 dict {('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('Q9CQV8', 1, 'S', 6, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'S', 6, 9606,...(truncated) 198,635 {} 2023-06-16 19:56:44
pypath.inputs.phosphosite.phosphosite_ptms 2023-06-16 19:56:50 2023-06-16 19:57:04 14.60 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 {} 2023-06-16 19:56:50
pypath.inputs.phosphosite.phosphosite_regsites 2023-06-16 19:57:05 2023-06-16 19:57:05 0.50 dict {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'phosphorylation', 'protein degradation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) 5,435 {} 2023-06-16 19:57:05
pypath.inputs.phosphosite.phosphosite_regsites_one_organism 2023-06-16 19:57:05 2023-06-16 19:58:09 64.17 dict {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21209006', '28052875', '24876223', '21148409'}, 'isoforms': {1}, 'process': {''}, 'function': {'intracellular localization', 'phosphorylation', 'protein stabilization', 'ubiquitination', 'protein degradation'}...(truncated) 3,619 {} 2023-06-16 19:57:05
pypath.inputs.phosphosite.regsites_tab 
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments.
 {} never
pypath.inputs.pisa.pisa_bonds 
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments.
 {} never
pypath.inputs.pisa.pisa_interfaces 
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments.
 {} never
pypath.inputs.pro.get_pro 2023-06-16 19:58:10 2023-06-16 20:04:10 360.02 Obo <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> 0 {} 2023-06-16 19:58:10
pypath.inputs.pro.pro_mapping 2023-06-16 20:04:10 2023-06-16 20:04:10 0.41 list [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) 320,143 {} 2023-06-16 20:04:10
pypath.inputs.progeny.progeny_annotations 2023-06-16 20:04:10 2023-06-16 20:04:16 5.58 dict {'P35250': {ProgenyAnnotation(pathway='Estrogen', weight=2.40982404059, p_value=0.0238138596584), ProgenyAnnotation(pathway='JAK-STAT', weight=0.0012188579040493524, p_value=0.998388257483376), ProgenyAnnotation(pathway='TGFb', weight=-0.430508102546081, p_value=0.6304595613186617), ProgenyAnnotatio...(truncated) 18,593 {} 2023-06-16 20:04:10
pypath.inputs.progeny.progeny_raw 2023-06-16 20:04:16 2023-06-16 20:04:18 1.73 DataFrame gene pathway weight p.value 1 RFC2 EGFR 1.470647 0.001655 2 ESRRA EGFR 0.178590 0.211838 3 HNRNPK EGFR 0.306699 0.084560 4 CBX6 EGFR -0.675507 0.017641 5 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) 274,143 {} 2023-06-16 20:04:16
pypath.inputs.proteinatlas.get_proteinatlas 2023-06-16 20:04:18 2023-06-16 20:04:25 6.93 dict {'normal': {'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 detected', 'Approved'...(truncated) 2 {} 2023-06-16 20:04:18
pypath.inputs.proteinatlas.proteinatlas_annotations 2023-06-16 20:04:26 2023-06-16 20:04:40 14.17 dict {'O43657': {ProtainatlasAnnotation(organ='smooth muscle', tissue='smooth muscle cells', 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(organ='pancreatic can...(truncated) 19,401 {} 2023-06-16 20:04:26
pypath.inputs.proteinatlas.proteinatlas_secretome_annotations 2023-06-16 20:04:43 2023-06-16 20:04:45 2.48 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 {} 2023-06-16 20:04:43
pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations 2023-06-16 20:04:45 2023-06-16 20:04:45 0.33 dict {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Microtubules', status='Uncertain'), ProteinatlasSubcellularAnnotation(location='Nuclear bodies', status='Uncertain')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellular...(truncated) 6,956 {} 2023-06-16 20:04:45
pypath.inputs.proteins.variants 2023-06-16 20:04:45 2023-06-16 20:16:59 733.59 list [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) 48,453 {} 2023-06-16 20:04:45
pypath.inputs.protmapper.get_protmapper 2023-06-16 20:17:00 2023-06-16 20:17:04 4.61 tuple ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) 2 {} 2023-06-16 20:17:00
pypath.inputs.protmapper.protmapper_enzyme_substrate 2023-06-16 20:17:05 2023-06-16 20:17:05 0.78 list [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'24727247', '25728676', '24357804', '25545367', '22304920'}, 'substrate': 'P15336', 'databases': {'Sparser', 'PhosphoSite', 'REACH', 'SIGNOR'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'23708658', '24727247'}, ...(truncated) 22,139 {} 2023-06-16 20:17:05
pypath.inputs.protmapper.protmapper_interactions 
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments.
 {} never
pypath.inputs.pubchem.pubchem_mapping 
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments.
 {} never
pypath.inputs.pubmed.get_pmid 
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments.
 {} never
pypath.inputs.pubmed.get_pubmeds 
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments.
 {} never
pypath.inputs.pubmed.only_pmids 
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments.
 {} never
pypath.inputs.pubmed.open_pubmed 
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments.
 {} never
pypath.inputs.pubmed.pmids_dict 
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments.
 {} never
pypath.inputs.pubmed.pmids_list 
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments.
 {} never
pypath.inputs.ramilowski2015.ramilowski_interactions 2023-06-16 20:17:06 2023-06-16 20:17:06 0.68 list [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) 1,894 {} 2023-06-16 20:17:06
pypath.inputs.ramilowski2015.ramilowski_locations 2023-06-16 20:17:06 2023-06-16 20:17:11 4.60 dict {'P04217': {RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), Ramilo...(truncated) 18,852 {} 2023-06-16 20:17:06
pypath.inputs.ramp._ramp_sqldump 2023-06-16 20:17:11 2023-06-16 20:17:15 4.06 TextIOWrapper <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/2ac9fe4b32649e946c59f28f74943748-38534654' encoding='utf-8'> 0 {} 2023-06-16 20:17:11
pypath.inputs.ramp.ramp_id_types 2023-06-16 20:17:15 2023-06-16 20:25:24 488.68 set {'chemspider', 'ncbiprotein', 'pubchem', 'plantfa', 'ensembl', 'entrez', 'kegg', 'CAS', 'brenda', 'wikidata', 'gene_symbol', 'LIPIDMAPS', 'uniprot', 'lipidbank', 'kegg_glycan', 'EN', 'swisslipids', 'chebi', 'hmdb'} 19 {} 2023-06-16 20:17:15
pypath.inputs.ramp.ramp_id_types_2 2023-06-16 20:25:24 2023-06-16 20:25:32 8.41 set {'chemspider', 'ncbiprotein', 'plantfa', 'pubchem', 'ensembl', 'entrez', 'kegg', 'CAS', 'brenda', 'wikidata', 'gene_symbol', 'LIPIDMAPS', 'uniprot', 'lipidbank', 'kegg_glycan', 'EN', 'swisslipids', 'hmdb', 'chebi'} 19 {} 2023-06-16 20:25:24
pypath.inputs.ramp.ramp_list_tables 2023-06-16 20:25:32 2023-06-16 20:25:35 2.56 dict {'analyte': ['rampId', 'type'], 'analytehasontology': ['rampCompoundId', 'rampOntologyId'], 'analytehaspathway': ['rampId', 'pathwayRampId', 'pathwaySource'], 'analytesynonym': ['Synonym', 'rampId', 'geneOrCompound', 'source'], 'catalyzed': ['rampCompoundId', 'rampGeneId'], 'chem_props': ['ramp_id',...(truncated) 13 {} 2023-06-16 20:25:32
pypath.inputs.ramp.ramp_mapping 
Not calling `pypath.inputs.ramp.ramp_mapping`, not enough arguments.
 {} never
pypath.inputs.ramp.ramp_raw 
Not calling `pypath.inputs.ramp.ramp_raw`, not enough arguments.
 {} never
pypath.inputs.ramp.ramp_show_tables 2023-06-16 20:25:35 2023-06-16 20:25:37 2.59 NoneType None 0 {} 2023-06-16 20:25:35
pypath.inputs.rdata._patch_rdata 2023-06-16 20:25:37 2023-06-16 20:25:37 0.00 NoneType None 0 {} 2023-06-16 20:25:37
pypath.inputs.rdata._rdata_data_frame_get_rownames 
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments.
 {} never
pypath.inputs.rdata._rdata_list_get_names 
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments.
 {} never
pypath.inputs.reaction._bp_collect_resources 
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments.
 {} never
pypath.inputs.reaction._process_controls 
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_collect_resources 
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_collect_species 
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_compartment 
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_extract_id 
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_extract_res 
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_id 
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_reaction 
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_reactions 2023-06-16 20:25:37 2023-06-16 20:25:52 14.32 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/reaction.py", line 986, in _reactome_reactions
    for i in sp.find('bqbiol:haspart').find_all('rdf:li'):
AttributeError: 'NoneType' object has no attribute 'find_all'
{} 2023-06-12 20:55:06
pypath.inputs.reaction._reactome_reactions_et 2023-06-16 20:25:52 2023-06-16 20:25:54 2.71 tuple ({}, {}, {}) 3 {} 2023-06-16 20:25:52
pypath.inputs.reaction._reactome_res 
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_species 
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments.
 {} never
pypath.inputs.reaction.acsn_biopax 2023-06-16 20:25:54 2023-06-16 20:25:55 0.80 list ['<?xml version="1.0" encoding="UTF-8"?>\n', '<rdf:RDF\n', ' xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n', ' xmlns:owl="http://www.w3.org/2002/07/owl#"\n', ' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n', ' xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"\n', ' xml:base="...(truncated) 190,854 {} 2023-06-16 20:25:54
pypath.inputs.reaction.acsn_interactions_2 
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments.
 {} never
pypath.inputs.reaction.get_acsn_effects 2023-06-16 20:25:55 2023-06-16 20:25:55 0.08 list [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) 37,288 {} 2023-06-16 20:25:55
pypath.inputs.reaction.get_controls 
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments.
 {} never
pypath.inputs.reaction.get_interactions 
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.get_reactions 2023-06-16 20:25:55 2023-06-16 20:25:58 2.44 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
    for i, rec in enumerate(value_gen):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/reaction.py", line 1187, in get_reactions
    rea.load_all()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/pyreact.py", line 1300, in load_all
    self.load_wikipathways()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/pyreact.py", line 1193, in load_wikipathways
    self.add_dataset(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/pyreact.py", line 1314, in add_dataset
    self.merge()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/pyreact.py", line 1350, in merge
    self.merge_modifications()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/pyreact.py", line 1582, in merge_modifications
    self.load_sequences()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/pyreact.py", line 2333, in load_sequences
    self.seq = seq.swissprot_seq(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/utils/seq.py", line 55, in swissprot_seq
    data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
{} 2023-06-12 20:55:22
pypath.inputs.reaction.get_soup 
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments.
 {} never
pypath.inputs.reaction.panther_biopax 2023-06-16 20:25:58 2023-06-16 20:26:06 8.89 dict {'BioPAX/Fructose_galactose_metabolism.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/B_cell_activation.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__202...(truncated) 178 {} 2023-06-16 20:25:58
pypath.inputs.reaction.panther_interactions 
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.pid_biopax 2023-06-16 20:26:06 2023-06-16 20:26:09 2.30 NoneType None 0 {} 2023-06-16 20:26:06
pypath.inputs.reaction.pid_interactions 
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.process_complex 
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments.
 {} never
pypath.inputs.reaction.process_controls 
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments.
 {} never
pypath.inputs.reaction.process_reactions 
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactions_biopax 
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_biopax 2023-06-16 20:26:09 2023-06-16 20:26:43 33.97 TextIOWrapper <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> 0 {'fixed': True} 2023-06-16 20:26:09
pypath.inputs.reaction.reactome_bs 2023-06-16 20:26:43 2023-06-16 20:33:48 425.72 list [('R-HSA-1059683', <?xml version='1.0' encoding='utf-8' standalone='no'?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 85 on 5/30/23, 5:13 PM using JSBML version 1....(truncated) 2,629 {} 2023-06-16 20:26:43
pypath.inputs.reaction.reactome_interactions 
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_sbml 2023-06-16 20:34:12 2023-06-16 20:34:14 2.29 dict {'R-HSA-1059683.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/9c...(truncated) 2,629 {} 2023-06-16 20:34:12
pypath.inputs.scconnect.scconnect_annotations 2023-06-16 20:34:14 2023-06-16 20:34:28 13.32 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='human'), ScconnectAnnota...(truncated) 3,286 {} 2023-06-16 20:34:14
pypath.inputs.scconnect.scconnect_complexes 2023-06-16 20:34:28 2023-06-16 20:34:28 0.03 set {Complex: COMPLEX:Q16552_Q96PD4, Complex: COMPLEX:P0DML2_P0DML3, Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:P05111_P08476, Complex: COMPLEX:P01562, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P01215_P01229, Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:O75462_Q9UBD9, Complex: CO...(truncated) 17 {} 2023-06-16 20:34:28
pypath.inputs.scconnect.scconnect_interactions 2023-06-16 20:34:28 2023-06-16 20:41:09 401.72 list [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) 1,766 {} 2023-06-16 20:34:28
pypath.inputs.science.science_download 
Not calling `pypath.inputs.science.science_download`, not enough arguments.
 {} never
pypath.inputs.signalink.signalink_annotations 2023-06-16 20:41:10 2023-06-16 20:41:11 1.79 dict {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(p...(truncated) 2 {} 2023-06-16 20:41:10
pypath.inputs.signalink.signalink_function_annotations 2023-06-16 20:41:11 2023-06-16 20:41:12 0.46 dict {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) 783 {} 2023-06-16 20:41:11
pypath.inputs.signalink.signalink_interactions 2023-06-16 20:41:12 2023-06-16 20:41:12 0.44 list [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) 1,939 {} 2023-06-16 20:41:12
pypath.inputs.signalink.signalink_pathway_annotations 2023-06-16 20:41:12 2023-06-16 20:41:13 0.46 dict {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Innate immune pathways'), SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Toll...(truncated) 835 {} 2023-06-16 20:41:12
pypath.inputs.signor.signor_complexes 2023-06-16 20:41:13 2023-06-16 20:41:14 1.13 dict {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4...(truncated) 4,867 {} 2023-06-16 20:41:13
pypath.inputs.signor.signor_enzyme_substrate 2023-06-16 20:41:14 2023-06-16 20:41:16 2.02 list [{'typ': 'phosphorylation', 'resnum': 74, 'instance': 'HKPLEGKYEWQEVEK', 'substrate': 'P46527', 'start': 67, 'end': 81, 'kinase': 'P12931', 'resaa': 'Y', 'motif': 'HKPLEGKYEWQEVEK', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'17254967'}}, {'typ': 'demethylation', 'resnum': 5, ...(truncated) 10,295 {'size': 2} 2023-06-16 20:41:14
pypath.inputs.signor.signor_interactions 2023-06-16 20:41:16 2023-06-16 20:41:16 0.54 list [SignorInteraction(source='P41567', target=Complex 43S_pre_initiation_complex: COMPLEX:CHEBI:15996_CHEBI:16635_O00303_O15371_O15372_O75821_O75822_P05198_P08708_P08865_P15880_P20042_P22090_P23396_P25398_P39019_P41091_P41567_P42677_P46781_P46782_P46783_P55010_P55884_P60228_P60866_P61247_P62081_P62241_...(truncated) 90,172 {'size': 14} 2023-06-16 20:41:16
pypath.inputs.signor.signor_pathway_annotations 2023-06-16 20:41:17 2023-06-16 20:41:33 16.10 dict {'Q00534': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q06124': {SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='Leptin Signaling'), SignorPathway(pathway='EGFR Signaling')}, 'P35222': {SignorPathway(pathway='Thyroid cancer'), SignorPathway(pathway='WNT Signaling'), S...(truncated) 672 {} 2023-06-16 20:41:17
pypath.inputs.signor.signor_pathways 
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments.
 {} never
pypath.inputs.signor.signor_protein_families 2023-06-16 20:41:33 2023-06-16 20:41:33 0.00 dict {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) 90 {} 2023-06-16 20:41:33
pypath.inputs.spike.spike_complexes 2023-06-16 20:41:33 2023-06-16 20:42:19 46.13 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 {} 2023-06-16 20:41:33
pypath.inputs.spike.spike_interactions 2023-06-16 20:42:19 2023-06-16 20:42:21 2.48 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 {} 2023-06-16 20:42:19
pypath.inputs.stitch.stitch_actions_interactions 2023-06-16 20:42:21 2023-06-16 20:43:38 76.66 list [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) 21,773,491 {} 2023-06-16 20:42:21
pypath.inputs.stitch.stitch_links_interactions 2023-06-16 20:43:38 2023-06-16 20:45:10 92.29 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 {} 2023-06-16 20:43:38
pypath.inputs.string.string_effects 2023-06-16 20:45:10 2023-06-16 20:45:20 9.20 list [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) 2,250,122 {} 2023-06-16 20:45:10
pypath.inputs.string.string_links_interactions 2023-06-16 20:45:21 2023-06-16 20:45:51 30.18 list [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000440005', neighborhood_score=0, fusion=0, cooccurence=50, coexpression=99, experimental=679, database=900, textmining=59, combined_score=969, physical_combined_score=740), StringLinksInteraction(protein_a='ENSP00000000233', prot...(truncated) 247,200 {} 2023-06-16 20:45:21
pypath.inputs.string.string_physical_interactions 2023-06-16 20:45:51 2023-06-16 20:45:53 1.70 list [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000221957', experimental=483, database=600, textmining=821, combined_score=959), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=932, database=0, textmining=0, combined_score=932...(truncated) 83,896 {} 2023-06-16 20:45:51
pypath.inputs.string.string_species 2023-06-16 20:45:53 2023-06-16 20:45:53 0.11 dict {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) 14,094 {} 2023-06-16 20:45:53
pypath.inputs.surfaceome.surfaceome_annotations 2023-06-16 20:45:53 2023-06-16 20:45:56 3.49 dict {'A0AV02': (0.8363, 'Transporters', {'SLC12', 'APC', 'SLC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC5', 'APC', 'SLC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) 2,808 {} 2023-06-16 20:45:53
pypath.inputs.switches_elm.get_switches_elm 2023-06-16 20:45:56 2023-06-16 20:46:02 5.97 list [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) 839 {} 2023-06-16 20:45:56
pypath.inputs.talklr.talklr_annotations 2023-06-16 20:46:02 2023-06-16 20:46:03 0.54 dict {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False)}, 'Q16613': {Talklr...(truncated) 1,345 {} 2023-06-16 20:46:02
pypath.inputs.talklr.talklr_interactions 2023-06-16 20:46:03 2023-06-16 20:46:03 0.04 list [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) 2,422 {} 2023-06-16 20:46:03
pypath.inputs.talklr.talklr_raw 2023-06-16 20:46:03 2023-06-16 20:46:03 0.03 DataFrame Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) 2,422 {} 2023-06-16 20:46:03
pypath.inputs.tcdb.tcdb_annotations 2023-06-16 20:46:03 2023-06-16 20:46:09 5.68 dict {'P60201': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.4'), 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(fam...(truncated) 2,223 {} 2023-06-16 20:46:03
pypath.inputs.tcdb.tcdb_classes 2023-06-16 20:46:09 2023-06-16 20:46:09 0.05 dict {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) 23,101 {'size': 14} 2023-06-16 20:46:09
pypath.inputs.tcdb.tcdb_families 2023-06-16 20:46:09 2023-06-16 20:46:09 0.01 dict {'1.A.1': 'Voltage-gated Ion Channel (VIC)', '1.A.10': 'Glutamate-gated Ion Channel (GIC) of Neurotransmitter Receptors', '1.A.100': 'Rhabdoviridae Putative Viroporin, U5 (RV-U5)', '1.A.101': 'Peroxisomal Pore-forming Pex11 (Pex11)', '1.A.102': 'Influenza A viroporin PB1-F2 (PB1-F2)', '1.A.103': 'Si...(truncated) 1,822 {'size': 1} 2023-06-16 20:46:09
pypath.inputs.tfcensus.tfcensus_annotations 2023-06-16 20:46:09 2023-06-16 20:46:09 0.21 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) 1,490 {} 2023-06-16 20:46:09
pypath.inputs.threedcomplex.threedcomplex_chains 2023-06-16 20:46:09 2023-06-16 20:46:15 5.76 dict {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) 174,325 {} 2023-06-16 20:46:09
pypath.inputs.threedcomplex.threedcomplex_contacts 2023-06-16 20:46:15 2023-06-16 20:46:39 23.90 set {ThreedcomplexContact(pdb='3cf5_1', uniprot_1='Q9RWB4', uniprot_2='Q9RXK2', chain_1='M', chain_2='B', n_residues=20.5, length_1=108, length_2=205, domain_s1=('50104',), domain_p1=('PF01245.15',), domain_s2=('50447',), domain_p2=('PF00297.17',), ident=False, homo=False), ThreedcomplexContact(pdb='1th...(truncated) 259,809 {} 2023-06-16 20:46:15
pypath.inputs.threedcomplex.threedcomplex_ddi 2023-06-16 20:46:40 2023-06-16 20:49:32 172.55 list [<pypath.internals.intera.DomainDomain object at 0x7f8ef26e1750>, <pypath.internals.intera.DomainDomain object at 0x7f8ef26e1960>, <pypath.internals.intera.DomainDomain object at 0x7f8ef26e18a0>, <pypath.internals.intera.DomainDomain object at 0x7f8ef26e1a50>, <pypath.internals.intera.DomainDomain o...(truncated) 524,460 {} 2023-06-16 20:46:40
pypath.inputs.threedcomplex.threedcomplex_nresidues 2023-06-16 20:49:33 2023-06-16 20:49:42 8.73 dict {'3cf5_1': {('Q9RWB4', 'Q9RXK2'): 20.5, ('Q9RXJ2', 'Q9RXK2'): 3.5, ('Q9RSK9', 'Q9RY64'): 2.5, ('Q9RX88', 'Q9RXJ5'): 13.0, ('Q9RSS7', 'Q9RX88'): 1.0, ('Q9RSW7', 'Q9RXY1'): 6.5, ('Q9RXJ5', 'Q9RY65'): 1.5, ('P49228', 'Q9RXJ7'): 8.5, ('Q9RSK9', 'Q9RSW6'): 3.0, ('Q9RXK2', 'Q9RXY1'): 2.5, ('Q9RSW7', 'Q9RY...(truncated) 81,193 {} 2023-06-16 20:49:33
pypath.inputs.threedid.get_3did 2023-06-16 20:49:42 2023-06-16 21:23:16 2,014.04 tuple ([<pypath.internals.intera.DomainDomain object at 0x7f8edc358c70>, <pypath.internals.intera.DomainDomain object at 0x7f8edc358250>, <pypath.internals.intera.DomainDomain object at 0x7f8edc35aa70>, <pypath.internals.intera.DomainDomain object at 0x7f8edc359db0>, <pypath.internals.intera.DomainDomain ...(truncated) 2 {} 2023-06-16 20:49:42
pypath.inputs.threedid.get_3did_ddi 2023-06-16 21:23:16 2023-06-16 21:23:19 2.58 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/threedid.py", line 59, in get_3did_ddi
    u_pfam, pfam_u = pfam_input.pfam_uniprot(organism = organism)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/pfam.py", line 100, in pfam_uniprot
    data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
{} 2023-06-12 21:49:16
pypath.inputs.topdb.topdb_annotations 2023-06-16 21:23:19 2023-06-16 21:23:22 3.44 dict {'P05067': {TopdbAnnotation(membrane='Plasma membrane', topology='Inside', score=89, tmregions=1), TopdbAnnotation(membrane='Plasma membrane', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplasm', topology='Inside', score=89, tmregions=1), TopdbAnnotation(membrane='Extra...(truncated) 1,245 {'size': -2} 2023-06-16 21:23:19
pypath.inputs.transmir.transmir_interactions 2023-06-16 21:23:22 2023-06-16 21:23:23 0.69 list [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) 2,678 {} 2023-06-16 21:23:22
pypath.inputs.trip.take_a_trip 2023-06-16 21:23:23 2023-06-16 21:23:23 0.01 dict {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) 5 {} 2023-06-16 21:23:23
pypath.inputs.trip.trip_find_uniprot 
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments.
 {} never
pypath.inputs.trip.trip_get_uniprot 
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments.
 {} never
pypath.inputs.trip.trip_interactions 2023-06-16 21:23:23 2023-06-16 21:23:23 0.01 list [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;12601176;11290752', 'Fluorescence probe labeling;Patch clamp;Fusion protein-pull down ...(truncated) 359 {} 2023-06-16 21:23:23
pypath.inputs.trip.trip_process 2023-06-16 21:23:23 2023-06-16 21:23:23 0.01 dict {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Porcine coronary artery', 'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell', 'HEK293'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) 359 {} 2023-06-16 21:23:23
pypath.inputs.trip.trip_process_table 
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments.
 {} never
pypath.inputs.unichem._unichem_mapping 
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.info 
Not calling `pypath.inputs.unichem.info`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_info 2023-06-16 21:23:23 2023-06-16 21:23:23 0.02 list [UnichemSource(number='1', label='chembl', name='ChEMBL', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) 41 {} 2023-06-16 21:23:23
pypath.inputs.unichem.unichem_mapping 
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_sources 2023-06-16 21:23:23 2023-06-16 21:23:23 0.02 dict {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma', '22': 'pubc...(truncated) 41 {} 2023-06-16 21:23:23
pypath.inputs.uniprot._all_uniprots 2023-06-16 21:23:23 2023-06-16 21:23:23 0.05 set {'D6RA70', 'A0A5C2GFF1', 'A0A5C2G2N7', 'B4DMD1', 'B7Z9U4', 'A0A3S6H8W3', 'G0Z8E4', 'H7C5P5', 'B4E0Z4', 'C9J1W4', 'H3BRQ8', 'D6MLI8', 'I3L448', 'Q6MZV6', 'A8K237', 'A0A5C2G943', 'Q3SY98', 'A0A0G2JS92', 'A0A8Q3WKT2', 'Q53EQ5', 'D0R7H5', 'F2VNC4', 'Q75NJ4', 'A0A024R1B6', 'A0A5C2GTX1', 'E3SWG5', 'C9JS50...(truncated) 207,780 {} 2023-06-16 21:23:23
pypath.inputs.uniprot._cleanup 2023-06-16 21:23:23 2023-06-16 21:23:23 0.00 NoneType None 0 {} 2023-06-16 21:23:23
pypath.inputs.uniprot._protein_datasheet 
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot._remove 
Not calling `pypath.inputs.uniprot._remove`, not enough arguments.
 {} never
pypath.inputs.uniprot._swissprot_param 
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments.
 {} never
pypath.inputs.uniprot.all_swissprots 2023-06-16 21:23:23 2023-06-16 21:23:23 0.00 set {'Q7Z4L0', 'Q6ZTQ3', 'O14609', 'Q8N8E1', 'K7EIQ3', 'Q6ZVT6', 'Q8TF01', 'O75129', 'Q9BTX7', 'O00461', 'Q0P5N6', 'Q9Y324', 'P0C7M4', 'Q4ZG55', 'Q13084', 'Q9H091', 'P23219', 'Q75NE6', 'Q99489', 'Q6ZVE7', 'Q8NAQ8', 'Q5T481', 'Q86X02', 'Q13349', 'Q5VTY9', 'Q99259', 'Q8NHZ8', 'Q8TDW4', 'Q8N0V1', 'Q9P275',...(truncated) 20,422 {} 2023-06-16 21:23:23
pypath.inputs.uniprot.all_trembls 2023-06-16 21:23:23 2023-06-16 21:24:02 39.34 set {'D6RA70', 'A0A5C2GFF1', 'A0A5C2G2N7', 'B4DMD1', 'B7Z9U4', 'A0A3S6H8W3', 'G0Z8E4', 'H7C5P5', 'B4E0Z4', 'C9J1W4', 'H3BRQ8', 'D6MLI8', 'I3L448', 'Q6MZV6', 'A8K237', 'A0A5C2G943', 'Q3SY98', 'A0A0G2JS92', 'A0A8Q3WKT2', 'Q53EQ5', 'D0R7H5', 'F2VNC4', 'Q75NJ4', 'A0A024R1B6', 'A0A5C2GTX1', 'E3SWG5', 'C9JS50...(truncated) 187,358 {} 2023-06-16 21:23:23
pypath.inputs.uniprot.all_uniprots 2023-06-16 21:24:02 2023-06-16 21:24:02 0.00 set {'D6RA70', 'A0A5C2GFF1', 'A0A5C2G2N7', 'B4DMD1', 'B7Z9U4', 'A0A3S6H8W3', 'G0Z8E4', 'H7C5P5', 'B4E0Z4', 'C9J1W4', 'H3BRQ8', 'D6MLI8', 'I3L448', 'Q6MZV6', 'A8K237', 'A0A5C2G943', 'Q3SY98', 'A0A0G2JS92', 'A0A8Q3WKT2', 'Q53EQ5', 'D0R7H5', 'F2VNC4', 'Q75NJ4', 'A0A024R1B6', 'A0A5C2GTX1', 'E3SWG5', 'C9JS50...(truncated) 207,780 {} 2023-06-16 21:24:02
pypath.inputs.uniprot.deleted_uniprot_genesymbol 
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments.
 {} never
pypath.inputs.uniprot.get_db 2023-06-16 21:24:02 2023-06-16 21:24:02 0.00 set {'D6RA70', 'A0A5C2GFF1', 'A0A5C2G2N7', 'B4DMD1', 'B7Z9U4', 'A0A3S6H8W3', 'G0Z8E4', 'H7C5P5', 'B4E0Z4', 'C9J1W4', 'H3BRQ8', 'D6MLI8', 'I3L448', 'Q6MZV6', 'A8K237', 'A0A5C2G943', 'Q3SY98', 'A0A0G2JS92', 'A0A8Q3WKT2', 'Q53EQ5', 'D0R7H5', 'F2VNC4', 'Q75NJ4', 'A0A024R1B6', 'A0A5C2GTX1', 'E3SWG5', 'C9JS50...(truncated) 207,780 {} 2023-06-16 21:24:02
pypath.inputs.uniprot.get_uniprot_sec 2023-06-16 21:24:03 2023-06-16 21:24:03 0.80 list [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZR6', 'Q9UII6'], ['A0A024R056', 'A0A140VJJ8'], ['A0A024R072', 'Q96S94'], ['A0A024R...(truncated) 72,055 {} 2023-06-16 21:24:03
pypath.inputs.uniprot.init_db 2023-06-16 21:24:03 2023-06-16 21:24:03 0.06 NoneType None 0 {} 2023-06-16 21:24:03
pypath.inputs.uniprot.is_swissprot 
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments.
 {} never
pypath.inputs.uniprot.is_trembl 
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments.
 {} never
pypath.inputs.uniprot.is_uniprot 
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments.
 {} never
pypath.inputs.uniprot.protein_datasheet 
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_data 
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_families 2023-06-16 21:24:03 2023-06-16 21:24:22 18.58 dict {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0B4J2F2': {UniprotFamily(family='Protein kinase superfamily, CAMK Ser/Thr protein kinase', subfamily='AMPK')}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M...(truncated) 14,420 {} 2023-06-16 21:24:03
pypath.inputs.uniprot.uniprot_history 
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_history_recent_datasheet 
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_keywords 2023-06-16 21:24:22 2023-06-16 21:24:39 16.56 dict {'A0A087X1C5': {UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Heme'), UniprotKeyword(keyword='Transmembrane helix'), UniprotKeyword(keyword='Transmembrane'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Monooxygenase'), UniprotKeyword(keyword='Reference proteome'),...(truncated) 20,422 {} 2023-06-16 21:24:22
pypath.inputs.uniprot.uniprot_locations 2023-06-16 21:24:39 2023-06-16 21:24:56 17.53 dict {'A0A087X1C5': {UniprotLocation(location='Mitochondrion', features=None), UniprotLocation(location='Membrane', features=('Multi-pass membrane protein',)), UniprotLocation(location='Cytoplasm', features=None)}, 'A0A0B4J2F0': {UniprotLocation(location='Mitochondrion outer membrane', features=('Single-...(truncated) 17,037 {} 2023-06-16 21:24:39
pypath.inputs.uniprot.uniprot_ncbi_taxids_2 2023-06-16 21:24:56 2023-06-16 21:24:57 0.35 dict {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) 27,305 {} 2023-06-16 21:24:56
pypath.inputs.uniprot.uniprot_preprocess 
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_recent_version 
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_taxonomy 2023-06-16 21:24:57 2023-06-16 21:24:59 2.10 dict {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Pinus balsamea', 'Abies balsamea', 'Balsam fir'}, 'H8ZM71': {'Pinus balsamea', 'Abies balsamea', 'Balsam fir'}, 'Q9MV51': {'Momi fir', 'Abies firma'}, 'O81086': {'Pinus grandis', 'Abies grandis', '...(truncated) 555,077 {} 2023-06-16 21:24:57
pypath.inputs.uniprot.uniprot_tissues 2023-06-16 21:24:59 2023-06-16 21:25:16 17.38 dict {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Skeletal muscle', level='undefined'), UniprotTissue(tissue='Plasma', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Myeloid dendritic cells', level='undefined'), UniprotTissue(ti...(truncated) 10,047 {} 2023-06-16 21:24:59
pypath.inputs.uniprot.uniprot_topology 2023-06-16 21:25:17 2023-06-16 21:26:31 74.12 dict {'A0A087X1C5': {UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', start=3, end=23), UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Cytoplasmic',...(truncated) 5,237 {} 2023-06-16 21:25:17
pypath.inputs.uniprot.valid_uniprot 
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments.
 {} never
pypath.inputs.wang._wang_process 
Not calling `pypath.inputs.wang._wang_process`, not enough arguments.
 {} never
pypath.inputs.wang.cui_interactions 2023-06-16 21:26:31 2023-06-16 21:26:35 4.56 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/common.py", line 112, in read_xls
    book = openpyxl.load_workbook(
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 344, in load_workbook
    reader = ExcelReader(filename, read_only, keep_vba,
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 123, in __init__
    self.archive = _validate_archive(fn)
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 95, in _validate_archive
    archive = ZipFile(filename, 'r')
  File "/usr/lib/python3.10/zipfile.py", line 1267, in __init__
    self._RealGetContents()
  File "/usr/lib/python3.10/zipfile.py", line 1334, in _RealGetContents
    raise BadZipFile("File is not a zip file")
zipfile.BadZipFile: File is not a zip file

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/wang.py", line 144, in cui_interactions
    raw = embo.embopress_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embopress.py", line 107, in embopress_supplementary
    inputs_common.read_xls(fname, sheet = sheet)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/common.py", line 120, in read_xls
    raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: <_io.BufferedReader name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/e2b39a322462f0f9978a1e2965dba6e1-downloadSupplement'>
{'broke': True} 2023-06-15 21:38:47
pypath.inputs.wang.hsn_interactions 2023-06-16 21:26:35 2023-06-16 21:26:36 0.41 list [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) 62,937 {} 2023-06-16 21:26:35
pypath.inputs.wang.wang_annotations 2023-06-16 21:26:36 2023-06-16 21:26:36 0.02 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/common.py", line 112, in read_xls
    book = openpyxl.load_workbook(
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 344, in load_workbook
    reader = ExcelReader(filename, read_only, keep_vba,
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 123, in __init__
    self.archive = _validate_archive(fn)
  File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-qaTZp30J-py3.10/lib/python3.10/site-packages/openpyxl/reader/excel.py", line 95, in _validate_archive
    archive = ZipFile(filename, 'r')
  File "/usr/lib/python3.10/zipfile.py", line 1267, in __init__
    self._RealGetContents()
  File "/usr/lib/python3.10/zipfile.py", line 1334, in _RealGetContents
    raise BadZipFile("File is not a zip file")
zipfile.BadZipFile: File is not a zip file

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/wang.py", line 267, in wang_annotations
    data = func()
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/wang.py", line 144, in cui_interactions
    raw = embo.embopress_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/embopress.py", line 107, in embopress_supplementary
    inputs_common.read_xls(fname, sheet = sheet)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/common.py", line 120, in read_xls
    raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: <_io.BufferedReader name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/cache/e2b39a322462f0f9978a1e2965dba6e1-downloadSupplement'>
{'broke': True} 2023-06-15 21:38:51
pypath.inputs.wang.wang_interactions 2023-06-16 21:26:36 2023-06-16 21:26:36 0.38 list [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) 62,937 {} 2023-06-16 21:26:36
pypath.inputs.wojtowicz2020._id_translate 
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments.
 {} never
pypath.inputs.wojtowicz2020.wojtowicz2020_interactions 2023-06-16 21:26:36 2023-06-16 21:26:36 0.10 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/wojtowicz2020.py", line 84, in wojtowicz2020_interactions
    for rec in wojtowicz2020_raw():
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/wojtowicz2020.py", line 42, in wojtowicz2020_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 21:52:42
pypath.inputs.wojtowicz2020.wojtowicz2020_raw 2023-06-16 21:26:36 2023-06-16 21:26:36 0.07 
Traceback (most recent call last):
  File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
    value = fun(*_args, **_kwargs)
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/wojtowicz2020.py", line 42, in wojtowicz2020_raw
    path = cell_input.cell_supplementary(
  File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230616-182602/pypath_git/pypath/inputs/cell.py", line 133, in cell_supplementary
    c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2023-06-12 21:52:42
pypath.inputs.zhong2015.zhong2015_annotations 2023-06-16 21:26:36 2023-06-16 21:26:37 0.47 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 {} 2023-06-16 21:26:36

The OmniPath Team • Saez Lab • 2023-06-16