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 2021-10-19 02:00:02 and 2021-10-19 05:07:26; pypath version: 0.12.0 (from git; 5e75930 )

Modules collected: 145
Modules failed to import: 0
Functions collected: 463
Functions run without error: 282
Functions returned empty value: 13
Functions skipped due to lack of arguments: 118
Functions run with error: 63

Function Started Finished Elapsed (s) Result type Result repr Result size Error
pypath.inputs.abs.abs_interactions 2021-10-19 02:00:09 2021-10-19 02:00:09 0.39 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
pypath.inputs.acsn.acsn_interactions 2021-10-19 02:00:09 2021-10-19 02:00:10 0.54 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
pypath.inputs.acsn.acsn_interactions_sif 2021-10-19 02:00:10 2021-10-19 02:00:10 0.34 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
pypath.inputs.adhesome.adhesome_annotations 2021-10-19 02:00:12 2021-10-19 02:01:06 54.68 defaultdict defaultdict(<class 'set'>, {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclas...(truncated) 239
pypath.inputs.adhesome.adhesome_interactions 2021-10-19 02:01:06 2021-10-19 02:01:07 0.25 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
pypath.inputs.almen2009.almen2009_annotations 2021-10-19 02:01:07 2021-10-19 02:01:09 2.43 defaultdict defaultdict(<class 'set'>, {'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_transme...(truncated) 4,828
pypath.inputs.baccin2019.baccin2019_annotations 2021-10-19 02:01:09 2021-10-19 02:09:18 488.78 dict {} 0
pypath.inputs.baccin2019.baccin2019_interactions 2021-10-19 02:09:18 2021-10-19 02:09:32 14.25 list [] 0
pypath.inputs.biogps.biogps_annotations 2021-10-19 02:09:32 2021-10-19 02:44:19 2,086.59 defaultdict defaultdict(<class 'set'>, {'Q08345': {BiogpsAnnotation(dataset='human_gene_atlas', sample='CerebellumPeduncles_1', probe='208779_x_at', expression=107.2), BiogpsAnnotation(dataset='human_nci60', sample='SN12C', probe='1007_s_at', expression=351.27), BiogpsAnnotation(dataset='human_gene_atlas', samp...(truncated) 13,237
pypath.inputs.biogps.biogps_datasets 2021-10-19 02:44:30 2021-10-19 02:44:30 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
pypath.inputs.biogps.biogps_download 
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments.
pypath.inputs.biogps.biogps_download_all 2021-10-19 02:44:30 2021-10-19 02:45:00 30.38 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
pypath.inputs.biogrid.biogrid_interactions 2021-10-19 02:45:01 2021-10-19 02:45:09 8.46 list [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridInteraction(partner_a='CDKN3', partner_b='CDK2', pmid='12745075'), BiogridInteraction(partner_a='PPARGC1B', partner_b='ESR1', pmid='11854298'), Biog...(truncated) 6,430
pypath.inputs.biomart.biomart_homology 2021-10-19 02:45:09 2021-10-19 02:45:42 32.34 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) 168,975
pypath.inputs.biomart.biomart_microarray 
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments.
pypath.inputs.biomart.biomart_microarray_types 2021-10-19 02:45:42 2021-10-19 02:45:42 0.00 list [{'array': 'OneArray', 'format': 'EXPRESSION', 'type': 'OLIGO', 'description': None, 'vendor': 'PHALANX', 'label': 'PHALANX OneArray'}, {'description': None, 'vendor': 'CODELINK', 'type': 'OLIGO', 'format': 'EXPRESSION', 'array': 'CODELINK', 'label': 'CODELINK CODELINK'}, {'array': 'HumanWG_6_V2', '...(truncated) 37
pypath.inputs.biomart.biomart_microarrays 2021-10-19 02:45:42 2021-10-19 03:36:35 3,053.49 dict {'ENSG00000198712': {Probe(array='agilent_sureprint_g3_ge_8x60k_v2', probe='A_23_P402751'), Probe(array='agilent_wholegenome_4x44k_v1', probe='A_23_P402751'), Probe(array='affy_hta_2_0', probe='TC0M000021.hg'), Probe(array='affy_huex_1_0_st_v2', probe='4037634'), Probe(array='agilent_wholegenome', p...(truncated) 64,002
pypath.inputs.biomart.biomart_query 
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments.
pypath.inputs.ca1.ca1_interactions 2021-10-19 03:36:37 2021-10-19 03:36:38 1.31 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/ca1.py", line 55, in ca1_interactions
    path = science_input.science_download(url = url)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/science.py", line 60, in science_download
    c_init = curl.Curl(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 935, in __init__
    self.curl_call()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1329, in curl_call
    self.remove_target()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1339, in remove_target
    os.remove(self.target.name)
PermissionError: [Errno 13] Permission denied: '/dev/null'
pypath.inputs.cancercellmap.ccmap_interactions 2021-10-19 03:36:38 2021-10-19 03:36:40 1.77 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
pypath.inputs.cancerdrugs_db.cancerdrugs_db_annotations 2021-10-19 03:36:40 2021-10-19 03:36:48 8.06 defaultdict defaultdict(<class 'set'>, {'46220502': {CancerDrugsAnnotation(label='Abemaciclib', indications='Advanced Breast Cancer; Metastatic Breast Cancer', last_updated='17/09/2020')}, '132971': {CancerDrugsAnnotation(label='Abiraterone', indications='Metastatic Castration Resistant Prostate Cancer', last_u...(truncated) 197
pypath.inputs.cancerdrugs_db.cancerdrugs_db_download 2021-10-19 03:36:48 2021-10-19 03:36:48 0.00 list [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', '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">CHEMBL3301610</...(truncated) 281
pypath.inputs.cancerdrugs_db.cancerdrugs_db_interactions 2021-10-19 03:36:48 2021-10-19 03:36:49 1.01 list [CancerDrugsInteraction(source={'46220502'}, target={'Q00534'}), CancerDrugsInteraction(source={'46220502'}, target={'P11802'}), CancerDrugsInteraction(source={'46220502'}, target={'P30281'}), CancerDrugsInteraction(source={'46220502'}, target={'Q8N726', 'P42771'}), CancerDrugsInteraction(source={'4...(truncated) 2,040
pypath.inputs.cancersea.cancersea_annotations 2021-10-19 03:36:49 2021-10-19 03:36:51 2.17 dict {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Angiogenesis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) 1,246
pypath.inputs.cell.cell_supplementary 
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments.
pypath.inputs.cellcall.cellcall_annotations 2021-10-19 03:36:51 2021-10-19 03:36:53 1.73 dict {'P98172': {CellcallAnnotation(role='ligand')}, 'O15197': {CellcallAnnotation(role='receptor')}, 'P03971': {CellcallAnnotation(role='ligand')}, 'O00238': {CellcallAnnotation(role='receptor')}, 'Q8IU54': {CellcallAnnotation(role='ligand')}, 'Q08334': {CellcallAnnotation(role='receptor')}, 'P05013': {...(truncated) 460
pypath.inputs.cellcall.cellcall_download 2021-10-19 03:36:53 2021-10-19 03:36:53 0.05 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
pypath.inputs.cellcall.cellcall_download_all 2021-10-19 03:36:53 2021-10-19 03:36:54 1.03 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
pypath.inputs.cellcall.cellcall_interactions 2021-10-19 03:36:54 2021-10-19 03:36:55 1.33 list [CellcallInteraction(ligand_uniprot='P98172', receptor_uniprot='O15197', core=True), CellcallInteraction(ligand_uniprot='P03971', receptor_uniprot='O00238', core=True), CellcallInteraction(ligand_uniprot='Q8IU54', receptor_uniprot='Q08334', core=True), CellcallInteraction(ligand_uniprot='P05013', re...(truncated) 797
pypath.inputs.cellcellinteractions.cellcellinteractions_annotations 2021-10-19 03:36:55 2021-10-19 03:36:57 1.63 dict {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='ECM')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor'), Cellcellinterac...(truncated) 3,427
pypath.inputs.cellchatdb._cellchatdb_organism 2021-10-19 03:36:57 2021-10-19 03:36:57 0.00 int 9606 None
pypath.inputs.cellchatdb._cellchatdb_process_cofactors 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments.
pypath.inputs.cellchatdb._cellchatdb_process_complexes 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments.
pypath.inputs.cellchatdb.cellchatdb_annotations 2021-10-19 03:36:57 2021-10-19 03:37:03 5.85 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 325, in cellchatdb_annotations
    interactions = cellchatdb_interactions(organism = organism)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 227, in cellchatdb_interactions
    raw = cellchatdb_download(organism = organism)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 70, in cellchatdb_download
    rownames = [
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 71, in <listcomp>
    rdata._rdata_data_frame_get_rownames(df_obj)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/rdata.py", line 28, in _rdata_data_frame_get_rownames
    for i, attr in enumerate(robj.attributes):
TypeError: 'RObject' object is not iterable
pypath.inputs.cellchatdb.cellchatdb_cofactors 2021-10-19 03:37:03 2021-10-19 03:37:08 4.93 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 142, in cellchatdb_cofactors
    raw = cellchatdb_download(organism = organism)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 70, in cellchatdb_download
    rownames = [
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 71, in <listcomp>
    rdata._rdata_data_frame_get_rownames(df_obj)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/rdata.py", line 28, in _rdata_data_frame_get_rownames
    for i, attr in enumerate(robj.attributes):
TypeError: 'RObject' object is not iterable
pypath.inputs.cellchatdb.cellchatdb_complexes 2021-10-19 03:37:08 2021-10-19 03:37:14 5.52 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 96, in cellchatdb_complexes
    raw = cellchatdb_download(organism = organism)['complex']
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 70, in cellchatdb_download
    rownames = [
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 71, in <listcomp>
    rdata._rdata_data_frame_get_rownames(df_obj)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/rdata.py", line 28, in _rdata_data_frame_get_rownames
    for i, attr in enumerate(robj.attributes):
TypeError: 'RObject' object is not iterable
pypath.inputs.cellchatdb.cellchatdb_download 2021-10-19 03:37:14 2021-10-19 03:37:19 4.97 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 70, in cellchatdb_download
    rownames = [
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 71, in <listcomp>
    rdata._rdata_data_frame_get_rownames(df_obj)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/rdata.py", line 28, in _rdata_data_frame_get_rownames
    for i, attr in enumerate(robj.attributes):
TypeError: 'RObject' object is not iterable
pypath.inputs.cellchatdb.cellchatdb_interactions 2021-10-19 03:37:19 2021-10-19 03:37:24 5.53 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 227, in cellchatdb_interactions
    raw = cellchatdb_download(organism = organism)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 70, in cellchatdb_download
    rownames = [
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/cellchatdb.py", line 71, in <listcomp>
    rdata._rdata_data_frame_get_rownames(df_obj)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/rdata.py", line 28, in _rdata_data_frame_get_rownames
    for i, attr in enumerate(robj.attributes):
TypeError: 'RObject' object is not iterable
pypath.inputs.cellinker._cellinker_interactions_raw 2021-10-19 03:37:24 2021-10-19 03:37:27 2.99 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
pypath.inputs.cellinker._cellinker_uniprots 
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments.
pypath.inputs.cellinker.cellinker_annotations 2021-10-19 03:37:27 2021-10-19 03:37:28 0.89 dict {'P08575': {CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), Cellink...(truncated) 1,921
pypath.inputs.cellinker.cellinker_complex_annotations 2021-10-19 03:37:28 2021-10-19 03:37:29 0.54 dict {Complex: COMPLEX:O75581_Q9ULV1: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, Complex: COMPLEX:P17181_P48551: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor interaction'), CellinkerAnnotatio...(truncated) 134
pypath.inputs.cellinker.cellinker_complexes 2021-10-19 03:37:29 2021-10-19 03:37:29 0.02 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
pypath.inputs.cellinker.cellinker_complexes_raw 2021-10-19 03:37:29 2021-10-19 03:37:29 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
pypath.inputs.cellinker.cellinker_lr_interactions 2021-10-19 03:37:29 2021-10-19 03:37:29 0.53 set {CellinkerInteraction(ligand='P08575', receptor='P20273', ligand_location='Membrane', receptor_location='Membrane', resources='CellPhoneDB', pmids='12115612', type='Cell adhesion'), CellinkerInteraction(ligand='O14904', receptor=Complex: COMPLEX:O75581_Q9ULV1, ligand_location='Secreted', receptor_lo...(truncated) 3,812
pypath.inputs.cellinker.cellinker_lr_interactions_raw 2021-10-19 03:37:29 2021-10-19 03:37:29 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
pypath.inputs.cellinker.cellinker_protein_annotations 2021-10-19 03:37:29 2021-10-19 03:37:30 0.54 dict {'P08575': {CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), Cellink...(truncated) 1,787
pypath.inputs.cellinker.cellinker_smol_interactions 2021-10-19 03:37:30 2021-10-19 03:37:30 0.68 set {CellinkerInteraction(ligand='5280939', receptor='Q86XQ3', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='21412339', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5283155', receptor='Q9NPC1', ligand_location=None, receptor_location='Membrane', ...(truncated) 315
pypath.inputs.cellinker.cellinker_smol_interactions_raw 2021-10-19 03:37:30 2021-10-19 03:37:30 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
pypath.inputs.cellinker.components_to_complex 
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments.
pypath.inputs.cellphonedb._cellphonedb_annotations 
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments.
pypath.inputs.cellphonedb._cellphonedb_get_entity 
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments.
pypath.inputs.cellphonedb._cellphonedb_hla 
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments.
pypath.inputs.cellphonedb.cellphonedb_complex_annotations 2021-10-19 03:37:30 2021-10-19 03:37:31 0.22 dict {Complex ACVL1_BMPR2: COMPLEX:P37023_Q13873: CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), Complex ACVR1_BMPR2: COMPLEX:Q04771_Q13873: CellPhoneDBAnnotation(receptor=True, receptor_class=('...(truncated) 112
pypath.inputs.cellphonedb.cellphonedb_complexes 2021-10-19 03:37:31 2021-10-19 03:37:31 0.02 dict {'COMPLEX:P37023_Q13873': Complex ACVL1_BMPR2: COMPLEX:P37023_Q13873, 'COMPLEX:Q04771_Q13873': Complex ACVR1_BMPR2: COMPLEX:Q04771_Q13873, 'COMPLEX:P27037_Q04771': Complex ACVR_1A2A receptor: COMPLEX:P27037_Q04771, 'COMPLEX:Q04771_Q13705': Complex ACVR_1A2B receptor: COMPLEX:Q04771_Q13705, 'COMPLEX:...(truncated) 112
pypath.inputs.cellphonedb.cellphonedb_interactions 2021-10-19 03:37:31 2021-10-19 03:37:31 0.60 list [CellphonedbInteraction(id_a=Complex IL12: COMPLEX:P29459_P29460, id_b=Complex IL12 receptor: COMPLEX:P42701_Q99665, sources='CellPhoneDB', references='', interaction_type='ligand-receptor', type_a='ligand', type_b='receptor'), CellphonedbInteraction(id_a=Complex Activin ligand ab: COMPLEX:P08476_P0...(truncated) 1,396
pypath.inputs.cellphonedb.cellphonedb_ligands_receptors 2021-10-19 03:37:31 2021-10-19 03:37:31 0.05 tuple ({'P01258', 'P05113', 'P49763', 'P15813', 'O95150', 'P12109', 'Q68D85', 'Q13740', 'P09681', 'P13598', 'Q9UBU3', 'O15444', Complex a4b1 complex: COMPLEX:P05556_P13612, 'Q6UVK1', 'O60258', 'P03971', 'P01732', 'Q14213', Complex a6b4 complex: COMPLEX:P16144_P23229, 'Q495A1', 'Q6UW32', 'Q13261', 'Q6UXX9'...(truncated) 2
pypath.inputs.cellphonedb.cellphonedb_protein_annotations 2021-10-19 03:37:31 2021-10-19 03:37:31 0.04 dict {'A4D1S0': CellPhoneDBAnnotation(receptor=True, receptor_class=('klr',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), 'A6NMZ7': CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transme...(truncated) 978
pypath.inputs.celltalkdb.celltalkdb_annotations 2021-10-19 03:37:31 2021-10-19 03:37:43 11.65 defaultdict defaultdict(<class 'set'>, {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='15721238'), CellTalkDBAnnotation(role='ligand', pmid='26156437')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='recep...(truncated) 1,598
pypath.inputs.celltalkdb.celltalkdb_download 2021-10-19 03:37:43 2021-10-19 03:37:43 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
pypath.inputs.celltalkdb.celltalkdb_interactions 2021-10-19 03:37:43 2021-10-19 03:37:43 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
pypath.inputs.compleat.compleat_complexes 2021-10-19 03:37:43 2021-10-19 03:37:47 3.83 dict {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) 9,693
pypath.inputs.compleat.compleat_raw 2021-10-19 03:37:47 2021-10-19 03:37:47 0.06 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
pypath.inputs.complexportal.complexportal_complexes 2021-10-19 03:37:47 2021-10-19 03:38:33 45.58 dict {'COMPLEX:P84022_Q13485_Q15796': Complex SMAD2-SMAD3-SMAD4 complex: COMPLEX:P84022_Q13485_Q15796, 'COMPLEX:P16220_P18848': Complex bZIP transcription factor complex, ATF4-CREB1: COMPLEX:P16220_P18848, 'COMPLEX:P18846_P18848': Complex bZIP transcription factor complex, ATF1-ATF4: COMPLEX:P18846_P1884...(truncated) 1,191
pypath.inputs.comppi.comppi_interaction_locations 2021-10-19 03:38:33 2021-10-19 03:39:29 56.21 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) 591,338
pypath.inputs.comppi.comppi_locations 2021-10-19 03:39:29 2021-10-19 03:40:25 56.42 dict {'Q8TES7': {ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation(location='membrane', score=0.96), ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='nucleus', score=0.9099999999999999), ComppiLocation...(truncated) 18,238
pypath.inputs.connectomedb.connectomedb_annotations 2021-10-19 03:40:25 2021-10-19 03:40:26 0.56 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
pypath.inputs.connectomedb.connectomedb_interactions 2021-10-19 03:40:26 2021-10-19 03:40:26 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
pypath.inputs.corum.corum_complexes 2021-10-19 03:40:26 2021-10-19 03:40:26 0.29 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
pypath.inputs.cosmic.cancer_gene_census_annotations 2021-10-19 03:40:26 2021-10-19 03:40:26 0.00 dict {} 0
pypath.inputs.cpad.cpad_annotations 2021-10-19 03:40:26 2021-10-19 03:40:40 14.25 defaultdict defaultdict(<class 'set'>, {'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 cyto...(truncated) 1,036
pypath.inputs.cpad.cpad_pathway_cancer 2021-10-19 03:40:40 2021-10-19 03:40:40 0.06 tuple (defaultdict(<class 'set'>, {'Glioma': {CpadPathwayCancer(pathway='AMPK signaling pathway', cancer='Glioma', pathway_category='AMPK signaling pathway', effect_on_cancer='Activating', effect_on_cancer_outcome='induce cell migration'), CpadPathwayCancer(pathway='EGFR signaling pathway', cancer='Glioma...(truncated) 2
pypath.inputs.cpad.get_cpad 2021-10-19 03:40:40 2021-10-19 03:40:40 0.00 DictReader <csv.DictReader object at 0x7f111e381e20> None
pypath.inputs.cpdb.cpdb_interactions 2021-10-19 03:40:40 2021-10-19 03:40:44 3.13 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 531,371
pypath.inputs.cpdb.cpdb_interactions_ltp 2021-10-19 03:40:44 2021-10-19 03:40:46 1.65 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
pypath.inputs.csa.get_csa 2021-10-19 03:40:46 2021-10-19 03:40:47 1.20 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/csa.py", line 40, in get_csa
    u_pdb, pdb_u = get_pdb_chains()
NameError: name 'get_pdb_chains' is not defined
pypath.inputs.cspa.cspa_annotations 2021-10-19 03:40:47 2021-10-19 03:40:49 1.55 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
pypath.inputs.cspa.cspa_cell_type_annotations 2021-10-19 03:40:49 2021-10-19 03:40:52 3.29 dict {'A1A5B4': {CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='MedB1', value=17.42748), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='HBL1', value=17.03274), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='NK', value...(truncated) 1,407
pypath.inputs.cspa.cspa_cell_types 2021-10-19 03:40:52 2021-10-19 03:40:54 2.45 defaultdict defaultdict(<function cspa_cell_types.<locals>.<lambda> at 0x7f1121cda3a0>, {'A431': defaultdict(<class 'dict'>, {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.1...(truncated) 47
pypath.inputs.dbptm.dbptm_enzyme_substrate 2021-10-19 03:40:54 2021-10-19 03:40:58 3.22 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
pypath.inputs.dbptm.dbptm_enzyme_substrate_old 2021-10-19 03:40:58 2021-10-19 03:41:01 2.81 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/dbptm.py", line 98, in dbptm_enzyme_substrate_old
    for k, data in iteritems(extra):
  File "/usr/lib/python3/dist-packages/future/utils/__init__.py", line 311, in iteritems
    func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
pypath.inputs.dbptm.dbptm_interactions 2021-10-19 03:41:01 2021-10-19 03:41:02 1.49 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
pypath.inputs.deathdomain.deathdomain_interactions 2021-10-19 03:41:02 2021-10-19 03:41:05 2.16 list [] 0
pypath.inputs.deathdomain.deathdomain_interactions_rescued 2021-10-19 03:41:05 2021-10-19 03:41:05 0.16 list [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) 184
pypath.inputs.depod.depod_enzyme_substrate 2021-10-19 03:41:05 2021-10-19 03:41:05 0.17 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
pypath.inputs.depod.depod_interactions 2021-10-19 03:41:05 2021-10-19 03:41:05 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
pypath.inputs.dgidb.dgidb_annotations 2021-10-19 03:41:05 2021-10-19 03:41:08 3.02 defaultdict defaultdict(<class 'set'>, {'Q9BXS1': {DgidbAnnotation(category='ENZYME')}, 'Q9BZH6': {DgidbAnnotation(category='TRANSCRIPTION FACTOR')}, 'Q96Q89': {DgidbAnnotation(category='ENZYME')}, 'Q99470': {DgidbAnnotation(category='DRUGGABLE GENOME')}, 'Q9H211': {DgidbAnnotation(category='KINASE')}, 'O95069'...(truncated) 10,494
pypath.inputs.dgidb.get_dgidb_old 2021-10-19 03:41:08 2021-10-19 03:42:12 63.61 set {'Q9BZJ6', 'P14207', 'P23946', 'Q99570', 'Q9BZL6', 'Q8TDU6', 'Q14123', 'P08913', 'P30613', 'Q9NRR5', 'Q9H0F6', 'Q8TE56', 'Q9NUT2', 'O14976', 'O43866', 'P20618', 'Q9HC96', 'Q13509', 'P78317', 'P43155', 'A8MPY1', 'P49711', 'Q96KG9', 'P01732', 'Q15004', 'Q9Y2G8', 'P23786', 'Q8NER5', 'Q495A1', 'Q8NGH3',...(truncated) 5,986
pypath.inputs.dip.dip_interactions 2021-10-19 03:42:12 2021-10-19 03:42:13 1.65 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/dip.py", line 55, in dip_interactions
    specA = int(l[9].split(':')[1].split('(')[0])
IndexError: list index out of range
pypath.inputs.dip.dip_login 
Not calling `pypath.inputs.dip.dip_login`, not enough arguments.
pypath.inputs.disgenet.disgenet_annotations 2021-10-19 03:42:13 2021-10-19 03:42:19 5.55 defaultdict defaultdict(<class 'set'>, {'P04217': {DisGeNetAnnotation(disease='Hepatomegaly', type='phenotype', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',)), DisGeNetAnnotation(disease='Schizophrenia', type='disease', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, sour...(truncated) 9,202
pypath.inputs.domino.domino_ddi 2021-10-19 03:42:19 2021-10-19 03:42:32 12.52 list [<pypath.internals.intera.DomainDomain object at 0x7f11571b19d0>, <pypath.internals.intera.DomainDomain object at 0x7f11571b19a0>, <pypath.internals.intera.DomainDomain object at 0x7f1157b59bb0>, <pypath.internals.intera.DomainDomain object at 0x7f1157b59d60>, <pypath.internals.intera.DomainDomain o...(truncated) 1,294
pypath.inputs.domino.domino_enzsub 2021-10-19 03:42:32 2021-10-19 03:42:32 0.81 dict {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f114ea62f70>, <pypath.internals.intera.DomainDomain object at 0x7f114ea62ee0>, <pypath.internals.intera.DomainDomain object at 0x7f10fec532b0>, <pypath.internals.intera.DomainDomain object at 0x7f10fec53f70>, <pypath.internals.intera.Domain...(truncated) 2
pypath.inputs.domino.domino_interactions 2021-10-19 03:42:32 2021-10-19 03:42:33 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
pypath.inputs.domino.get_domino 2021-10-19 03:42:33 2021-10-19 03:42:33 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
pypath.inputs.dorothea._process_resources 
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments.
pypath.inputs.dorothea.dorothea_full_raw 2021-10-19 03:42:33 2021-10-19 03:42:42 8.36 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
pypath.inputs.dorothea.dorothea_interactions 2021-10-19 03:42:42 2021-10-19 03:42:50 7.88 list [DorotheaInteraction(tf='AHR', target='ASAP1', effect=0, level='B', curated=False, chipseq=True, predicted=True, coexp=True, curated_sources='', chipseq_sources='ReMap', predicted_sources='HOCOMOCO', coexp_sources='ARACNe-GTEx', all_sources='ReMap,HOCOMOCO,ARACNe-GTEx', pubmed='', kegg_pathways=''),...(truncated) 15,252
pypath.inputs.dorothea.dorothea_old_csv 2021-10-19 03:42:50 2021-10-19 03:42:50 0.32 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 556, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/dorothea.py", line 211, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
pypath.inputs.dorothea.dorothea_old_csv 2021-10-19 03:42:50 2021-10-19 03:42:50 0.14 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 556, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/dorothea.py", line 211, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
pypath.inputs.dorothea.dorothea_rda_raw 2021-10-19 03:42:50 2021-10-19 03:42:52 1.87 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
pypath.inputs.dorothea.get_dorothea_old 2021-10-19 03:42:52 2021-10-19 03:42:52 0.38 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
pypath.inputs.dorothea.dorothea_rda_raw 2021-10-19 03:42:52 2021-10-19 03:42:53 1.26 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
pypath.inputs.dorothea.dorothea_interactions 2021-10-19 03:42:54 2021-10-19 03:43:01 7.94 list [DorotheaInteraction(tf='AHR', target='ASAP1', effect=0, level='B', curated=False, chipseq=True, predicted=True, coexp=True, curated_sources='', chipseq_sources='ReMap', predicted_sources='HOCOMOCO', coexp_sources='ARACNe-GTEx', all_sources='ReMap,HOCOMOCO,ARACNe-GTEx', pubmed='', kegg_pathways=''),...(truncated) 15,252
pypath.inputs.dorothea.dorothea_old_csv 2021-10-19 03:43:01 2021-10-19 03:43:02 0.18 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 556, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/dorothea.py", line 211, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
pypath.inputs.ebi.ebi_rest 
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments.
pypath.inputs.elm.elm_classes 2021-10-19 03:43:02 2021-10-19 03:43:15 13.00 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) 317
pypath.inputs.elm.elm_domains 2021-10-19 03:43:15 2021-10-19 03:43:16 0.87 dict {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')]}} 2
pypath.inputs.elm.elm_instances 2021-10-19 03:43:16 2021-10-19 03:46:28 192.37 list [ELMInstance(accession='Accession', type='ELMType', identifier='ELMIdentifier', uniprot_id='ProteinName', uniprot='Primary_Acc', synonyms='Accessions', start='Start', end='End', references='References', methods='Methods', logic='InstanceLogic', pdb='PDB', organism='Organism'), ELMInstance(accession=...(truncated) 3,935
pypath.inputs.elm.elm_interactions 2021-10-19 03:46:28 2021-10-19 03:47:45 76.84 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) 2,394
pypath.inputs.embrace._embrace_id_translation 
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments.
pypath.inputs.embrace.embrace_annotations 2021-10-19 03:47:45 2021-10-19 03:48:01 16.45 dict {'P01023': {EmbraceAnnotation(mainclass='ligand', neuron=True, mural_cell=False, microglia=False, endothelial_cell=False)}, 'Q07954': {EmbraceAnnotation(mainclass='receptor', neuron=True, mural_cell=False, microglia=True, endothelial_cell=False)}, 'P12821': {EmbraceAnnotation(mainclass='ligand', neu...(truncated) 942
pypath.inputs.embrace.embrace_interactions 2021-10-19 03:48:01 2021-10-19 03:48:01 0.25 list [EmbraceInteraction(ligand='P01023', receptor='Q07954'), EmbraceInteraction(ligand='P12821', receptor='P30411'), EmbraceInteraction(ligand='O14672', receptor='P30530'), EmbraceInteraction(ligand='O14672', receptor='P29320'), EmbraceInteraction(ligand='O43184', receptor='Q13797'), EmbraceInteraction(...(truncated) 1,688
pypath.inputs.embrace.embrace_raw 2021-10-19 03:48:01 2021-10-19 03:48:02 0.10 list [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) 1,710
pypath.inputs.embrace.embrace_translated 2021-10-19 03:48:02 2021-10-19 03:48:02 0.25 list [EmbraceRawRecord(ligand_symbol='P01023', receptor_symbol='Q07954', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='P12821', receptor_symbol='P30411', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_recepto...(truncated) 1,770
pypath.inputs.encode.encode_tf_mirna_interactions 2021-10-19 03:48:02 2021-10-19 03:48:03 0.73 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
pypath.inputs.ensembl.ensembl_organisms 2021-10-19 03:48:03 2021-10-19 03:48:03 0.14 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) 310
pypath.inputs.exocarta._get_exocarta_vesiclepedia 2021-10-19 03:48:03 2021-10-19 03:48:12 8.90 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
pypath.inputs.exocarta.get_exocarta 2021-10-19 03:48:12 2021-10-19 03:48:12 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
pypath.inputs.exocarta.get_vesiclepedia 2021-10-19 03:48:12 2021-10-19 03:48:29 17.04 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
pypath.inputs.genecards.genecards_datasheet 
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments.
pypath.inputs.genecards.genecards_soup 
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments.
pypath.inputs.genecards.genecards_summaries 
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments.
pypath.inputs.go.get_go_desc 
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments.
pypath.inputs.go.get_go_quick 2021-10-19 03:48:29 2021-10-19 03:48:29 0.41 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 846, in get_go_quick
    _ = next(c.result)
TypeError: 'NoneType' object is not an iterator
pypath.inputs.go.get_goslim 2021-10-19 03:48:29 2021-10-19 03:48:30 1.21 list ['GO:0000003', 'GO:0000228', 'GO:0000229', 'GO:0000278', 'GO:0000902', 'GO:0002376', 'GO:0003013', 'GO:0003674', 'GO:0003677', 'GO:0003700', 'GO:0003723', 'GO:0003729', 'GO:0003735', 'GO:0003924', 'GO:0004386', 'GO:0004518', 'GO:0005198', 'GO:0005575', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0...(truncated) 145
pypath.inputs.go.go_ancestors_quickgo 2021-10-19 03:48:30 2021-10-19 04:00:53 742.25 dict {'C': defaultdict(<class 'set'>, {'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009429': {('GO:0030694', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0009426': {('GO:0030694', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0030691': {('GO:0030689', 'is_a'), ('GO:0030687'...(truncated) 3
pypath.inputs.go.go_ancestors_goose 2021-10-19 04:00:53 2021-10-19 04:00:55 2.69 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 137, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
pypath.inputs.go.go_ancestors_quickgo 2021-10-19 04:00:55 2021-10-19 04:00:59 3.51 dict {'C': defaultdict(<class 'set'>, {'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009429': {('GO:0030694', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0009426': {('GO:0030694', 'part_of'), ('GO:0110165', 'is_a')}, 'GO:0030691': {('GO:0030689', 'is_a'), ('GO:0030687'...(truncated) 3
pypath.inputs.go.go_annotations_goa 2021-10-19 04:00:59 2021-10-19 04:01:01 2.33 dict {'C': defaultdict(<class 'set'>, {'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'}, 'A0A...(truncated) 3
pypath.inputs.go.go_annotations_goa 2021-10-19 04:01:01 2021-10-19 04:01:02 1.06 dict {'C': defaultdict(<class 'set'>, {'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'}, 'A0A...(truncated) 3
pypath.inputs.go.go_annotations_goose 2021-10-19 04:01:02 2021-10-19 04:01:05 2.66 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 781, in go_annotations_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
pypath.inputs.go.go_annotations_solr 2021-10-19 04:01:05 2021-10-19 04:01:07 1.59 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 667, in go_annotations_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.go.go_annotations_uniprot 2021-10-19 04:01:07 2021-10-19 04:01:13 6.75 dict {'Entry': ['Gene ontology IDs'], 'Q00266': ['GO:0000096', 'GO:0001887', 'GO:0004478', 'GO:0005524', 'GO:0005829', 'GO:0006556', 'GO:0006730', 'GO:0009087', 'GO:0032259', 'GO:0042802', 'GO:0046872', 'GO:0051289'], 'Q8NB16': ['GO:0004672', 'GO:0004706', 'GO:0005524', 'GO:0005634', 'GO:0005737', 'GO:00...(truncated) 20,387
pypath.inputs.go.go_descendants_quickgo 2021-10-19 04:01:13 2021-10-19 04:01:17 3.41 dict {'C': defaultdict(<class 'set'>, {'GO:0042627': {('GO:0034359', 'is_a'), ('GO:0034360', 'is_a')}, 'GO:0030694': {('GO:0009429', 'part_of'), ('GO:0009426', 'part_of')}, 'GO:0030689': {('GO:0030691', 'is_a'), ('GO:0030692', 'is_a'), ('GO:0030690', 'is_a')}, 'GO:0030681': {('GO:0005655', 'is_a'), ('GO:...(truncated) 3
pypath.inputs.go.go_descendants_goose 2021-10-19 04:01:17 2021-10-19 04:01:20 2.64 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 209, in go_descendants_goose
    anc = go_ancestors_goose(aspects = aspects)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 137, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
pypath.inputs.go.go_descendants_quickgo 2021-10-19 04:01:20 2021-10-19 04:01:23 3.40 dict {'C': defaultdict(<class 'set'>, {'GO:0042627': {('GO:0034359', 'is_a'), ('GO:0034360', 'is_a')}, 'GO:0030694': {('GO:0009429', 'part_of'), ('GO:0009426', 'part_of')}, 'GO:0030689': {('GO:0030691', 'is_a'), ('GO:0030692', 'is_a'), ('GO:0030690', 'is_a')}, 'GO:0030681': {('GO:0005655', 'is_a'), ('GO:...(truncated) 3
pypath.inputs.go.go_descendants_to_ancestors 
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments.
pypath.inputs.go.go_terms_quickgo 2021-10-19 04:01:23 2021-10-19 04:01:26 2.76 dict {'C': {'GO:0042627': 'chylomicron', 'GO:0042629': 'mast cell granule', 'GO:0042622': 'photoreceptor outer segment membrane', 'GO:0030692': 'Noc4p-Nop14p complex', 'GO:0030694': 'bacterial-type flagellum basal body, rod', 'GO:0030691': 'Noc2p-Noc3p complex', 'GO:0030690': 'Noc1p-Noc2p complex', 'GO:0...(truncated) 3
pypath.inputs.go.go_terms_goose 2021-10-19 04:01:26 2021-10-19 04:01:28 2.68 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 505, in go_terms_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
pypath.inputs.go.go_terms_quickgo 2021-10-19 04:01:28 2021-10-19 04:01:31 2.77 dict {'C': {'GO:0042627': 'chylomicron', 'GO:0042629': 'mast cell granule', 'GO:0042622': 'photoreceptor outer segment membrane', 'GO:0030692': 'Noc4p-Nop14p complex', 'GO:0030694': 'bacterial-type flagellum basal body, rod', 'GO:0030691': 'Noc2p-Noc3p complex', 'GO:0030690': 'Noc1p-Noc2p complex', 'GO:0...(truncated) 3
pypath.inputs.go.go_terms_solr 2021-10-19 04:01:31 2021-10-19 04:01:32 0.62 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/go.py", line 363, in go_terms_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.gpcrdb.gpcrdb_annotations 2021-10-19 04:01:32 2021-10-19 04:01:32 0.25 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) 402
pypath.inputs.graphviz.graphviz_attrs 2021-10-19 04:01:32 2021-10-19 04:01:34 1.35 tuple ({'_background': {'type': 'string', 'default': '<none>', 'min': '', 'notes': ''}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'write only'}, 'bgcolor': {'type': 'colorcolorList', 'default': '<none>', 'min': '', 'notes': ''}, 'center': {'type': 'bool', 'default': 'false', 'min': '', 'no...(truncated) 3
pypath.inputs.guide2pharma.guide2pharma_complexes 
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments.
pypath.inputs.guide2pharma.guide2pharma_download 2021-10-19 04:01:34 2021-10-19 04:01:38 4.82 tuple ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=9606, target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=True, pubmed_ids=[]), GuideToPharmacologyI...(truncated) 2
pypath.inputs.guide2pharma.guide2pharma_interactions 
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments.
pypath.inputs.havugimana.get_havugimana 2021-10-19 04:01:38 2021-10-19 04:01:40 1.81 list [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) 622
pypath.inputs.havugimana.havugimana_complexes 2021-10-19 04:01:40 2021-10-19 04:01:40 0.04 dict {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) 622
pypath.inputs.hgnc.hgnc_genegroups 2021-10-19 04:01:40 2021-10-19 04:01:49 8.76 defaultdict defaultdict(<class 'set'>, {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='C3 and PZP like, alpha-2-macroglobulin domain containing')}...(truncated) 14,975
pypath.inputs.hippie.hippie_interactions 2021-10-19 04:01:49 2021-10-19 04:02:05 16.33 list [HippieInteraction(id_a='P48436', id_b='P0DMV9', score=0.84, methods=None, references=('11356186', '16713569'), sources=None, organisms=None), HippieInteraction(id_a='Q9UNM6', id_b='P43686', score=0.96, methods=None, references=('17353931', '22863883', '22939629', '26344197'), sources=None, organism...(truncated) 39,764
pypath.inputs.homologene.get_homologene 2021-10-19 04:02:05 2021-10-19 04:02:05 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
pypath.inputs.homologene.homologene_dict 
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments.
pypath.inputs.homologene.homologene_uniprot_dict 
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments.
pypath.inputs.hpmr.get_hpmr 2021-10-19 04:02:05 2021-10-19 04:02:05 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
pypath.inputs.hpmr.hpmr_annotations 2021-10-19 04:02:05 2021-10-19 04:02:05 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
pypath.inputs.hpmr.hpmr_complexes 2021-10-19 04:02:05 2021-10-19 04:02:05 0.00 dict {'COMPLEX:P26992_P40189_P42702': Complex: COMPLEX:P26992_P40189_P42702, 'COMPLEX:P26441_Q9UBD9': Complex: COMPLEX:P26441_Q9UBD9, 'COMPLEX:O75462_P26992_P40189_P42702': Complex: COMPLEX:O75462_P26992_P40189_P42702, 'COMPLEX:P40189_Q14626': Complex: COMPLEX:P40189_Q14626, 'COMPLEX:P08887_P40189': Comp...(truncated) 101
pypath.inputs.hpmr.hpmr_interactions 2021-10-19 04:02:05 2021-10-19 04:02:05 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
pypath.inputs.hprd.get_hprd 2021-10-19 04:02:05 2021-10-19 04:02:11 5.93 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
pypath.inputs.hprd.hprd_enzyme_substrate 2021-10-19 04:02:11 2021-10-19 04:02:13 1.64 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
pypath.inputs.hprd.hprd_interactions 2021-10-19 04:02:13 2021-10-19 04:02:15 1.63 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
pypath.inputs.hprd.hprd_interactions_htp 2021-10-19 04:02:15 2021-10-19 04:02:16 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
pypath.inputs.htri.htri_interactions 2021-10-19 04:02:16 2021-10-19 04:02:20 3.83 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
pypath.inputs.humancellmap.humancellmap_annotations 2021-10-19 04:02:20 2021-10-19 04:02:22 1.96 dict {'Q9NRG9': {HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='peroxisome', method='NMF'), HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) 4,371
pypath.inputs.humap.humap2_complexes 2021-10-19 04:02:22 2021-10-19 04:02:24 2.17 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) 6,950
pypath.inputs.humap.humap_complexes 2021-10-19 04:02:24 2021-10-19 04:02:26 1.47 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) 4,502
pypath.inputs.huri._huri_interactions 
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments.
pypath.inputs.huri.hi_i_interactions 2021-10-19 04:02:26 2021-10-19 04:02:28 2.33 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) 5,714
pypath.inputs.huri.hi_ii_interactions 2021-10-19 04:02:28 2021-10-19 04:02:38 9.82 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='P59797', uniprot_b='Q8NF64', isoform_a=1, isoform_b=3, score=None), HuriInteractio...(truncated) 46,953
pypath.inputs.huri.hi_iii_old 2021-10-19 04:02:38 2021-10-19 04:02:38 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 556, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/huri.py", line 92, in hi_iii_old
    url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
pypath.inputs.huri.hi_union_interactions 2021-10-19 04:02:38 2021-10-19 04:03:27 49.08 list [HuriInteraction(uniprot_a='P0DP25', uniprot_b='Q9H0B3', isoform_a=1, isoform_b=1, score=0.899116271005), 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....(truncated) 231,268
pypath.inputs.huri.huri_interactions 2021-10-19 04:03:27 2021-10-19 04:04:01 34.00 list [HuriInteraction(uniprot_a='P0DP25', uniprot_b='Q9H0B3', isoform_a=1, isoform_b=1, score=0.899116271005), 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....(truncated) 167,764
pypath.inputs.huri.lit_bm_13_interactions 2021-10-19 04:04:01 2021-10-19 04:04:02 1.53 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
pypath.inputs.huri.lit_bm_17_interactions 2021-10-19 04:04:02 2021-10-19 04:04:04 1.60 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
pypath.inputs.huri.lit_bm_interactions 2021-10-19 04:04:04 2021-10-19 04:05:26 81.70 list [LitBmInteraction(uniprot_a='P23511', uniprot_b='Q13952'), LitBmInteraction(uniprot_a='P23511', uniprot_b='P25208'), LitBmInteraction(uniprot_a='P43351', uniprot_b='P43351'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q92843'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q07817'), LitBmInte...(truncated) 13,677
pypath.inputs.huri.rolland_hi_ii_14 2021-10-19 04:05:26 2021-10-19 04:05:29 3.54 list [['14', '6293', 'AAMP', 'VPS52', '1'], ['14', '8553', 'AAMP', 'BHLHE40', '1'], ['14', '64782', 'AAMP', 'AEN', '2'], ['15', '4188', 'AANAT', 'MDFI', '1'], ['15', '8553', 'AANAT', 'BHLHE40', '1'], ['28', '65983', 'ABO', 'GRAMD3', '2'], ['28', '84283', 'ABO', 'TMEM79', '1'], ['39', '39', 'ACAT2', 'ACAT...(truncated) 13,944
pypath.inputs.huri.vidal_hi_iii_old 
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments.
pypath.inputs.huri.yang2016_interactions 2021-10-19 04:05:29 2021-10-19 04:05:31 1.30 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) 2,829
pypath.inputs.huri.yu2011_interactions 2021-10-19 04:05:31 2021-10-19 04:05:33 2.15 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) 7,426
pypath.inputs.i3d.get_i3d 2021-10-19 04:05:33 2021-10-19 04:05:36 3.23 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/i3d.py", line 40, in get_i3d
    non_digit = re.compile(r'[^\d.-]+')
NameError: name 're' is not defined
pypath.inputs.icellnet._icellnet_get_components 
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments.
pypath.inputs.icellnet._icellnet_get_entity 
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments.
pypath.inputs.icellnet._icellnet_get_references 
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments.
pypath.inputs.icellnet._icellnet_get_resources 
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments.
pypath.inputs.icellnet.icellnet_annotations 2021-10-19 04:05:36 2021-10-19 04:05:36 0.37 defaultdict defaultdict(<class 'set'>, {'P03971': {IcellnetAnnotation(role='ligand', family='Cytokine', subfamily=None, classification=('Cytokine', 'Tgf'))}, Complex: COMPLEX:P36894_Q16671: {IcellnetAnnotation(role='receptor', family='Cytokine', subfamily=None, classification=('Cytokine', 'Tgf'))}, 'P36894': {I...(truncated) 688
pypath.inputs.icellnet.icellnet_complexes 2021-10-19 04:05:36 2021-10-19 04:05:36 0.10 dict {'COMPLEX:P36894_Q16671': Complex: COMPLEX:P36894_Q16671, 'COMPLEX:Q04771_Q16671': Complex: COMPLEX:Q04771_Q16671, 'COMPLEX:P27037_P37023': Complex: COMPLEX:P27037_P37023, 'COMPLEX:P37023_Q13705': Complex: COMPLEX:P37023_Q13705, 'COMPLEX:P37023_Q13873': Complex: COMPLEX:P37023_Q13873, 'COMPLEX:O0023...(truncated) 117
pypath.inputs.icellnet.icellnet_interactions 2021-10-19 04:05:36 2021-10-19 04:05:37 0.10 list [IcellnetRecord(ligand='P03971', receptor=Complex: COMPLEX:P36894_Q16671, family='Cytokine', subfamily=None, classification=['Cytokine', 'Tgf'], resources=None, references=['32333774']), IcellnetRecord(ligand='P03971', receptor=Complex: COMPLEX:Q04771_Q16671, family='Cytokine', subfamily=None, class...(truncated) 743
pypath.inputs.ielm.get_ielm 
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments.
pypath.inputs.ielm.get_ielm_huge 
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments.
pypath.inputs.imweb._get_imweb 2021-10-19 04:05:37 2021-10-19 04:05:38 1.57 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/imweb.py", line 74, in _get_imweb
    hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
  File "/usr/lib/python3.9/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
pypath.inputs.imweb.get_imweb 2021-10-19 04:05:38 2021-10-19 04:05:39 0.31 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/imweb.py", line 113, in get_imweb
    token = json.loads(fp.read())['token']
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/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)
pypath.inputs.imweb.get_imweb_req 2021-10-19 04:05:39 2021-10-19 04:05:39 0.54 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/imweb.py", line 140, in get_imweb_req
    token = json.loads(r0.text)['token']
  File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/lib/python3.9/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)
pypath.inputs.innatedb.innatedb_interactions 2021-10-19 04:05:39 2021-10-19 04:05:41 1.73 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
pypath.inputs.instruct.get_instruct 2021-10-19 04:05:41 2021-10-19 04:05:44 3.30 list [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) 11,470
pypath.inputs.instruct.get_instruct_offsets 2021-10-19 04:05:44 2021-10-19 04:05:45 0.51 dict {('10gs', 'P09211'): 0, ('11gs', 'P09211'): 0, ('12gs', 'P09211'): 0, ('13gs', 'P09211'): 0, ('14gs', 'P09211'): 0, ('16gs', 'P09211'): 0, ('17gs', 'P09211'): 0, ('18gs', 'P09211'): 0, ('19gs', 'P09211'): 0, ('1a00', 'P68871'): 0, ('1a00', 'P69905'): 0, ('1a01', 'P68871'): 0, ('1a01', 'P69905'): 0, ...(truncated) 11,620
pypath.inputs.intact._try_isoform 
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments.
pypath.inputs.intact.intact_interactions 2021-10-19 04:05:45 2021-10-19 04:06:59 73.80 list [IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, mi_score='0.77', isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}...(truncated) 70,176
pypath.inputs.integrins.get_integrins 2021-10-19 04:06:59 2021-10-19 04:07:00 1.01 set {'P26012', 'P11215', 'P26010', 'P23229', 'Q13349', 'P17301', 'P08514', 'P53708', 'Q9UKX5', 'P05107', 'P20702', 'P16144', 'P56199', 'P05556', 'O75578', 'P05106', 'P26006', 'P38570', 'Q13797', 'P18564', 'P06756', 'Q13683', 'P08648', 'P20701', 'P18084'} 25
pypath.inputs.intogen.intogen_annotations 2021-10-19 04:07:00 2021-10-19 04:07:00 0.73 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/intogen.py", line 60, in intogen_annotations
    __ = c.result['Drivers_type_role.tsv'].readline()
TypeError: 'NoneType' object is not subscriptable
pypath.inputs.ipi._ipi_uniprot_pairs 
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments.
pypath.inputs.ipi.ipi_uniprot 2021-10-19 04:07:00 2021-10-19 04:07:01 0.33 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
pypath.inputs.iptmnet.iptmnet_interactions 2021-10-19 04:07:01 2021-10-19 04:07:12 11.39 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) 16,686
pypath.inputs.italk.italk_annotations 2021-10-19 04:07:12 2021-10-19 04:07:13 0.83 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
pypath.inputs.italk.italk_interactions 2021-10-19 04:07:13 2021-10-19 04:07:13 0.20 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
pypath.inputs.italk.italk_raw 2021-10-19 04:07:13 2021-10-19 04:07:13 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
pypath.inputs.kea.kea_enzyme_substrate 2021-10-19 04:07:13 2021-10-19 04:07:18 4.83 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) 35,196
pypath.inputs.kea.kea_interactions 2021-10-19 04:07:18 2021-10-19 04:07:21 2.53 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) 35,196
pypath.inputs.kegg.kegg_dbget 
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments.
pypath.inputs.kegg.kegg_interactions 2021-10-19 04:07:21 2021-10-19 04:09:26 125.36 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) 14,427
pypath.inputs.kegg.kegg_medicus 2021-10-19 04:09:26 2021-10-19 04:09:41 14.61 set {KeggMedicusRawInteraction(id_a='5211', id_b='229', name_a='PFKL', name_b='ALDOB', effect='enzyme_enzyme', itype='post_translational', pw_type='variant', type_a='gene', type_b='gene', network_id='N00735'), KeggMedicusRawInteraction(id_a=('7322', '9978', '8454', '6500', '23291'), id_b='4792', name_a=...(truncated) 12,600
pypath.inputs.kegg.kegg_medicus_complexes 2021-10-19 04:09:41 2021-10-19 04:09:42 1.37 dict {'COMPLEX:O00401_Q8TF74': Complex: COMPLEX:O00401_Q8TF74, 'COMPLEX:O15488_P54840': Complex: COMPLEX:O15488_P54840, 'COMPLEX:Q9NPP4_Q9ULZ3': Complex: COMPLEX:Q9NPP4_Q9ULZ3, 'COMPLEX:P15336': Complex: COMPLEX:P15336, 'COMPLEX:P27540_P35869': Complex: COMPLEX:P27540_P35869, 'COMPLEX:Q6UXL0_Q9UHF4': Com...(truncated) 267
pypath.inputs.kegg.kegg_medicus_interactions 2021-10-19 04:09:42 2021-10-19 04:09:44 1.41 list [KeggMedicusInteraction(id_a='P17858', id_b='P05062', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='enzyme_enzyme'), KeggMedicusInteraction(id_a=Complex: COMPLEX:P62837_P62877_P63208_Q13616_Q9UKB1, id_b='P25963', entity_type_a='complex', entity_type...(truncated) 9,383
pypath.inputs.kegg.kegg_pathway_annotations 2021-10-19 04:09:44 2021-10-19 04:09:51 6.94 defaultdict defaultdict(<class 'set'>, {'P62070': {KeggPathway(pathway='Ras signaling pathway'), KeggPathway(pathway='Mitophagy - animal'), KeggPathway(pathway='Proteoglycans in cancer'), KeggPathway(pathway='Autophagy - animal'), KeggPathway(pathway='Regulation of actin cytoskeleton'), KeggPathway(pathway='Ape...(truncated) 2,567
pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons 2021-10-19 04:09:51 2021-10-19 04:09:51 0.44 defaultdict defaultdict(<class 'set'>, {'A8K7J7': {KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Butirosin and neom...(truncated) 813
pypath.inputs.kegg.kegg_pathways 2021-10-19 04:09:51 2021-10-19 04:09:58 6.96 tuple ({'MAPK signaling pathway': {'P62070', 'Q7RTX0', 'P36507', 'Q13164', 'P35813', 'O95257', 'Q12988', 'O75676', 'Q13387', 'Q13153', 'Q12852', 'Q9HBH9', 'Q96NL6', 'P0DMV8', 'P0C869', 'P10398', 'Q8WTQ7', 'Q12968', 'P19838', 'Q9UBE8', 'P01375', 'P16949', 'Q96KG9', 'Q16637', 'Q06413', 'Q9UDY8', 'P50897', '...(truncated) 2
pypath.inputs.kinasedotcom.kinasedotcom_annotations 2021-10-19 04:09:58 2021-10-19 04:10:03 4.89 defaultdict defaultdict(<class 'set'>, {'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(g...(truncated) 503
pypath.inputs.kirouac2010.kirouac2010_interactions 2021-10-19 04:10:03 2021-10-19 04:10:08 4.69 list [('ADIPOQ', 'ADIPOR'), ('AGRP', 'ATRN'), ('AREG', 'EGFR'), ('ANGPTL1', 'TEK'), ('ANGPTL2', 'TEK'), ('ANGPTL3', 'TEK'), ('ANGPTL4', 'TEK'), ('ANGPTL5', 'TEK'), ('ANGPTL6', 'TEK'), ('BTC', 'EGFR'), ('BMP1', 'BMPR'), ('BMP10', 'BMPR'), ('BMP15', 'BMPR'), ('BMP2', 'BMPR'), ('BMP3', 'BMPR'), ('BMP4', 'BM...(truncated) 267
pypath.inputs.laudanna.laudanna_directions 2021-10-19 04:10:08 2021-10-19 04:10:08 0.39 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/laudanna.py", line 54, in laudanna_directions
    LaudannaDirection(
TypeError: <lambda>() missing 1 required positional argument: 'target_genesymbol'
pypath.inputs.laudanna.laudanna_effects 2021-10-19 04:10:08 2021-10-19 04:10:08 0.40 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
pypath.inputs.li2012.get_li2012 2021-10-19 04:10:08 2021-10-19 04:10:33 25.11 filter <filter object at 0x7f1120120970> None
pypath.inputs.li2012.li2012_dmi 2021-10-19 04:10:33 2021-10-19 04:10:33 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/li2012.py", line 132, in li2012_dmi
    se = uniprot_input.swissprot_seq(isoforms = True)
AttributeError: module 'pypath.inputs.uniprot' has no attribute 'swissprot_seq'
pypath.inputs.li2012.li2012_enzyme_substrate 2021-10-19 04:10:33 2021-10-19 04:10:33 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
pypath.inputs.li2012.li2012_interactions 2021-10-19 04:10:34 2021-10-19 04:10:34 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
pypath.inputs.lincs.lincs_compounds 2021-10-19 04:10:34 2021-10-19 04:10:42 8.01 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
pypath.inputs.lmpid.lmpid_dmi 2021-10-19 04:10:42 2021-10-19 04:10:43 1.16 list [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) 1,170
pypath.inputs.lmpid.lmpid_interactions 2021-10-19 04:10:43 2021-10-19 04:10:44 0.90 list [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) 1,170
pypath.inputs.lmpid.load_lmpid 2021-10-19 04:10:44 2021-10-19 04:10:44 0.66 list [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) 1,170
pypath.inputs.lncdisease.lncdisease_interactions 2021-10-19 04:10:44 2021-10-19 04:10:44 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
pypath.inputs.lncrnadb.lncrnadb_interactions 2021-10-19 04:10:44 2021-10-19 04:10:45 0.49 list [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism='Paramecium tetraurelia', pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism='Loris tardigradus', pmid='17175535'), LncrnadbInteraction(lncrna='G22'...(truncated) 773
pypath.inputs.locate.locate_localizations 2021-10-19 04:10:45 2021-10-19 04:10:45 0.33 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/locate.py", line 63, in locate_localizations
    c.result[fname]
TypeError: 'NoneType' object is not subscriptable
pypath.inputs.lrdb.lrdb_annotations 2021-10-19 04:10:45 2021-10-19 04:10:46 0.88 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=('10608878',)), LrdbAnnotation(role='receptor', cell_type=None, source...(truncated) 1,536
pypath.inputs.lrdb.lrdb_interactions 2021-10-19 04:10:46 2021-10-19 04:10:46 0.04 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
pypath.inputs.macrophage._trim_gname 
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments.
pypath.inputs.macrophage.macrophage_interactions 2021-10-19 04:10:46 2021-10-19 04:10:47 0.42 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
pypath.inputs.matrisome.__matrisome_annotations_2 2021-10-19 04:10:47 2021-10-19 04:11:02 15.03 set {'S100a6', 'Serpinh1', 'PODN', 'FBN3', 'Itih2', 'CXCL3', 'SERPINE1', 'LAMC3', 'Col5a2', 'Serpina3k', 'Sftpd', 'LPA', 'Scube2', 'PRG3', 'P4ha1', 'ITIH2', 'HABP2', 'MFAP4', 'Try10', 'Lama2', 'Ecm1', 'Plod1', 'Dmbt1', 'Vwa5a', 'ADAM15', 'Lgals4', 'IGFALS', 'ADAMTSL2', 'Gpc4', 'Ndnf', 'Col6a6', 'COL15A1...(truncated) 744
pypath.inputs.matrisome.matrisome_annotations 2021-10-19 04:11:02 2021-10-19 04:11:02 0.78 dict {'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) 1,064
pypath.inputs.matrixdb._matrixdb_protein_list 
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments.
pypath.inputs.matrixdb.matrixdb_annotations 2021-10-19 04:11:03 2021-10-19 04:11:06 3.10 dict {'Q9BZJ6': {MatrixdbAnnotation(mainclass='membrane')}, 'Q9BZL6': {MatrixdbAnnotation(mainclass='membrane')}, 'Q8TDU6': {MatrixdbAnnotation(mainclass='membrane')}, 'P08913': {MatrixdbAnnotation(mainclass='membrane')}, 'O15259': {MatrixdbAnnotation(mainclass='membrane')}, 'Q00973': {MatrixdbAnnotation...(truncated) 10,100
pypath.inputs.matrixdb.matrixdb_ecm_proteins 2021-10-19 04:11:06 2021-10-19 04:11:06 0.06 set {'Q8N135', 'P51888', 'Q6UX34', 'P12109', 'Q8WWZ8', 'Q92832', 'Q075Z2', 'Q8TE56', 'Q3B7J2', 'Q9Y251', 'O14905', 'Q06828', 'P03956', 'Q6UXH8', 'P08493', 'P21941', 'Q96HD1', 'Q7L985', 'Q6UXX9', 'Q96BH3', 'Q8TB73', 'Q9Y6C2', 'Q96FE5', 'Q8TE57', 'Q99102', 'Q2UY09', 'Q9NS15', 'O94898', 'Q15848', 'Q6NUI6',...(truncated) 483
pypath.inputs.matrixdb.matrixdb_interactions 2021-10-19 04:11:06 2021-10-19 04:11:06 0.16 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
pypath.inputs.matrixdb.matrixdb_membrane_proteins 2021-10-19 04:11:06 2021-10-19 04:11:08 1.86 set {'Q9BZJ6', 'Q9BZL6', 'Q8TDU6', 'P08913', 'O15259', 'Q00973', 'Q9NUT2', 'Q9BTV4', 'Q5VUD6', 'O14976', 'Q96KG9', 'Q13011', 'Q8NGH3', 'P78344', 'B9A6J9', 'P23470', 'A6NLU5', 'O60488', 'P09104', 'Q8IVI9', 'Q9NR77', 'Q99102', 'Q99665', 'Q9NPY3', 'Q9P032', 'Q9Y5Z9', 'P48067', 'Q5PT55', 'P25024', 'Q6ZT12',...(truncated) 8,242
pypath.inputs.matrixdb.matrixdb_secreted_proteins 2021-10-19 04:11:08 2021-10-19 04:11:08 0.31 set {'Q00887', 'P14207', 'P23946', 'Q93070', 'P0CJ68', 'P13010', 'P0CJ74', 'Q13231', 'Q075Z2', 'P10809', 'Q8TE56', 'Q96SM3', 'Q3B7J2', 'P09681', 'Q9Y251', 'O43866', 'P20618', 'P67809', 'Q9UJ98', 'P03971', 'P01763', 'P01732', 'Q6UXX9', 'P14555', 'Q96BH3', 'Q9UQ74', 'P09104', 'Q9Y6C2', 'P35916', 'Q6JVE5',...(truncated) 2,925
pypath.inputs.mcam.mcam_cell_adhesion_molecules 2021-10-19 04:11:08 2021-10-19 04:11:09 1.48 set {'Q49MI3', 'P56856', 'Q92729', 'Q13835', 'Q9HDB5', 'Q13740', 'P16284', 'Q8WWQ8', 'P13612', 'Q8TD84', 'P01732', 'Q13308', 'Q86WK6', 'Q5ZPR3', 'P07359', 'Q6MZF4', 'P35443', 'P78325', 'P30203', 'Q9NPY3', 'P16150', 'O95471', 'P11215', 'O00548', 'P22105', 'Q9BY67', 'Q86WK7', 'Q9NY15', 'Q13797', 'Q8TES5',...(truncated) 103
pypath.inputs.membranome.membranome_annotations 2021-10-19 04:11:09 2021-10-19 04:11:31 21.67 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) 2,527
pypath.inputs.mimp.get_kinase_class 2021-10-19 04:11:31 2021-10-19 04:11:32 0.91 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
pypath.inputs.mimp.mimp_enzyme_substrate 2021-10-19 04:11:32 2021-10-19 04:11:35 2.87 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
pypath.inputs.mimp.mimp_interactions 2021-10-19 04:11:35 2021-10-19 04:11:36 0.61 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
pypath.inputs.mir2disease.mir2disease_interactions 2021-10-19 04:11:36 2021-10-19 04:11:36 0.21 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
pypath.inputs.mirbase.get_mirbase_aliases 2021-10-19 04:11:36 2021-10-19 04:11:36 0.09 tuple ({'MIMAT0000062': {'hsa-let-7a-5p', 'hsa-let-7a'}, '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', 'hsa-let-7f-5p'}, 'MIM...(truncated) 2
pypath.inputs.mirbase.mirbase_ids 2021-10-19 04:11:36 2021-10-19 04:11:36 0.09 list [('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000068', 'MI...(truncated) 3,027
pypath.inputs.mirbase.mirbase_mature 2021-10-19 04:11:36 2021-10-19 04:11:36 0.06 list [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('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
pypath.inputs.mirbase.mirbase_mature_all 2021-10-19 04:11:36 2021-10-19 04:11:36 0.09 list ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) 3,027
pypath.inputs.mirbase.mirbase_precursor 2021-10-19 04:11:36 2021-10-19 04:11:36 0.06 list [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7cL'), ('MI0000064', 'hsa-le...(truncated) 2,173
pypath.inputs.mirbase.mirbase_precursor_all 2021-10-19 04:11:36 2021-10-19 04:11:36 0.09 list ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000115', 'MI0000070', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000075', 'MI0000074', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) 3,027
pypath.inputs.mirbase.mirbase_precursor_to_mature 2021-10-19 04:11:36 2021-10-19 04:11:36 0.15 list [('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT0010195'), ('hsa-let-7a-2L', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0000062'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMA...(truncated) 3,361
pypath.inputs.mirdeathdb.mirdeathdb_interactions 2021-10-19 04:11:36 2021-10-19 04:11:37 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
pypath.inputs.mirecords.mirecords_interactions 2021-10-19 04:11:37 2021-10-19 04:11:41 4.19 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
pypath.inputs.mirtarbase._mirtarbase_interactions 
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments.
pypath.inputs.mirtarbase.mirtarbase_interactions 2021-10-19 04:11:41 2021-10-19 04:12:01 20.63 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
pypath.inputs.mitab.mitab_field_list 
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments.
pypath.inputs.mitab.mitab_field_uniprot 
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments.
pypath.inputs.mppi.mppi_interactions 2021-10-19 04:12:02 2021-10-19 04:12:02 0.43 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
pypath.inputs.msigdb.msigdb_annotations 2021-10-19 04:12:02 2021-10-19 04:12:02 0.42 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/msigdb.py", line 295, in msigdb_annotations
    collection_data = msigdb_download_collections(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/msigdb.py", line 252, in msigdb_download_collections
    msigdb_download(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/msigdb.py", line 96, in msigdb_download
    c_login_1 = curl.Curl(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 935, in __init__
    self.curl_call()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1329, in curl_call
    self.remove_target()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1339, in remove_target
    os.remove(self.target.name)
PermissionError: [Errno 13] Permission denied: '/dev/null'
pypath.inputs.msigdb.msigdb_download 2021-10-19 04:12:02 2021-10-19 04:12:03 0.40 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/msigdb.py", line 96, in msigdb_download
    c_login_1 = curl.Curl(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 935, in __init__
    self.curl_call()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1329, in curl_call
    self.remove_target()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1339, in remove_target
    os.remove(self.target.name)
PermissionError: [Errno 13] Permission denied: '/dev/null'
pypath.inputs.msigdb.msigdb_download_collections 2021-10-19 04:12:03 2021-10-19 04:12:04 1.45 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/msigdb.py", line 252, in msigdb_download_collections
    msigdb_download(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/msigdb.py", line 96, in msigdb_download
    c_login_1 = curl.Curl(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 935, in __init__
    self.curl_call()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1329, in curl_call
    self.remove_target()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1339, in remove_target
    os.remove(self.target.name)
PermissionError: [Errno 13] Permission denied: '/dev/null'
pypath.inputs.ncrdeathdb.ncrdeathdb_interactions 2021-10-19 04:12:04 2021-10-19 04:12:07 2.61 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/ncrdeathdb.py", line 71, in ncrdeathdb_interactions
    NcrdeathdbInteraction(
TypeError: <lambda>() got an unexpected keyword argument 'protein'
pypath.inputs.negatome.negatome_interactions 2021-10-19 04:12:07 2021-10-19 04:12:07 0.09 list [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) 2,171
pypath.inputs.netbiol._netbiol_interactions 
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments.
pypath.inputs.netbiol.arn_interactions 2021-10-19 04:12:07 2021-10-19 04:12:07 0.14 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
pypath.inputs.netbiol.nrf2ome_interactions 2021-10-19 04:12:07 2021-10-19 04:12:07 0.15 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
pypath.inputs.netpath.netpath_interactions 2021-10-19 04:12:07 2021-10-19 04:12:10 2.26 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
pypath.inputs.netpath.netpath_names 2021-10-19 04:12:10 2021-10-19 04:12:10 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
pypath.inputs.netpath.netpath_pathway_annotations 2021-10-19 04:12:10 2021-10-19 04:12:26 16.31 defaultdict defaultdict(<class 'set'>, {'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(...(truncated) 1,868
pypath.inputs.ontology.listof_ontologies 2021-10-19 04:12:26 2021-10-19 04:12:30 4.07 dict {'aeo': 'Anatomical Entity Ontology', 'agro': 'Agronomy Ontology', 'amphx': 'Amphioxus Development and Anatomy Ontology (AMPHX)', 'atol': 'Animal Trait Ontology for Livestock', 'bcio': 'The Behaviour Change Intervention Ontology', 'bco': 'Biological Collections Ontology', 'bfo': 'Basic Formal Ontolo...(truncated) 266
pypath.inputs.ontology.ontology 
Not calling `pypath.inputs.ontology.ontology`, not enough arguments.
pypath.inputs.opm.opm_annotations 2021-10-19 04:12:30 2021-10-19 04:12:40 9.61 defaultdict defaultdict(<class 'set'>, {'Q5T2W1': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P59666': {OpmAnnotation(membrane='Secreted', family='Vertebrate defens...(truncated) 405
pypath.inputs.oreganno.oreganno_interactions 2021-10-19 04:12:40 2021-10-19 04:14:39 119.12 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
pypath.inputs.oreganno.oreganno_raw 2021-10-19 04:14:39 2021-10-19 04:14:51 12.73 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
pypath.inputs.pathwaycommons._create_single_resource_method 
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons.pathwaycommons_interactions 2021-10-19 04:14:51 2021-10-19 04:15:05 14.04 list [PathwayCommonsInteraction(id_a='A2M', interaction_type='in-complex-with', id_b='BCL2L1', resource='WikiPathways'), PathwayCommonsInteraction(id_a='A2M', interaction_type='in-complex-with', id_b='CRP', resource='WikiPathways'), PathwayCommonsInteraction(id_a='A2M', interaction_type='in-complex-with'...(truncated) 1,261,865
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
pypath.inputs.pazar.pazar_interactions 2021-10-19 04:15:06 2021-10-19 04:15:07 0.25 list [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) 16,386
pypath.inputs.pdb.pdb_chains 2021-10-19 04:15:07 2021-10-19 04:15:12 5.80 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
pypath.inputs.pdb.pdb_complexes 2021-10-19 04:15:15 2021-10-19 04:15:21 6.66 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) 38,526
pypath.inputs.pdb.pdb_uniprot 2021-10-19 04:15:21 2021-10-19 04:15:25 3.49 tuple ({'P02185': {('2zsr', 'X-ray', 1.21), ('3ed9', 'X-ray', 1.21), ('2mgg', 'X-ray', 1.8), ('1mlq', 'X-ray', 2.0), ('1ufp', 'X-ray', 2.1), ('2cmm', 'X-ray', 1.8), ('1n9h', 'X-ray', 1.8), ('2e2y', 'X-ray', 1.6), ('3nml', 'X-ray', 1.68), ('5kd1', 'X-ray', 1.7), ('2mgh', 'X-ray', 2.0), ('1wvp', 'X-ray', 1....(truncated) 2
pypath.inputs.pdzbase.pdzbase_interactions 2021-10-19 04:15:25 2021-10-19 04:15:26 0.66 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
pypath.inputs.pepcyber.pepcyber_details 
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments.
pypath.inputs.pepcyber.pepcyber_interactions 2021-10-19 04:15:26 2021-10-19 04:15:27 1.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/pepcyber.py", line 112, in pepcyber_interactions
    c = curl.Curl(url, silent = False, timeout = 600, encoding = 'utf-8')
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 951, in __init__
    self.process_file()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1668, in process_file
    self.extract_file()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 1698, in extract_file
    self.extract()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 619, in extract
    getattr(self, 'open_%s' % self.type)()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 746, in open_plain
    self.result = self.fileobj.read()
  File "/usr/lib/python3.9/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd5 in position 7716714: invalid continuation byte
pypath.inputs.pfam._pfam_uniprot 
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments.
pypath.inputs.pfam.pfam_names 2021-10-19 04:15:27 2021-10-19 04:15:28 0.73 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
pypath.inputs.pfam.pfam_pdb 2021-10-19 04:15:28 2021-10-19 04:15:30 2.37 tuple (defaultdict(<class 'dict'>, {'101m': {'PF00042': PfamDomain(chain='A', start=7, end=113)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=7, end=113)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': ...(truncated) 2
pypath.inputs.pfam.pfam_regions 2021-10-19 04:15:30 2021-10-19 04:21:31 360.51 tuple ({}, {}) 2
pypath.inputs.pfam.pfam_uniprot 2021-10-19 04:21:31 2021-10-19 04:26:15 284.53 tuple ({'Q9UNH6': {'PF00787'}, 'O43761': {'PF01284'}, 'P33176': {'PF00225'}, 'Q3LI63': {'PF11759'}, 'Q9H3Y8': {'PF15060'}, 'Q8IXQ8': {'PF00595'}, 'Q8WVE7': {'PF10190'}, 'Q9NRZ5': {'PF01553', 'PF16076'}, 'Q8NEY3': {'PF06294'}, 'Q96NB2': {'PF03820'}, 'Q9H0T7': {'PF00071'}, 'Q9BWN1': {'PF15386'}, 'Q96GD3': {...(truncated) 2
pypath.inputs.phobius.phobius_annotations 2021-10-19 04:26:15 2021-10-19 04:26:16 0.40 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
pypath.inputs.phosphatome.phosphatome_annotations 2021-10-19 04:26:16 2021-10-19 04:26:16 0.20 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphatome.py", line 50, in phosphatome_annotations
    tbl = inputs_common.read_xls(c.result['aag1796_Tables S1 to S23.xlsx'])
TypeError: 'NoneType' object is not subscriptable
pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate 2021-10-19 04:26:16 2021-10-19 04:26:18 1.85 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
pypath.inputs.phosphoelm.phosphoelm_interactions 2021-10-19 04:26:18 2021-10-19 04:26:19 0.55 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
pypath.inputs.phosphoelm.phosphoelm_kinases 2021-10-19 04:26:19 2021-10-19 04:26:19 0.11 dict {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) 247
pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate 2021-10-19 04:26:19 2021-10-19 04:26:20 1.18 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
pypath.inputs.phosphonetworks.phosphonetworks_interactions 2021-10-19 04:26:20 2021-10-19 04:26:20 0.02 list [['PRKCA', 'HRH1'], ['PRKCD', 'PRKCD'], ['CAMK4', 'VPS72'], ['CDK4', 'RPA2'], ['STK38L', 'EIF4B'], ['CAMKK2', 'CAMKK1'], ['PAK1', 'LIMK1'], ['CDK4', 'PKM2'], ['CSNK2A1', 'ZCRB1'], ['CSNK1E', 'PPP1R13L'], ['CDK4', 'RBL1'], ['PDPK1', 'TBC1D22A'], ['STK17A', 'RPA2'], ['PRKCA', 'EIF6'], ['MAPK8', 'HNRPK...(truncated) 1,821
pypath.inputs.phosphopoint.phosphopoint_directions 2021-10-19 04:26:20 2021-10-19 04:26:20 0.27 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
pypath.inputs.phosphopoint.phosphopoint_interactions 2021-10-19 04:26:20 2021-10-19 04:26:20 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
pypath.inputs.phosphosite._phosphosite_filter_organism 
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments.
pypath.inputs.phosphosite.phosphosite_directions 2021-10-19 04:26:20 2021-10-19 04:26:20 0.08 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 1125, in phosphosite_directions
    curated, noref = phosphosite_interactions()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 679, in phosphosite_interactions
    bpax = c.gzfile
AttributeError: 'Curl' object has no attribute 'gzfile'
pypath.inputs.phosphosite.phosphosite_enzyme_substrate 2021-10-19 04:26:20 2021-10-19 04:26:20 0.06 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 69, in phosphosite_enzyme_substrate
    data = inputs_common.read_table(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 228, in read_table
    _ = next(fileObject)
TypeError: 'NoneType' object is not an iterator
pypath.inputs.phosphosite.phosphosite_interactions 2021-10-19 04:26:20 2021-10-19 04:26:20 0.05 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 679, in phosphosite_interactions
    bpax = c.gzfile
AttributeError: 'Curl' object has no attribute 'gzfile'
pypath.inputs.phosphosite.phosphosite_interactions_all 2021-10-19 04:26:20 2021-10-19 04:26:20 0.06 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 1134, in phosphosite_interactions_all
    return phosphosite_interactions_curated() + phosphosite_interactions_noref()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 1094, in phosphosite_interactions_curated
    curated, noref = phosphosite_interactions(ncbi_tax_id = ncbi_tax_id)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 679, in phosphosite_interactions
    bpax = c.gzfile
AttributeError: 'Curl' object has no attribute 'gzfile'
pypath.inputs.phosphosite.phosphosite_interactions_curated 2021-10-19 04:26:20 2021-10-19 04:26:20 0.06 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 1094, in phosphosite_interactions_curated
    curated, noref = phosphosite_interactions(ncbi_tax_id = ncbi_tax_id)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 679, in phosphosite_interactions
    bpax = c.gzfile
AttributeError: 'Curl' object has no attribute 'gzfile'
pypath.inputs.phosphosite.phosphosite_interactions_new 2021-10-19 04:26:20 2021-10-19 04:26:21 0.06 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 948, in phosphosite_interactions_new
    bpax = c.gzfile
AttributeError: 'Curl' object has no attribute 'gzfile'
pypath.inputs.phosphosite.phosphosite_interactions_noref 2021-10-19 04:26:21 2021-10-19 04:26:21 0.05 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 1111, in phosphosite_interactions_noref
    curated, noref = phosphosite_interactions(ncbi_tax_id = ncbi_tax_id)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 679, in phosphosite_interactions
    bpax = c.gzfile
AttributeError: 'Curl' object has no attribute 'gzfile'
pypath.inputs.phosphosite.phosphosite_ptm_orthology 2021-10-19 04:26:21 2021-10-19 04:26:21 0.05 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 219, in phosphosite_ptm_orthology
    for _ in xrange(4):
NameError: name 'xrange' is not defined
pypath.inputs.phosphosite.phosphosite_ptms 2021-10-19 04:26:21 2021-10-19 04:26:21 0.05 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 290, in phosphosite_ptms
    for _ in xrange(4):
NameError: name 'xrange' is not defined
pypath.inputs.phosphosite.phosphosite_regsites 2021-10-19 04:26:21 2021-10-19 04:26:21 0.05 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 373, in phosphosite_regsites
    data = inputs_common.read_table(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 228, in read_table
    _ = next(fileObject)
TypeError: 'NoneType' object is not an iterator
pypath.inputs.phosphosite.phosphosite_regsites_one_organism 2021-10-19 04:26:21 2021-10-19 04:26:21 0.05 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 480, in phosphosite_regsites_one_organism
    regsites = phosphosite_regsites()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/phosphosite.py", line 373, in phosphosite_regsites
    data = inputs_common.read_table(
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 228, in read_table
    _ = next(fileObject)
TypeError: 'NoneType' object is not an iterator
pypath.inputs.phosphosite.regsites_tab 
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments.
pypath.inputs.pisa.pisa_bonds 
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments.
pypath.inputs.pisa.pisa_interfaces 
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments.
pypath.inputs.pro.get_pro 2021-10-19 04:26:21 2021-10-19 04:26:38 17.69 Obo <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> None
pypath.inputs.pro.pro_mapping 2021-10-19 04:26:38 2021-10-19 04:26:39 0.44 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) 315,413
pypath.inputs.proteinatlas.get_proteinatlas 2021-10-19 04:26:39 2021-10-19 04:27:37 58.31 dict {'normal': defaultdict(<class 'dict'>, {'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':...(truncated) 2
pypath.inputs.proteinatlas.proteinatlas_annotations 2021-10-19 04:27:39 2021-10-19 04:29:24 105.76 defaultdict defaultdict(<class 'set'>, {'O43657': {ProtainatlasAnnotation(organ='placenta', tissue='trophoblastic cells', level='High', 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='...(truncated) 19,095
pypath.inputs.proteinatlas.proteinatlas_secretome_annotations 2021-10-19 04:29:27 2021-10-19 04:29:27 0.06 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/proteinatlas.py", line 254, in proteinatlas_secretome_annotations
    reader = inputs_common.read_xls(c.fileobj.name)[1:]
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations 2021-10-19 04:29:27 2021-10-19 04:29:28 0.95 dict {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Nuclear bodies', status='Uncertain'), ProteinatlasSubcellularAnnotation(location='Microtubules', status='Uncertain')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellular...(truncated) 6,634
pypath.inputs.protmapper.get_protmapper 2021-10-19 04:29:28 2021-10-19 04:29:33 5.50 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
pypath.inputs.protmapper.protmapper_enzyme_substrate 2021-10-19 04:29:34 2021-10-19 04:29:34 0.63 list [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'22304920', '25545367', '24727247', '25728676', '24357804'}, 'substrate': 'P15336', 'databases': {'Sparser', 'SIGNOR', 'PhosphoSite', 'REACH'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'23708658', '24727247'}, ...(truncated) 22,139
pypath.inputs.protmapper.protmapper_interactions 
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments.
pypath.inputs.pubchem.pubchem_mapping 
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments.
pypath.inputs.pubmed.get_pmid 
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments.
pypath.inputs.pubmed.get_pubmeds 
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments.
pypath.inputs.pubmed.only_pmids 
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments.
pypath.inputs.pubmed.open_pubmed 
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments.
pypath.inputs.pubmed.pmids_dict 
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments.
pypath.inputs.pubmed.pmids_list 
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments.
pypath.inputs.ramilowski2015.ramilowski_interactions 2021-10-19 04:29:34 2021-10-19 04:29:35 0.56 list [['A2M', 'LRP1', '', 'HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'], ['AANAT', 'MTNR1A', '', 'HPMR;literature supported'], ['AANAT', 'MTNR1B', '', 'HPMR;literature supported'], ['ACE', 'AGTR2', '', 'HPRD;literature supported'], ['ACE', 'BDKRB2', '', 'HPRD;literature supported'], ...(truncated) 1,894
pypath.inputs.ramilowski2015.ramilowski_locations 2021-10-19 04:29:35 2021-10-19 04:29:42 7.24 defaultdict defaultdict(<class 'set'>, {'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='Consensus6', tmh=0, note=N...(truncated) 18,872
pypath.inputs.rdata._patch_rdata 2021-10-19 04:29:42 2021-10-19 04:29:42 0.00 NoneType None None
pypath.inputs.rdata._rdata_data_frame_get_rownames 
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments.
pypath.inputs.rdata._rdata_list_get_names 
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments.
pypath.inputs.reaction._bp_collect_resources 
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments.
pypath.inputs.reaction._process_controls 
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments.
pypath.inputs.reaction._reactome_collect_resources 
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments.
pypath.inputs.reaction._reactome_collect_species 
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments.
pypath.inputs.reaction._reactome_compartment 
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments.
pypath.inputs.reaction._reactome_extract_id 
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments.
pypath.inputs.reaction._reactome_extract_res 
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments.
pypath.inputs.reaction._reactome_id 
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments.
pypath.inputs.reaction._reactome_reaction 
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments.
pypath.inputs.reaction._reactome_reactions 2021-10-19 04:29:42 2021-10-19 04:29:45 2.81 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 954, in _reactome_reactions
    soup = reactome_bs()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 132, in reactome_bs
    sbml = reactome_sbml()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 60, in reactome_sbml
    sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.reaction._reactome_reactions_et 2021-10-19 04:29:45 2021-10-19 04:29:47 2.27 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 1011, in _reactome_reactions_et
    sbml = reactome_sbml()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 60, in reactome_sbml
    sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.reaction._reactome_res 
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments.
pypath.inputs.reaction._reactome_species 
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments.
pypath.inputs.reaction.acsn_biopax 2021-10-19 04:29:47 2021-10-19 04:29:49 1.25 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
pypath.inputs.reaction.acsn_interactions_2 
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments.
pypath.inputs.reaction.get_acsn_effects 2021-10-19 04:29:49 2021-10-19 04:29:49 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 1116, in get_acsn_effects
    data = acsn_interactions()
NameError: name 'acsn_interactions' is not defined
pypath.inputs.reaction.get_controls 
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments.
pypath.inputs.reaction.get_interactions 
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments.
pypath.inputs.reaction.get_reactions 2021-10-19 04:29:49 2021-10-19 04:32:16 147.41 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 556, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 1153, in get_reactions
    rea.load_all()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/utils/pyreact.py", line 1301, in load_all
    self.load_pid()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/utils/pyreact.py", line 1156, in load_pid
    parser.process()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/utils/pyreact.py", line 248, in process
    self.open_biopax()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/utils/pyreact.py", line 292, in open_biopax
    self.opener = curl.FileOpener(self.biopax, **opener_args)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/share/curl.py", line 581, in __init__
    if type(file_param) in common.char_types else file_param.name
AttributeError: 'NoneType' object has no attribute 'name'
pypath.inputs.reaction.get_soup 
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments.
pypath.inputs.reaction.panther_biopax 2021-10-19 04:32:16 2021-10-19 04:32:16 0.18 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 118, in panther_biopax
    c = curl.Curl(url, silent = False, large = True).values()
AttributeError: 'Curl' object has no attribute 'values'
pypath.inputs.reaction.panther_interactions 
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments.
pypath.inputs.reaction.pid_biopax 2021-10-19 04:32:16 2021-10-19 04:32:18 1.68 NoneType None None
pypath.inputs.reaction.pid_interactions 
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments.
pypath.inputs.reaction.process_complex 
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments.
pypath.inputs.reaction.process_controls 
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments.
pypath.inputs.reaction.process_reactions 
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments.
pypath.inputs.reaction.reactions_biopax 
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments.
pypath.inputs.reaction.reactome_biopax 2021-10-19 04:32:18 2021-10-19 04:32:33 15.15 TextIOWrapper <_io.TextIOWrapper name='/home/omnipath/testing/pypath_inputs_status__20211019-020002/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> None
pypath.inputs.reaction.reactome_bs 2021-10-19 04:32:33 2021-10-19 04:32:35 2.19 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 132, in reactome_bs
    sbml = reactome_sbml()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 60, in reactome_sbml
    sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.reaction.reactome_interactions 
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments.
pypath.inputs.reaction.reactome_sbml 2021-10-19 04:32:35 2021-10-19 04:32:39 3.17 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/reaction.py", line 60, in reactome_sbml
    sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
pypath.inputs.science.science_download 
Not calling `pypath.inputs.science.science_download`, not enough arguments.
pypath.inputs.signalink.signalink_annotations 2021-10-19 04:32:39 2021-10-19 04:32:40 1.59 dict {'pathway': defaultdict(<class 'set'>, {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='JAK/STA...(truncated) 2
pypath.inputs.signalink.signalink_function_annotations 2021-10-19 04:32:40 2021-10-19 04:32:41 1.27 defaultdict defaultdict(<class 'set'>, {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(functi...(truncated) 784
pypath.inputs.signalink.signalink_interactions 2021-10-19 04:32:41 2021-10-19 04:32:42 0.42 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
pypath.inputs.signalink.signalink_pathway_annotations 2021-10-19 04:32:42 2021-10-19 04:32:42 0.67 defaultdict defaultdict(<class 'set'>, {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='JAK/STAT'), Signali...(truncated) 836
pypath.inputs.signor.signor_complexes 2021-10-19 04:32:42 2021-10-19 04:32:43 0.61 dict {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4, 'COMPLEX:P63...(truncated) 2,978
pypath.inputs.signor.signor_enzyme_substrate 2021-10-19 04:32:43 2021-10-19 04:32:46 3.18 list [{'typ': 'cleavage', 'resnum': 36, 'instance': 'TNRSSKGRSLIGKVD', 'substrate': 'P55085', 'start': 29, 'end': 43, 'kinase': 'P35030', 'resaa': 'R', 'motif': 'TNRSSKGRSLIGKVD', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'10978167'}}, {'typ': 'cleavage', 'resnum': 34, 'instance':...(truncated) 9,884
pypath.inputs.signor.signor_interactions 2021-10-19 04:32:46 2021-10-19 04:32:47 0.41 list [SignorInteraction(source='P34969', target='P09471', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates activity', mechanism='binding', ncbi_tax_id='9606', pubmeds='31160049', direct=True, ptm_type='binding', ptm_residue='', ptm_motif=''), Si...(truncated) 30,683
pypath.inputs.signor.signor_pathway_annotations 2021-10-19 04:32:47 2021-10-19 04:33:11 24.15 defaultdict defaultdict(<class 'set'>, {'O14980': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q6N021': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'Q969H0': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P10415': {SignorPathway(pathway='Autophagy'), SignorPathway(pathway='Mitochondrial Contr...(truncated) 547
pypath.inputs.signor.signor_pathways 
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments.
pypath.inputs.signor.signor_protein_families 2021-10-19 04:33:11 2021-10-19 04:33:11 0.00 dict {'SIGNOR-PF1': ['P28482', 'P27361'], 'SIGNOR-PF2': ['Q9HBW0', 'Q9UBY5', 'Q92633'], 'SIGNOR-PF3': ['O14610', 'O60262', 'Q9P2W3', 'P63215', 'P63211', 'P50150', 'P59768', 'P63218', 'P61952', 'Q9UK08', 'Q9UBI6', 'P50151'], 'SIGNOR-PF4': ['P28482', 'P27361'], 'SIGNOR-PF5': ['P01137', 'P10600', 'P61812'],...(truncated) 75
pypath.inputs.spike.spike_interactions 2021-10-19 04:33:11 2021-10-19 04:33:22 10.80 list [['836', 'CASP3', '8669', 'EIF3J', '1', '10672017', '1', '2', '', 'Published research', '', 'Proteolytic Processing'], ['836', 'CASP3', '3691', 'ITGB4', '1', '17178732', '1', '2', '', 'Published research', '', 'Proteolytic Processing'], ['407042', 'MIR34C', '4609', 'MYC', '1', '20212154', '1', '2', ...(truncated) 3,842
pypath.inputs.stitch.stitch_interactions 2021-10-19 04:33:22 2021-10-19 04:34:39 77.69 list [StitchInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action='', score=150), StitchInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action='', score=150), StitchInteraction(partner_a='23627457', partner_b='ENSP00000353915'...(truncated) 21,773,491
pypath.inputs.string.string_effects 2021-10-19 04:34:39 2021-10-19 04:34:49 9.11 list [StringInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringInteraction(source='ENSP00000000233', target...(truncated) 2,250,122
pypath.inputs.surfaceome.surfaceome_annotations 2021-10-19 04:34:50 2021-10-19 04:34:54 3.72 dict {'A0AV02': (0.8363, 'Transporters', {'APC', 'SLC', 'SLC12'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'APC', 'SLC5', 'SLC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) 2,809
pypath.inputs.switches_elm.get_switches_elm 2021-10-19 04:34:54 2021-10-19 04:34:54 0.07 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/switches_elm.py", line 84, in get_switches_elm
    sep2 = subf,
NameError: name 'subf' is not defined
pypath.inputs.talklr.talklr_annotations 2021-10-19 04:34:54 2021-10-19 04:34:54 0.70 defaultdict defaultdict(<class 'set'>, {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative...(truncated) 1,346
pypath.inputs.talklr.talklr_interactions 2021-10-19 04:34:54 2021-10-19 04:34:54 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
pypath.inputs.talklr.talklr_raw 2021-10-19 04:34:54 2021-10-19 04:34:55 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
pypath.inputs.tcdb.tcdb_annotations 2021-10-19 04:34:55 2021-10-19 04:34:59 4.72 defaultdict defaultdict(<class 'set'>, {'P60201': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(family='Synaptosomal Vesicle Fusion Pore (SVF-Pore)', t...(truncated) 2,020
pypath.inputs.tcdb.tcdb_classes 2021-10-19 04:34:59 2021-10-19 04:34:59 0.03 dict {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) 21,572
pypath.inputs.tcdb.tcdb_families 2021-10-19 04:34:59 2021-10-19 04:34:59 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) 1,635
pypath.inputs.tfcensus.tfcensus_annotations 2021-10-19 04:34:59 2021-10-19 04:35:00 0.35 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) 1,886
pypath.inputs.threedcomplex.threedcomplex_chains 2021-10-19 04:35:00 2021-10-19 04:35:06 6.53 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
pypath.inputs.threedcomplex.threedcomplex_contacts 2021-10-19 04:35:06 2021-10-19 04:35:43 36.23 set {ThreedcomplexContact(pdb='3sld_2', uniprot_1='Q5EGK8', uniprot_2='Q5EGK8', chain_1='E', chain_2='B', n_residues=32.5, length_1=309, length_2=308, domain_s1=('',), domain_p1=('PF00915.15', 'PF08435.6'), domain_s2=('',), domain_p2=('PF00915.15', 'PF08435.6'), ident=True, homo=True), ThreedcomplexCont...(truncated) 260,286
pypath.inputs.threedcomplex.threedcomplex_ddi 2021-10-19 04:35:44 2021-10-19 04:38:40 176.17 list [<pypath.internals.intera.DomainDomain object at 0x7f111fcdb1c0>, <pypath.internals.intera.DomainDomain object at 0x7f111fcdb100>, <pypath.internals.intera.DomainDomain object at 0x7f111fcdb160>, <pypath.internals.intera.DomainDomain object at 0x7f111fcdb2b0>, <pypath.internals.intera.DomainDomain o...(truncated) 525,728
pypath.inputs.threedcomplex.threedcomplex_nresidues 2021-10-19 04:38:40 2021-10-19 04:38:48 7.55 dict {'3sld_2': {('Q5EGK8', 'Q5EGK8'): 32.5}, '4tni_1': {('P0A444', 'Q8DIN8'): 5.0, ('P0A431', 'Q9F1L5'): 9.5, ('Q8DIN8', 'Q8DIQ1'): 11.5, ('P59087', 'Q8DJI1'): 1.5, ('Q8CM25', 'Q8DIF8'): 16.5, ('Q8DHA7', 'Q8DIQ0'): 1.0, ('P0A444', 'Q8DIP0'): 6.0, ('Q8DIF8', 'Q9F1K9'): 15.5, ('Q8DHA7', 'Q8DIN8'): 15.5, (...(truncated) 81,358
pypath.inputs.threedid.get_3did 2021-10-19 04:38:48 2021-10-19 04:38:48 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/threedid.py", line 174, in get_3did
    resultfile = os.path.join(settings.get('cachedir'), '3did_ddi.pickle')
NameError: name 'settings' is not defined
pypath.inputs.threedid.get_3did_ddi 2021-10-19 04:38:48 2021-10-19 04:38:56 7.44 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/threedid.py", line 49, in get_3did_ddi
    u_pdb, pdb_u = pdb_input.pdb_chains()
NameError: name 'pdb_input' is not defined
pypath.inputs.threedid.get_3did_dmi 2021-10-19 04:38:56 2021-10-19 04:38:56 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/threedid.py", line 323, in get_3did_dmi
    resultfile = os.path.join(settings.get('cachedir'), '3did_dmi.pickle')
NameError: name 'settings' is not defined
pypath.inputs.threedid.process_3did_dmi 2021-10-19 04:38:56 2021-10-19 04:38:56 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/threedid.py", line 431, in process_3did_dmi
    dmi = get_3did_dmi()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/threedid.py", line 323, in get_3did_dmi
    resultfile = os.path.join(settings.get('cachedir'), '3did_dmi.pickle')
NameError: name 'settings' is not defined
pypath.inputs.topdb.topdb_annotations 2021-10-19 04:38:56 2021-10-19 04:39:01 5.84 defaultdict defaultdict(<class 'set'>, {'P05067': {TopdbAnnotation(membrane='Cytoplasm', topology='Outside', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplasm', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplasm', topology='Inside', score=89, tmregions=1), TopdbAnnotation...(truncated) 1,247
pypath.inputs.transmir.transmir_interactions 2021-10-19 04:39:02 2021-10-19 04:39:03 1.28 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
pypath.inputs.trip.take_a_trip 2021-10-19 04:39:03 2021-10-19 04:39:53 50.27 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/trip.py", line 78, in take_a_trip
    mainsoup = bs4.BeautifulSoup(mainhtml, 'html.parser')
  File "/usr/lib/python3/dist-packages/bs4/__init__.py", line 287, in __init__
    elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
pypath.inputs.trip.trip_find_uniprot 
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments.
pypath.inputs.trip.trip_get_uniprot 
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments.
pypath.inputs.trip.trip_interactions 2021-10-19 04:39:53 2021-10-19 04:40:43 49.91 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/trip.py", line 297, in trip_interactions
    data = trip_process(exclude_methods, predictions, species, strict)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/trip.py", line 210, in trip_process
    data = take_a_trip()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/trip.py", line 78, in take_a_trip
    mainsoup = bs4.BeautifulSoup(mainhtml, 'html.parser')
  File "/usr/lib/python3/dist-packages/bs4/__init__.py", line 287, in __init__
    elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
pypath.inputs.trip.trip_process 2021-10-19 04:40:43 2021-10-19 04:41:33 49.93 
Traceback (most recent call last):
  File "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/trip.py", line 210, in trip_process
    data = take_a_trip()
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/trip.py", line 78, in take_a_trip
    mainsoup = bs4.BeautifulSoup(mainhtml, 'html.parser')
  File "/usr/lib/python3/dist-packages/bs4/__init__.py", line 287, in __init__
    elif len(markup) <= 256 and (
TypeError: object of type 'NoneType' has no len()
pypath.inputs.trip.trip_process_table 
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments.
pypath.inputs.unichem._unichem_mapping 
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments.
pypath.inputs.unichem.info 
Not calling `pypath.inputs.unichem.info`, not enough arguments.
pypath.inputs.unichem.unichem_info 2021-10-19 04:41:33 2021-10-19 04:41:33 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
pypath.inputs.unichem.unichem_mapping 
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments.
pypath.inputs.unichem.unichem_sources 2021-10-19 04:41:33 2021-10-19 04:41:33 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', '11': 'ibm', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma'...(truncated) 41
pypath.inputs.uniprot._all_uniprots 2021-10-19 04:41:33 2021-10-19 04:41:33 0.05 set {'M9P959', 'Q9BVC5', 'Q6FGN1', 'Q9NRR5', 'A0A1U9X7X2', 'A0A0A7CAM6', 'A1L1A2', 'A0A6B7G189', 'Q00973', 'A0A0B6XK48', 'Q540I6', 'R9Y259', 'A0A5C2G2K1', 'P30085', 'E9PLA7', 'Q96KG9', 'Q7KZ29', 'H7C1F6', 'Q30041', 'B4DM91', 'A0A5C2GIX7', 'A0A024R5I9', 'K7ER52', 'C7SJI3', 'E5RIZ4', 'G3V599', 'A0A5C2GA09...(truncated) 202,160
pypath.inputs.uniprot._cleanup 2021-10-19 04:41:33 2021-10-19 04:41:33 0.00 NoneType None None
pypath.inputs.uniprot._protein_datasheet 
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments.
pypath.inputs.uniprot._remove 
Not calling `pypath.inputs.uniprot._remove`, not enough arguments.
pypath.inputs.uniprot._swissprot_param 
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments.
pypath.inputs.uniprot.all_swissprots 2021-10-19 04:41:33 2021-10-19 04:41:33 0.00 set {'Q9BVC5', 'P30613', 'Q8IUR6', 'Q9NRR5', 'Q9BUG6', 'Q00973', 'O14976', 'Q13509', 'O94887', 'P30085', 'Q8N8Z8', 'Q96KG9', 'Q96BH3', 'Q8TE57', 'Q9P032', 'Q12857', 'P25024', 'P02766', 'B7Z6K7', 'P50542', 'Q7Z478', 'Q96SI9', 'Q9NYM9', 'O75602', 'P49913', 'Q9HBT6', 'Q8TF63', 'Q9H6T0', 'Q9BT78', 'Q68CR7',...(truncated) 20,386
pypath.inputs.uniprot.all_trembls 2021-10-19 04:41:33 2021-10-19 04:42:03 29.60 set {'M9P959', 'Q6FGN1', 'A0A1U9X7X2', 'A0A0A7CAM6', 'A1L1A2', 'A0A6B7G189', 'A0A0B6XK48', 'Q540I6', 'R9Y259', 'A0A5C2G2K1', 'E9PLA7', 'Q7KZ29', 'H7C1F6', 'Q30041', 'B4DM91', 'A0A5C2GIX7', 'A0A024R5I9', 'K7ER52', 'C7SJI3', 'E5RIZ4', 'G3V599', 'A0A5C2GA09', 'B4DKZ8', 'D3VVR0', 'A0A7S5C1F6', 'D6RIY4', 'Q5...(truncated) 181,774
pypath.inputs.uniprot.all_uniprots 2021-10-19 04:42:03 2021-10-19 04:42:03 0.00 set {'M9P959', 'Q9BVC5', 'Q6FGN1', 'Q9NRR5', 'A0A1U9X7X2', 'A0A0A7CAM6', 'A1L1A2', 'A0A6B7G189', 'Q00973', 'A0A0B6XK48', 'Q540I6', 'R9Y259', 'A0A5C2G2K1', 'P30085', 'E9PLA7', 'Q96KG9', 'Q7KZ29', 'H7C1F6', 'Q30041', 'B4DM91', 'A0A5C2GIX7', 'A0A024R5I9', 'K7ER52', 'C7SJI3', 'E5RIZ4', 'G3V599', 'A0A5C2GA09...(truncated) 202,160
pypath.inputs.uniprot.deleted_uniprot_genesymbol 
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments.
pypath.inputs.uniprot.get_db 2021-10-19 04:42:03 2021-10-19 04:42:03 0.00 set {'M9P959', 'Q9BVC5', 'Q6FGN1', 'Q9NRR5', 'A0A1U9X7X2', 'A0A0A7CAM6', 'A1L1A2', 'A0A6B7G189', 'Q00973', 'A0A0B6XK48', 'Q540I6', 'R9Y259', 'A0A5C2G2K1', 'P30085', 'E9PLA7', 'Q96KG9', 'Q7KZ29', 'H7C1F6', 'Q30041', 'B4DM91', 'A0A5C2GIX7', 'A0A024R5I9', 'K7ER52', 'C7SJI3', 'E5RIZ4', 'G3V599', 'A0A5C2GA09...(truncated) 202,160
pypath.inputs.uniprot.get_uniprot_sec 2021-10-19 04:42:03 2021-10-19 04:42:04 0.76 list [['A0A023IN41', 'H0Y5F6'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZR6', 'Q9UII6'], ['A0A024R056', 'A0A140VJJ8'], ['A0A024R072', 'Q96S94'], ['A0A024R077', 'Q96S94'], ['A0A024R079', 'G3V1E2'], ['A0A024R081', 'J3QRY6'], ['A0A024R...(truncated) 71,842
pypath.inputs.uniprot.init_db 2021-10-19 04:42:04 2021-10-19 04:42:04 0.05 NoneType None None
pypath.inputs.uniprot.is_swissprot 
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments.
pypath.inputs.uniprot.is_trembl 
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments.
pypath.inputs.uniprot.is_uniprot 
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments.
pypath.inputs.uniprot.protein_datasheet 
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments.
pypath.inputs.uniprot.uniprot_data 
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments.
pypath.inputs.uniprot.uniprot_families 2021-10-19 04:42:04 2021-10-19 04:42:09 5.52 defaultdict defaultdict(<class 'set'>, {'Q00266': {UniprotFamily(family='AdoMet synthase', subfamily=None)}, 'Q8NB16': {UniprotFamily(family='Protein kinase', subfamily=None)}, 'O94851': {UniprotFamily(family='Mical', subfamily=None)}, 'Q8TDZ2': {UniprotFamily(family='Mical', subfamily=None)}, 'Q9NPJ6': {Unipro...(truncated) 14,350
pypath.inputs.uniprot.uniprot_history 
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments.
pypath.inputs.uniprot.uniprot_history_recent_datasheet 
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments.
pypath.inputs.uniprot.uniprot_keywords 2021-10-19 04:42:09 2021-10-19 04:42:16 7.19 defaultdict defaultdict(<class 'set'>, {'Q00266': {UniprotKeyword(keyword='Disease variant'), UniprotKeyword(keyword='Reference proteome'), UniprotKeyword(keyword='Nucleotide-binding'), UniprotKeyword(keyword='Potassium'), UniprotKeyword(keyword='One-carbon metabolism'), UniprotKeyword(keyword='Disulfide bond')...(truncated) 20,386
pypath.inputs.uniprot.uniprot_locations 2021-10-19 04:42:16 2021-10-19 04:42:24 7.46 defaultdict defaultdict(<class 'set'>, {'Q8NB16': {UniprotLocation(location='Nucleus', features=None), UniprotLocation(location='Cell membrane', features=None), UniprotLocation(location='Cytoplasm', features=None)}, 'O94851': {UniprotLocation(location='Nucleus', features=None)}, 'Q8TDZ2': {UniprotLocation(locat...(truncated) 16,797
pypath.inputs.uniprot.uniprot_ncbi_taxids 2021-10-19 04:42:24 2021-10-19 05:06:45 1,461.25 dict {1980042: Taxon(ncbi_id=1980042, latin='1,4-dioxane-degrading enrichment culture', english='', latin_synonym=None), 85621: Taxon(ncbi_id=85621, latin='16SrII (Peanut WB group)', english='', latin_synonym=None), 85623: Taxon(ncbi_id=85623, latin='16SrIII (X-disease group)', english='', latin_synonym=...(truncated) 2,658,466
pypath.inputs.uniprot.uniprot_ncbi_taxids_2 2021-10-19 05:06:47 2021-10-19 05:06:47 0.09 dict {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) 26,658
pypath.inputs.uniprot.uniprot_preprocess 
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments.
pypath.inputs.uniprot.uniprot_recent_version 
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments.
pypath.inputs.uniprot.uniprot_taxonomy 2021-10-19 05:06:47 2021-10-19 05:06:50 2.65 defaultdict defaultdict(<class 'set'>, {'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': {'Abies firma', 'Momi fir'}, 'O81086': {'Abies g...(truncated) 551,169
pypath.inputs.uniprot.uniprot_tissues 2021-10-19 05:06:50 2021-10-19 05:06:58 7.55 defaultdict defaultdict(<class 'set'>, {'Q00266': {UniprotTissue(tissue='Liver', level='undefined')}, 'Q8TDZ2': {UniprotTissue(tissue='Kidney', level='undefined'), UniprotTissue(tissue='Spleen', level='undefined'), UniprotTissue(tissue='Testis', level='undefined'), UniprotTissue(tissue='Thymus', level='undefine...(truncated) 9,891
pypath.inputs.uniprot.uniprot_topology 2021-10-19 05:06:58 2021-10-19 05:07:22 24.29 defaultdict defaultdict(<class 'set'>, {'Q8NCK7': {UniprotTopology(topology='Cytoplasmic', start=428, end=471), UniprotTopology(topology='Transmembrane', start=198, end=218), UniprotTopology(topology='Transmembrane', start=407, end=427), UniprotTopology(topology='Transmembrane', start=273, end=293), UniprotTopo...(truncated) 5,212
pypath.inputs.uniprot.valid_uniprot 
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments.
pypath.inputs.wang.get_hsn 2021-10-19 05:07:22 2021-10-19 05:07:23 0.47 list [['1909', 'EDNRA', '4683', 'NBN', 'Pos'], ['7040', 'TGFB1', '7040', 'TGFB1', 'Neg'], ['9669', 'EIF5B', '6135', 'RPL11', 'Pos'], ['367', 'AR', '7337', 'UBE3A', 'Phy'], ['5291', 'PIK3CB', '57580', 'PREX1', 'Pos'], ['5568', 'PRKACG', '1499', 'CTNNB1', 'Pos'], ['156', 'ADRBK1', '155', 'ADRB3', 'Pos'], [...(truncated) 62,937
pypath.inputs.wang.wang_interactions 2021-10-19 05:07:23 2021-10-19 05:07:23 0.31 list [['EDNRA', 'NBN', '+'], ['TGFB1', 'TGFB1', '-'], ['EIF5B', 'RPL11', '+'], ['AR', 'UBE3A', '0'], ['PIK3CB', 'PREX1', '+'], ['PRKACG', 'CTNNB1', '+'], ['ADRBK1', 'ADRB3', '+'], ['ITGA2B', 'ACTN4', '0'], ['MCM7', 'UBE3A', '-'], ['CD4', 'ITK', '+'], ['STAT3', 'MYC', '+'], ['ZBTB17', 'NDRG2', '-'], ['CSN...(truncated) 62,937
pypath.inputs.wojtowicz2020._id_translate 
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments.
pypath.inputs.wojtowicz2020.wojtowicz2020_interactions 2021-10-19 05:07:23 2021-10-19 05:07:25 1.78 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 103, in read_xls
    book = openpyxl.load_workbook(
  File "/usr/local/lib/python3.9/dist-packages/openpyxl/reader/excel.py", line 315, in load_workbook
    reader = ExcelReader(filename, read_only, keep_vba,
  File "/usr/local/lib/python3.9/dist-packages/openpyxl/reader/excel.py", line 124, in __init__
    self.archive = _validate_archive(fn)
  File "/usr/local/lib/python3.9/dist-packages/openpyxl/reader/excel.py", line 96, in _validate_archive
    archive = ZipFile(filename, 'r')
  File "/usr/lib/python3.9/zipfile.py", line 1257, in __init__
    self._RealGetContents()
  File "/usr/lib/python3.9/zipfile.py", line 1324, 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 "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/wojtowicz2020.py", line 81, in wojtowicz2020_interactions
    for rec in wojtowicz2020_raw():
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/wojtowicz2020.py", line 44, in wojtowicz2020_raw
    content = inputs_common.read_xls(path)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 111, in read_xls
    raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: /home/omnipath/testing/pypath_inputs_status__20211019-020002/cache/9d0df0fb6df21b617036bed66b2693a1-mmc4.xlsx
pypath.inputs.wojtowicz2020.wojtowicz2020_raw 2021-10-19 05:07:25 2021-10-19 05:07:25 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 103, in read_xls
    book = openpyxl.load_workbook(
  File "/usr/local/lib/python3.9/dist-packages/openpyxl/reader/excel.py", line 315, in load_workbook
    reader = ExcelReader(filename, read_only, keep_vba,
  File "/usr/local/lib/python3.9/dist-packages/openpyxl/reader/excel.py", line 124, in __init__
    self.archive = _validate_archive(fn)
  File "/usr/local/lib/python3.9/dist-packages/openpyxl/reader/excel.py", line 96, in _validate_archive
    archive = ZipFile(filename, 'r')
  File "/usr/lib/python3.9/zipfile.py", line 1257, in __init__
    self._RealGetContents()
  File "/usr/lib/python3.9/zipfile.py", line 1324, 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 "/home/omnipath/testing/./status-report.py", line 544, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/wojtowicz2020.py", line 44, in wojtowicz2020_raw
    content = inputs_common.read_xls(path)
  File "/home/omnipath/testing/pypath_inputs_status__20211019-020002/pypath/inputs/common.py", line 111, in read_xls
    raise ValueError('Could not open xls: %s' % xls_file)
ValueError: Could not open xls: /home/omnipath/testing/pypath_inputs_status__20211019-020002/cache/9d0df0fb6df21b617036bed66b2693a1-mmc4.xlsx
pypath.inputs.zhong2015.zhong2015_annotations 2021-10-19 05:07:25 2021-10-19 05:07:26 0.60 defaultdict defaultdict(<class 'set'>, {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM'...(truncated) 466

The OmniPath Team • Saez Lab • 2021-10-19