Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.
Compiled between 2023-08-25 18:26:53 and 2023-08-25 21:46:01; pypath version: 0.15.7 (from git, installed by poetry; d732a52 )
| Modules collected: | 180 |
|---|---|
| Modules failed to import: | 2 |
| Functions collected: | 611 |
| Functions run without error: | 348 |
| Functions returned empty value: | 21 |
| Functions skipped due to lack of arguments: | 173 |
| Functions run with error: | 90 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2023-08-25 18:26:54 | 2023-08-25 18:26:55 | 0.41 | list | [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) | 650 | {} | 2023-08-25 18:26:54 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2023-08-25 18:26:55 | 2023-08-25 18:26:55 | 0.65 | list | [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) | 37,725 | {} | 2023-08-25 18:26:55 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2023-08-25 18:26:55 | 2023-08-25 18:26:56 | 0.35 | list | [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) | 9,570 | {} | 2023-08-25 18:26:55 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2023-08-25 18:26:56 | 2023-08-25 18:29:13 | 137.53 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {} | 2023-08-25 18:26:56 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2023-08-25 18:29:13 | 2023-08-25 18:29:14 | 1.20 | list | [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) | 6,542 | {} | 2023-08-25 18:29:13 | |
| ¶ | pypath.inputs.adrecs._adrecs_base |
Not calling `pypath.inputs.adrecs._adrecs_base`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.adrecs._adrecs_drug_adr | 2023-08-25 18:29:14 | 2023-08-25 18:29:41 | 26.47 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2023-08-25 18:29:14 | |
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.adrecs.<lambda> |
Not calling `pypath.inputs.adrecs.<lambda>`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.adrecs.adrecs_adr_ontology | 2023-08-25 18:29:41 | 2023-08-25 18:29:48 | 7.57 | list | [AdrecsTerm(adrecs_class='01', badd='BADD_A00503', name='Blood and lymphatic system disorders', synonyms=(), meddra=10005329), AdrecsTerm(adrecs_class='01.01', badd='BADD_A06244', name='Coagulopathies and bleeding diatheses (excl thrombocytopenic)', synonyms=(), meddra=10064477), AdrecsTerm(adrecs_c...(truncated) | 13,855 | {} | 2023-08-25 18:29:41 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_adr | 2023-08-25 18:29:49 | 2023-08-25 18:29:49 | 0.85 | list | [AdrecsDrugAdr(drug_badd='BADD_D01250', drug='Lasofoxifene', adr_badd='BADD_A00001', adr="5'nucleotidase increased"), AdrecsDrugAdr(drug_badd='BADD_D00006', drug='4r,6r-dorzolamide', adr_badd='BADD_A00002', adr='Cardiac conduction disorders'), AdrecsDrugAdr(drug_badd='BADD_D00013', drug='Abciximab',...(truncated) | 809,346 | {} | 2023-08-25 18:29:49 | |
| ¶ | pypath.inputs.adrecs.adrecs_drug_identifiers | 2023-08-25 18:29:49 | 2023-08-25 18:29:52 | 2.92 | list | [AdrecsDrug(badd='BADD_D00001', drug='1,2-hexanediol', synonyms=('1,2-hexanediol',), drugbank='DB14108', pubchem_cid='94335', mesh='C119102', kegg=None, tdd=None), AdrecsDrug(badd='BADD_D00002', drug='2-hydroxy-3-phenylpropanoic acid', synonyms=('3-phenyllactate', '3-phenyllactic acid', '3-phenyllac...(truncated) | 2,526 | {} | 2023-08-25 18:29:49 | |
| ¶ | pypath.inputs.adrecs.adrecs_hierarchy | 2023-08-25 18:29:52 | 2023-08-25 18:29:54 | 1.47 | set | {AdrecsChildParent(child=AdrecsAdr(adr_class='07.04.07', badd='BADD_A03346'), parent=AdrecsAdr(adr_class='07.04', badd='BADD_A01798')), AdrecsChildParent(child=AdrecsAdr(adr_class='14.06', badd='BADD_A01857'), parent=AdrecsAdr(adr_class='14', badd='BADD_A02756')), AdrecsChildParent(child=AdrecsAdr(a...(truncated) | 13,828 | {} | 2023-08-25 18:29:52 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2023-08-25 18:29:54 | 2023-08-25 18:29:55 | 0.95 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/almen2009.py", line 63, in almen2009_annotations
uniprots = mapping.map_name(row[0], 'ipi', 'uniprot')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 3564, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/share/common.py", line 2772, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 1982, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 2514, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 1575, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 3212, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 257, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 287, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 449, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 560, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/ipi.py", line 68, in _ipi_uniprot_pairs
for ipi, uniprots in iteritems(ipi_uniprot()):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/ipi.py", line 40, in ipi_uniprot
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 18:29:55 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2023-08-25 18:29:55 | 2023-08-25 18:29:55 | 0.57 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/baccin2019.py", line 190, in baccin2019_annotations
ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/baccin2019.py", line 121, in baccin2019_interactions
data = inputs_common.read_xls(c.fileobj.name, sheet = 'SuppTable3')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-07-28 18:29:56 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2023-08-25 18:29:55 | 2023-08-25 18:29:56 | 0.37 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/baccin2019.py", line 121, in baccin2019_interactions
data = inputs_common.read_xls(c.fileobj.name, sheet = 'SuppTable3')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-07-28 18:29:57 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2023-08-25 18:29:56 | 2023-08-25 18:29:56 | 0.00 | list | [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) | 9 | {} | 2023-08-25 18:29:56 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2023-08-25 18:29:56 | 2023-08-25 18:30:31 | 35.61 | dict | {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) | 9 | {} | 2023-08-25 18:29:56 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2023-08-25 18:30:32 | 2023-08-25 18:31:11 | 39.01 | list | [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855', experimental_system='Two-hybrid', experimental_system_type='physical', ltp=True, htp_score=None, multi_validated=True, tax_a='9606', tax_b='9606'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272', experimen...(truncated) | 8,277 | {} | 2023-08-25 18:30:32 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2023-08-25 18:31:11 | 2023-08-25 18:31:12 | 1.23 | list | [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) | 7,038 | {} | 2023-08-25 18:31:11 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2023-08-25 18:31:12 | 2023-08-25 18:31:51 | 38.26 | 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) | 177,409 | {} | 2023-08-25 18:31:12 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2023-08-25 18:31:51 | 2023-08-25 18:31:57 | 6.06 | list | [{'format': 'EXPRESSION', 'description': None, 'vendor': 'PHALANX', 'type': 'OLIGO', 'array': 'OneArray', 'label': 'PHALANX OneArray'}, {'description': None, 'array': 'CODELINK', 'type': 'OLIGO', 'vendor': 'CODELINK', 'format': 'EXPRESSION', 'label': 'CODELINK CODELINK'}, {'format': 'EXPRESSION', 't...(truncated) | 35 | {} | 2023-08-25 18:31:51 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomodels._get_biomodels | 2023-08-25 18:31:57 | 2023-08-25 18:31:57 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/biomodels.py", line 101, in _get_biomodels
loginurl = urls.urls['biomodels']['login'] % t
KeyError: 'login'
|
{} | 2023-07-28 18:32:04 | |||
| ¶ | pypath.inputs.biomodels.download_single_model |
Not calling `pypath.inputs.biomodels.download_single_model`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomodels.get_biomodels | 2023-08-25 18:31:57 | 2023-08-25 18:31:57 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/biomodels.py", line 160, in get_biomodels
c0.perform()
pycurl.error: (3, '')
|
{} | 2023-07-28 18:32:04 | |||
| ¶ | pypath.inputs.biomodels.get_biomodels_req | 2023-08-25 18:31:57 | 2023-08-25 18:31:58 | 0.84 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/biomodels.py", line 193, in get_biomodels_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-07-28 18:32:04 | |||
| ¶ | pypath.inputs.biomodels.get_single_model |
Not calling `pypath.inputs.biomodels.get_single_model`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2023-08-25 18:31:58 | 2023-08-25 18:31:58 | 0.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/ca1.py", line 53, in ca1_interactions
path = science_input.science_download(url = url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 18:32:05 | |||
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2023-08-25 18:31:58 | 2023-08-25 18:32:00 | 1.81 | list | [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) | 47,644 | {} | 2023-08-25 18:31:58 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2023-08-25 18:32:00 | 2023-08-25 18:32:11 | 10.81 | dict | {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) | 186 | {} | 2023-08-25 18:32:00 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2023-08-25 18:32:11 | 2023-08-25 18:32:11 | 0.00 | list | [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) | 304 | {} | 2023-08-25 18:32:11 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2023-08-25 18:32:11 | 2023-08-25 18:32:11 | 0.01 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='Q8N726', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 2,268 | {} | 2023-08-25 18:32:11 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2023-08-25 18:32:11 | 2023-08-25 18:32:13 | 2.47 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Inflammation'), CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,247 | {} | 2023-08-25 18:32:11 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2023-08-25 18:32:13 | 2023-08-25 18:32:30 | 16.49 | dict | {'O00548': {CellcallAnnotation(role='ligand')}, 'Q9UM47': {CellcallAnnotation(role='receptor')}, 'P52798': {CellcallAnnotation(role='ligand')}, 'P29322': {CellcallAnnotation(role='receptor')}, 'Q9H1J5': {CellcallAnnotation(role='ligand')}, 'Q9H461': {CellcallAnnotation(role='receptor')}, 'P20800': {...(truncated) | 460 | {} | 2023-08-25 18:32:13 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2023-08-25 18:32:30 | 2023-08-25 18:32:30 | 0.04 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2023-08-25 18:32:30 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2023-08-25 18:32:30 | 2023-08-25 18:32:31 | 0.96 | list | [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) | 38,645 | {} | 2023-08-25 18:32:30 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2023-08-25 18:32:31 | 2023-08-25 18:32:31 | 0.11 | list | [CellcallInteraction(ligand_uniprot='O00548', receptor_uniprot='Q9UM47', core=True), CellcallInteraction(ligand_uniprot='P52798', receptor_uniprot='P29322', core=True), CellcallInteraction(ligand_uniprot='Q9H1J5', receptor_uniprot='Q9H461', core=True), CellcallInteraction(ligand_uniprot='P20800', re...(truncated) | 797 | {} | 2023-08-25 18:32:31 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2023-08-25 18:32:31 | 2023-08-25 18:32:32 | 0.76 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Receptor')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM'), Cellcellinteractions...(truncated) | 3,425 | {} | 2023-08-25 18:32:31 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2023-08-25 18:32:32 | 2023-08-25 18:32:32 | 0.00 | int | 9606 | 0 | {} | 2023-08-25 18:32:32 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_cofactors |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_process_complexes |
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_annotations | 2023-08-25 18:32:32 | 2023-08-25 18:32:40 | 8.55 | dict | {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P19883': {CellChatDBAnnotation(role='agonist', pathway='TGFb', category=...(truncated) | 1,067 | {} | 2023-08-25 18:32:32 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2023-08-25 18:32:40 | 2023-08-25 18:32:45 | 5.26 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O75610', 'O60565', 'P12645', 'Q9H772', 'O00292', 'Q9H2X0', 'P41271', 'Q13253'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 31 | {} | 2023-08-25 18:32:40 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2023-08-25 18:32:45 | 2023-08-25 18:32:51 | 5.15 | dict | {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) | 153 | {} | 2023-08-25 18:32:45 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2023-08-25 18:32:51 | 2023-08-25 18:32:56 | 5.82 | dict | {'interaction': interaction_name ... rownames TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 TGFB1_ACVR1B_TGF...(truncated) | 4 | {} | 2023-08-25 18:32:51 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2023-08-25 18:32:56 | 2023-08-25 18:33:02 | 5.24 | list | [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) | 11,113 | {} | 2023-08-25 18:32:56 | |
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.32 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.18 | dict | {'P02776': {CellinkerAnnotation(role='ligand', location='Secreted', type='Cytokine-cytokine receptor interaction')}, 'P34741': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='...(truncated) | 1,921 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.05 | dict | {Complex: COMPLEX:P05556_P26006: {CellinkerAnnotation(role='receptor', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction')}, Complex: COMPLEX:O75581_Q9ULV1: {CellinkerAnnotation(role='receptor', location='Membrane', t...(truncated) | 134 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.00 | dict | {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) | 143 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.00 | list | [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) | 145 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.05 | set | {CellinkerInteraction(ligand='P02776', receptor='P34741', ligand_location='Secreted', receptor_location='Membrane', resources=None, pmids='7524669', type='Cytokine-cytokine receptor interaction'), CellinkerInteraction(ligand='P01903', receptor='P21926', ligand_location='Membrane', receptor_location=...(truncated) | 3,812 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.01 | list | [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) | 3,744 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2023-08-25 18:33:02 | 2023-08-25 18:33:02 | 0.06 | dict | {'P02776': {CellinkerAnnotation(role='ligand', location='Secreted', type='Cytokine-cytokine receptor interaction')}, 'P34741': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='receptor', location='Membrane', type='...(truncated) | 1,787 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2023-08-25 18:33:02 | 2023-08-25 18:33:03 | 0.14 | set | {CellinkerInteraction(ligand='5202', receptor='P30939', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='8380639', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5282411', receptor='P34995', ligand_location=None, receptor_location='Membrane', reso...(truncated) | 314 | {} | 2023-08-25 18:33:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2023-08-25 18:33:03 | 2023-08-25 18:33:03 | 0.00 | list | [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) | 341 | {} | 2023-08-25 18:33:03 | |
| ¶ | pypath.inputs.cellinker.components_to_complex |
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_annotations |
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_get_entity |
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb._cellphonedb_hla |
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complex_annotations | 2023-08-25 18:33:03 | 2023-08-25 18:33:03 | 0.21 | dict | {Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transmembrane=False, integrin=False), Complex DHEAsulfate_bySULT2B: COMPLEX:P50225: CellPhoneDBAnnotation(receptor=False, rec...(truncated) | 359 | {} | 2023-08-25 18:33:03 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2023-08-25 18:33:03 | 2023-08-25 18:33:03 | 0.01 | dict | {'COMPLEX:Q8TF42': Complex Dehydroepiandrosterone_bySTS: COMPLEX:Q8TF42, 'COMPLEX:P50225': Complex DHEAsulfate_bySULT2B: COMPLEX:P50225, 'COMPLEX:Q9H8P0': Complex Dihydrotestosterone_bySRD5A3: COMPLEX:Q9H8P0, 'COMPLEX:P18405': Complex Dihydrotestosterone_bySRD5A1: COMPLEX:P18405, 'COMPLEX:P31213': C...(truncated) | 359 | {} | 2023-08-25 18:33:03 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2023-08-25 18:33:03 | 2023-08-25 18:33:03 | 0.71 | list | [CellphonedbInteraction(id_a=Complex 12oxoLeukotrieneB4_byPTGR1: COMPLEX:Q14914, id_b='Q15722', sources='CellPhoneDB', references='', interaction_type='ligand-receptor', type_a='ligand', type_b='receptor'), CellphonedbInteraction(id_a=Complex 12oxoLeukotrieneB4_byPTGR1: COMPLEX:Q14914, id_b='Q9NPC1'...(truncated) | 2,915 | {} | 2023-08-25 18:33:03 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2023-08-25 18:33:03 | 2023-08-25 18:33:04 | 0.02 | tuple | ({'P01308', 'P55075', 'Q07325', 'O95407', 'P35247', 'Q01959', Complex LTC4_byLTC4S: COMPLEX:Q16873, 'O95715', Complex FZD1_LRP6: COMPLEX:O75581_Q9UP38, 'P10912', 'P39060', Complex Calcitriol_byCYP27B1: COMPLEX:O15528, 'Q96T91', 'P01571', 'P09544', 'Q02297', Complex FZD3_LRP6: COMPLEX:O75581_Q9NPG1, ...(truncated) | 2 | {} | 2023-08-25 18:33:03 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2023-08-25 18:33:04 | 2023-08-25 18:33:04 | 0.02 | dict | {'P03372': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=True, secreted=False, secreted_class=(), transmembrane=False, integrin=False), 'Q92753': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), tr...(truncated) | 1,354 | {} | 2023-08-25 18:33:04 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2023-08-25 18:33:04 | 2023-08-25 18:35:04 | 120.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/celltalkdb.py", line 177, in celltalkdb_annotations
for rec in celltalkdb_download(organism = ncbi_tax_id):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/celltalkdb.py", line 83, in celltalkdb_download
soup = bs4.BeautifulSoup(c_init.fileobj, 'html.parser')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-08-14 18:32:36 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2023-08-25 18:35:04 | 2023-08-25 18:35:14 | 10.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/celltalkdb.py", line 83, in celltalkdb_download
soup = bs4.BeautifulSoup(c_init.fileobj, 'html.parser')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-08-14 18:32:53 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2023-08-25 18:35:14 | 2023-08-25 18:35:24 | 10.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/celltalkdb.py", line 141, in celltalkdb_interactions
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/celltalkdb.py", line 141, in <listcomp>
return [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/celltalkdb.py", line 83, in celltalkdb_download
soup = bs4.BeautifulSoup(c_init.fileobj, 'html.parser')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-08-14 18:32:53 | |||
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2023-08-25 18:35:24 | 2023-08-25 18:35:24 | 0.25 | dict | {'P15391': {CelltypistAnnotation(cell_type='Cycling cells', cell_subtype='Cycling B cells', cell_ontology='CL:0000236', marker_type='curated_marker', tissues=('Intestine',), datasets=('Smillie et al. 2019',)), CelltypistAnnotation(cell_type='B cells', cell_subtype='B cells', cell_ontology='CL:000023...(truncated) | 459 | {} | 2023-08-25 18:35:24 | |
| ¶ | pypath.inputs.chembl.chembl_activities |
Not calling `pypath.inputs.chembl.chembl_activities`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.chembl.chembl_documents | 2023-08-25 18:35:24 | 2023-08-25 18:36:55 | 91.60 | dict | {'CHEMBL1139451': 14695813, 'CHEMBL1148466': 14695814, 'CHEMBL1139452': 14695824, 'CHEMBL1139453': 14695825, 'CHEMBL1139454': 14695826, 'CHEMBL1139455': 14695827, 'CHEMBL1139456': 14695815, 'CHEMBL1139457': 14695828, 'CHEMBL1139458': 14695816, 'CHEMBL1148467': 14695833, 'CHEMBL1139459': 14695834, 'C...(truncated) | 80,293 | {} | 2023-08-25 18:35:24 | |
| ¶ | pypath.inputs.chembl.chembl_drug_indications | 2023-08-25 18:36:55 | 2023-08-25 18:37:57 | 61.07 | list | [ChemblIndication(efo_id='EFO:0000404', efo_term='diffuse scleroderma', max_phase=2.0, mesh_heading='Scleroderma, Diffuse', mesh_id='D045743', molecule_chembl='CHEMBL1201823'), ChemblIndication(efo_id='EFO:0000685', efo_term='rheumatoid arthritis', max_phase=4.0, mesh_heading='Arthritis, Rheumatoid'...(truncated) | 51,582 | {} | 2023-08-25 18:36:55 | |
| ¶ | pypath.inputs.chembl.chembl_mechanisms | 2023-08-25 18:37:57 | 2023-08-25 18:38:08 | 11.28 | list | [ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_action='Carbonic anhydrase VII inhibitor', chembl='CHEMBL19', target_chembl='CHEMBL2326'), ChemblMechanism(action_type='INHIBITOR', direct_interaction=True, disease_efficacy=True, mechanism_of_acti...(truncated) | 7,098 | {} | 2023-08-25 18:37:57 | |
| ¶ | pypath.inputs.chembl.chembl_targets | 2023-08-25 18:38:08 | 2023-08-25 18:40:10 | 122.41 | list | [ChemblTarget(accession='O43451', target_chembl_id='CHEMBL2074'), ChemblTarget(accession='O60706', target_chembl_id='CHEMBL1971'), ChemblTarget(accession='O76074', target_chembl_id='CHEMBL1827'), ChemblTarget(accession='O95180', target_chembl_id='CHEMBL1859'), ChemblTarget(accession='O96760', target...(truncated) | 15,398 | {} | 2023-08-25 18:38:08 | |
| ¶ | pypath.inputs.clinvar.clinvar_citations | 2023-08-25 18:40:10 | 2023-08-25 18:40:33 | 22.57 | list | [Citation(allele='1056169', variation_id='1068254', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='523785', variation_id='528159', nsv='', citation_source='PubMed', citation_id='28492532'), Citation(allele='334658', variation_id='310628', nsv='', citation_source='PubMed'...(truncated) | 2,734,421 | {'fixed': True} | 2023-08-25 18:40:10 | |
| ¶ | pypath.inputs.clinvar.clinvar_raw | 2023-08-25 18:40:37 | 2023-08-25 18:42:43 | 126.85 | list | [Variant(allele='1111014', type='single nucleotide variant', variant='NM_006267.5(RANBP2):c.156C>T (p.Tyr52=)', entrez='5903', genesymbol='RANBP2', clinical_significance='Likely benign', review_status='criteria provided, single submitter', rs='-1', phenotype_ids=('MONDO:MONDO:0011953', 'MedGen:C2675...(truncated) | 4,607,659 | {'fixed': True} | 2023-08-25 18:40:37 | |
| ¶ | pypath.inputs.collectri.collectri_interactions | 2023-08-25 18:53:46 | 2023-08-25 18:53:49 | 2.32 | list | [CollectriInteraction(tf='P01106', target='O14746', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;...(truncated) | 64,969 | {} | 2023-08-25 18:53:46 | |
| ¶ | pypath.inputs.collectri.collectri_raw | 2023-08-25 18:53:49 | 2023-08-25 18:53:49 | 0.08 | list | [CollectriRecord(tf='MYC', target='TERT', effect=1, tf_category='dbTF', resources='ExTRI;HTRI;TRRUST;TFactS;NTNU.Curated;Pavlidis2021;DoRothEA-A', pubmed='10022128;10491298;10606235;10637317;10723141;10786671;10914736;11274400;11279234;11287602;11435602;11606399;11916966;12044867;12646176;12695333;1...(truncated) | 43,416 | {} | 2023-08-25 18:53:49 | |
| ¶ | pypath.inputs.compath._compath_mappings | 2023-08-25 18:53:49 | 2023-08-25 18:53:49 | 0.12 | list | [CompathPathwayToPathway(pathway1='2-Oxocarboxylic acid metabolism - Homo sapiens (human)', pathway_id_1='hsa01210', source_db='kegg', relation='isPartOf', pathway2='Amino Acid metabolism', pathway_id_2='WP3925', target_db='wikipathways'), CompathPathwayToPathway(pathway1='AMPK signaling pathway - H...(truncated) | 1,592 | {} | 2023-08-25 18:53:49 | |
| ¶ | pypath.inputs.compath.compath_mappings | 2023-08-25 18:53:49 | 2023-08-25 18:53:49 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/compath.py", line 55, in compath_mappings
return pd.DataFrame(result) if return_df else result
NameError: name 'return_df' is not defined
|
{} | 2023-07-28 19:06:32 | |||
| ¶ | pypath.inputs.compleat.compleat_complexes | 2023-08-25 18:53:49 | 2023-08-25 18:53:50 | 0.98 | dict | {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) | 9,692 | {'size': 1} | 2023-08-25 18:53:49 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2023-08-25 18:53:50 | 2023-08-25 18:53:50 | 0.04 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2023-08-25 18:53:50 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2023-08-25 18:53:50 | 2023-08-25 18:55:06 | 75.90 | dict | {'COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0': Complex Shelterin complex: COMPLEX:P54274_Q15554_Q96AP0_Q9BSI4_Q9NUX5_Q9NYB0, 'COMPLEX:Q86XT2_Q99816_Q9NZ09_Q9UK41': Complex ESCRT-I complex, VPS37D-UBAP1 variant: COMPLEX:Q86XT2_Q99816_Q9NZ09_Q9UK41, 'COMPLEX:Q86XE3_Q8NE86_Q9BPX6_Q9H4I9': Comple...(truncated) | 1,620 | {} | 2023-08-25 18:53:50 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2023-08-25 18:55:06 | 2023-08-25 18:55:21 | 14.83 | 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) | 588,829 | {} | 2023-08-25 18:55:06 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2023-08-25 18:55:21 | 2023-08-25 18:55:36 | 15.46 | dict | {'Q8TES7': {ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation(location='nucleus', score=0.9099999999999999), ComppiLocation(location='membrane', score=0.96), ComppiLocation...(truncated) | 18,254 | {} | 2023-08-25 18:55:21 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2023-08-25 18:55:37 | 2023-08-25 18:55:37 | 0.31 | dict | {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) | 1,428 | {} | 2023-08-25 18:55:37 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2023-08-25 18:55:37 | 2023-08-25 18:55:37 | 0.01 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2023-08-25 18:55:37 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2023-08-25 18:55:37 | 2023-08-25 18:55:38 | 0.82 | dict | {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) | 2,734 | {} | 2023-08-25 18:55:37 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2023-08-25 18:55:38 | 2023-08-25 18:55:40 | 2.35 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cosmic.py", line 132, in cancer_gene_census_annotations
data = csv.DictReader(c.fileobj, delimiter = ',')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:08:21 | |||
| ¶ | pypath.inputs.cpad.cpad_annotations | 2023-08-25 18:55:40 | 2023-08-25 18:55:45 | 4.54 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cpad.py", line 69, in cpad_annotations
mirbase = mapping.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 3564, in map_name
return mapper.map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/share/common.py", line 2772, in wrapper
return func(*args, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 1982, in map_name
mapped_names = self._map_name(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 2514, in _map_name
tbl = self.which_table(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 1575, in which_table
self.load_mapping(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 3212, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 257, in __init__
self.load()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 287, in load
self.read()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 449, in read
getattr(self, method)()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/mapping.py", line 560, in read_mapping_file
for i, line in enumerate(infile):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 76, in mirbase_mature
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 19:08:25 | |||
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2023-08-25 18:55:45 | 2023-08-25 18:55:45 | 0.08 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='NF-kappa B signaling pathway', cancer='Glioma', pathway_category='NF-kappa B signaling pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='sensitize human glioma cells to ionizing radiation'), CpadPathwayCancer(pathway='TGF-beta/Smad3 signaling ...(truncated) | 2 | {} | 2023-08-25 18:55:45 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2023-08-25 18:55:45 | 2023-08-25 18:55:45 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2023-08-25 18:55:45 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2023-08-25 18:55:45 | 2023-08-25 18:55:51 | 6.65 | 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) | 531,371 | {} | 2023-08-25 18:55:45 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2023-08-25 18:55:52 | 2023-08-25 18:55:55 | 2.76 | list | [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) | 482,222 | {} | 2023-08-25 18:55:52 | |
| ¶ | pypath.inputs.credentials.credentials |
Not calling `pypath.inputs.credentials.credentials`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cspa.cspa_annotations | 2023-08-25 18:55:55 | 2023-08-25 18:55:56 | 0.73 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cspa.py", line 58, in cspa_annotations
raw = inputs_common.read_xls(xlsname, sheets[str_organism])[1:]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-07-28 19:08:41 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2023-08-25 18:55:56 | 2023-08-25 18:55:56 | 0.35 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cspa.py", line 127, in cspa_cell_type_annotations
cell_type_data = cspa_cell_types(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cspa.py", line 92, in cspa_cell_types
raw = inputs_common.read_xls(xlsname, sheets[str_organism])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'float' object has no attribute 'value'
|
{} | 2023-07-28 19:08:42 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2023-08-25 18:55:56 | 2023-08-25 18:55:56 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cspa.py", line 92, in cspa_cell_types
raw = inputs_common.read_xls(xlsname, sheets[str_organism])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'float' object has no attribute 'value'
|
{} | 2023-07-28 19:08:42 | |||
| ¶ | pypath.inputs.ctdbase._ctdbase_download |
Not calling `pypath.inputs.ctdbase._ctdbase_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase._map_keys |
Not calling `pypath.inputs.ctdbase._map_keys`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase._modify_dict |
Not calling `pypath.inputs.ctdbase._modify_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_relations |
Not calling `pypath.inputs.ctdbase.ctdbase_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ctdbase.ctdbase_vocabulary |
Not calling `pypath.inputs.ctdbase.ctdbase_vocabulary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2023-08-25 18:55:56 | 2023-08-25 18:55:58 | 2.26 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='O43508', score=0.0196893398245272, cytokine_genesymbol='TWEAK', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P15018', score=0.172277014442499, cytokine_genesymbol='LIF', target_genesymbol='A4GALT'), CytosigAnnotation(cytokine='P22004', score=0.0187...(truncated) | 4,889 | {} | 2023-08-25 18:55:56 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2023-08-25 18:55:59 | 2023-08-25 18:55:59 | 0.04 | DataFrame | Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) | 4,881 | {} | 2023-08-25 18:55:59 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2023-08-25 18:55:59 | 2023-08-25 18:56:01 | 2.53 | list | [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) | 223,135 | {} | 2023-08-25 18:55:59 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2023-08-25 18:56:02 | 2023-08-25 18:56:05 | 2.97 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/dbptm.py", line 97, in dbptm_enzyme_substrate_old
for k, data in iteritems(extra):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-FlMyD3yS-py3.10/lib/python3.10/site-packages/future/utils/__init__.py", line 314, in iteritems
func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2023-07-28 19:08:47 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2023-08-25 18:56:05 | 2023-08-25 18:56:06 | 1.07 | list | [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) | 2,071 | {} | 2023-08-25 18:56:05 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2023-08-25 18:56:06 | 2023-08-25 18:56:07 | 0.93 | list | [] | 0 | {} | 2023-08-25 18:56:06 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2023-08-25 18:56:07 | 2023-08-25 18:56:07 | 0.17 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2023-08-25 18:56:07 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2023-08-25 18:56:07 | 2023-08-25 18:56:07 | 0.08 | list | [{'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1054, 'references': ['11201744'], 'substrate': 'P29597', 'start': None, 'end': None, 'typ': 'dephosphorylation'}, {'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1055, 'references': ['11201744'], 'substrate': 'P29597', 's...(truncated) | 537 | {} | 2023-08-25 18:56:07 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2023-08-25 18:56:07 | 2023-08-25 18:56:07 | 0.01 | list | [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) | 832 | {} | 2023-08-25 18:56:07 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2023-08-25 18:56:07 | 2023-08-25 18:56:09 | 2.25 | dict | {'Q9BXS1': {DgidbAnnotation(category='ENZYME')}, 'Q9BZH6': {DgidbAnnotation(category='TRANSCRIPTION FACTOR')}, 'Q96Q89': {DgidbAnnotation(category='ENZYME')}, 'Q99470': {DgidbAnnotation(category='DRUGGABLE GENOME')}, 'Q9H211': {DgidbAnnotation(category='KINASE')}, 'O95069': {DgidbAnnotation(category...(truncated) | 10,494 | {} | 2023-08-25 18:56:07 | |
| ¶ | pypath.inputs.dgidb.dgidb_interactions | 2023-08-25 18:56:09 | 2023-08-25 18:56:14 | 4.81 | list | [DgidbInteraction(genesymbol='GABRQ', entrez='55879', resource='ChemblInteractions', type='positive modulator', drug_name='CLONAZEPAM', drug_chembl='chembl:CHEMBL452', score='0.15', pmid=None), DgidbInteraction(genesymbol='RACGAP1', entrez='29127', resource='DTC', type=None, drug_name='MITOXANTRONE ...(truncated) | 85,022 | {} | 2023-08-25 18:56:09 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2023-08-25 18:56:14 | 2023-08-25 18:57:17 | 62.56 | set | {'P51452', 'P51160', 'Q9BSJ1', 'Q16281', 'Q01959', 'P08183', 'Q01970', 'Q01433', 'P24864', 'Q8NGP9', 'Q9NRK6', 'Q8WZ94', 'Q01860', 'Q8NGG4', 'Q9UI42', 'Q9Y5P0', 'O95672', 'Q96A70', 'P36776', 'P01106', 'P56705', 'A6NDH6', 'P46734', 'Q9NZV8', 'Q15233', 'Q8NBS3', 'Q9H981', 'Q8NGL0', 'O75629', 'P42081',...(truncated) | 5,907 | {} | 2023-08-25 18:56:14 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.28 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2023-08-25 18:57:17 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases._diseases_general |
Not calling `pypath.inputs.diseases._diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.diseases_general |
Not calling `pypath.inputs.diseases.diseases_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.diseases.experiments_filtered | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-07-28 19:10:00 | |||
| ¶ | pypath.inputs.diseases.experiments_full | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-07-28 19:10:00 | |||
| ¶ | pypath.inputs.diseases.knowledge_filtered | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-07-28 19:10:00 | |||
| ¶ | pypath.inputs.diseases.knowledge_full | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-07-28 19:10:00 | |||
| ¶ | pypath.inputs.diseases.textmining_filtered | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-07-28 19:10:00 | |||
| ¶ | pypath.inputs.diseases.textmining_full | 2023-08-25 18:57:17 | 2023-08-25 18:57:17 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/diseases.py", line 78, in _diseases_general
url = urls['diseases']['url'] % (data_origin, query_type)
TypeError: 'module' object is not subscriptable
|
{} | 2023-07-28 19:10:00 | |||
| ¶ | pypath.inputs.domino.domino_ddi | 2023-08-25 18:57:17 | 2023-08-25 18:57:22 | 5.15 | list | [<pypath.internals.intera.DomainDomain object at 0x7fbe42748160>, <pypath.internals.intera.DomainDomain object at 0x7fbe425bbac0>, <pypath.internals.intera.DomainDomain object at 0x7fbe425bb790>, <pypath.internals.intera.DomainDomain object at 0x7fbe425bafb0>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2023-08-25 18:57:17 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2023-08-25 18:57:22 | 2023-08-25 18:57:23 | 0.93 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7fbe425b9db0>, <pypath.internals.intera.DomainDomain object at 0x7fbe425bb7c0>, <pypath.internals.intera.DomainDomain object at 0x7fbe425ba1d0>, <pypath.internals.intera.DomainDomain object at 0x7fbe425babc0>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2023-08-25 18:57:22 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2023-08-25 18:57:23 | 2023-08-25 18:57:24 | 0.41 | list | [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) | 6,687 | {} | 2023-08-25 18:57:23 | |
| ¶ | pypath.inputs.domino.get_domino | 2023-08-25 18:57:24 | 2023-08-25 18:57:24 | 0.38 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2023-08-25 18:57:24 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2023-08-25 18:57:24 | 2023-08-25 18:57:33 | 8.60 | DataFrame | tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) | 1,019,220 | {} | 2023-08-25 18:57:24 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2023-08-25 18:57:33 | 2023-08-25 18:57:47 | 13.80 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2023-08-25 18:57:33 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-08-25 18:57:47 | 2023-08-25 18:57:47 | 0.50 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-08-25 18:57:47 | 2023-08-25 18:57:47 | 0.26 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2023-08-25 18:57:47 | 2023-08-25 18:57:49 | 1.72 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2023-08-25 18:57:47 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2023-08-25 18:57:49 | 2023-08-25 18:57:49 | 0.36 | list | [['AHR', 'CYP1A1', '0', 'A', True, False, True, False, 'HTRIdb,trrust_signed', '', 'hocomoco_v11', '', 'HTRIdb,trrust_signed,hocomoco_v11'], ['AHR', 'CYP1A2', '0', 'A', True, False, False, False, 'HTRIdb,trrust_signed', '', '', '', 'HTRIdb,trrust_signed'], ['AHR', 'CYP1B1', '0', 'A', True, False, Tr...(truncated) | 14,260 | {} | 2023-08-25 18:57:49 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2023-08-25 18:57:49 | 2023-08-25 18:57:51 | 1.19 | DataFrame | tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) | 454,504 | {} | 2023-08-25 18:57:49 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2023-08-25 18:57:51 | 2023-08-25 18:58:05 | 13.95 | list | [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) | 309,009 | {} | 2023-08-25 18:57:51 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2023-08-25 18:58:05 | 2023-08-25 18:58:05 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/dorothea.py", line 208, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.drugbank._drugbank_credentials | 2023-08-25 18:58:05 | 2023-08-25 18:58:05 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/drugbank.py", line 49, in _drugbank_credentials
return credentials.credentials(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/credentials.py", line 115, in credentials
raise RuntimeError(msg)
RuntimeError: Failed to obtain credentials for resource `DrugBank`
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.drugbank._drugbank_download |
Not calling `pypath.inputs.drugbank._drugbank_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_annotations | 2023-08-25 18:58:05 | 2023-08-25 18:58:05 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/drugbank.py", line 352, in drugbank_annotations
drugs = drugbank_drugs(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.drugbank.drugbank_drugs | 2023-08-25 18:58:05 | 2023-08-25 18:58:05 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.drugbank.drugbank_interactions | 2023-08-25 18:58:05 | 2023-08-25 18:58:05 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/drugbank.py", line 198, in drugbank_interactions
for d in drugbank_drugs(user = user, passwd = passwd)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/drugbank.py", line 303, in drugbank_drugs
for dbid, struct in raw['structure'].items():
KeyError: 'structure'
|
{} | 2023-07-28 19:10:51 | |||
| ¶ | pypath.inputs.drugbank.drugbank_mapping |
Not calling `pypath.inputs.drugbank.drugbank_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.drugbank.drugbank_raw_interactions | 2023-08-25 18:58:05 | 2023-08-25 18:58:05 | 0.00 | list | [] | 0 | {} | 2023-08-25 18:58:05 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_drugs | 2023-08-25 18:58:05 | 2023-08-25 18:58:06 | 1.09 | list | [DrugcentralDrug(drugcentral='5392', inn='capmatinib', cas='1029712-80-8', smiles='CNC(=O)C1=C(C=C(C=C1)C2=NN3C(=CN=C3N=C2)CC4=CC5=C(C=C4)N=CC=C5)F', inchikey='LIOLIMKSCNQPLV-UHFFFAOYSA-N', inchi='InChI=1S/C23H17FN6O/c1-25-22(31)18-6-5-16(11-19(18)24)21-13-28-23-27-12-17(30(23)29-21)10-14-4-7-20-15(...(truncated) | 4,099 | {} | 2023-08-25 18:58:05 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_interactions | 2023-08-25 18:58:06 | 2023-08-25 18:58:07 | 1.21 | list | [DrugcentralInteraction(drug=DrugcentralDrug(drugcentral='4', inn='levobupivacaine', cas='27262-47-1', smiles='CCCCN1CCCC[C@H]1C(=O)NC1=C(C)C=CC=C1C', inchikey='LEBVLXFERQHONN-INIZCTEOSA-N', inchi='InChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,...(truncated) | 23,115 | {} | 2023-08-25 18:58:06 | |
| ¶ | pypath.inputs.drugcentral.drugcentral_mapping |
Not calling `pypath.inputs.drugcentral.drugcentral_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2023-08-25 18:58:07 | 2023-08-25 18:58:08 | 0.93 | 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) | 330 | {} | 2023-08-25 18:58:07 | |
| ¶ | pypath.inputs.elm.elm_domains | 2023-08-25 18:58:08 | 2023-08-25 18:58:08 | 0.35 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')], 'LIG_APCC_KENbox_2': [('182', '480'), ('220', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')], 'LIG_BIR_III_3': [('258', '323')], 'LIG_BIR_III_2': [('258', '323')], 'LIG_BIR_III_4': [('258', '323')], 'LIG_BIR_III_1': [('258', '323')]}, '...(truncated) | 604 | {} | 2023-08-25 18:58:08 | |
| ¶ | pypath.inputs.elm.elm_instances | 2023-08-25 18:58:08 | 2023-08-25 18:59:52 | 103.57 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 4,075 | {} | 2023-08-25 18:58:08 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2023-08-25 18:59:52 | 2023-08-25 19:01:04 | 72.41 | 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) | 2,511 | {} | 2023-08-25 18:59:52 | |
| ¶ | pypath.inputs.embopress.embopress_supplementary |
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2023-08-25 19:01:04 | 2023-08-25 19:01:04 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 158, in embrace_annotations
for rec in embrace_translated(organism = organism):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:15:30 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2023-08-25 19:01:04 | 2023-08-25 19:01:04 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 124, in embrace_interactions
for rec in embrace_translated(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:15:30 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2023-08-25 19:01:04 | 2023-08-25 19:01:04 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:15:30 | |||
| ¶ | pypath.inputs.embrace.embrace_translated | 2023-08-25 19:01:04 | 2023-08-25 19:01:05 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 82, in embrace_translated
raw = embrace_raw()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embrace.py", line 37, in embrace_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:15:30 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2023-08-25 19:01:05 | 2023-08-25 19:01:05 | 0.45 | list | [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) | 1,237 | {} | 2023-08-25 19:01:05 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2023-08-25 19:01:05 | 2023-08-25 19:01:06 | 0.58 | 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) | 317 | {} | 2023-08-25 19:01:05 | |
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2023-08-25 19:01:06 | 2023-08-25 19:01:15 | 9.79 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {} | 2023-08-25 19:01:06 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2023-08-25 19:01:15 | 2023-08-25 19:01:15 | 0.03 | list | [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) | 32,085 | {} | 2023-08-25 19:01:15 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2023-08-25 19:01:15 | 2023-08-25 19:02:14 | 58.90 | list | [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) | 290,197 | {} | 2023-08-25 19:01:15 | |
| ¶ | pypath.inputs.expasy.expasy_enzyme_classes | 2023-08-25 19:02:14 | 2023-08-25 19:02:14 | 0.05 | list | [('1', None, None, 'Oxidoreductases'), ('1', '1', None, 'Acting on the CH-OH group of donors'), ('1', '1', '1', 'With NAD(+) or NADP(+) as acceptor'), ('1', '1', '2', 'With a cytochrome as acceptor'), ('1', '1', '3', 'With oxygen as acceptor'), ('1', '1', '4', 'With a disulfide as acceptor'), ('1', ...(truncated) | 353 | {} | 2023-08-25 19:02:14 | |
| ¶ | pypath.inputs.expasy.expasy_enzymes | 2023-08-25 19:02:14 | 2023-08-25 19:02:15 | 0.96 | dict | {'1.1.1.1': {'uniprots': ['P07327', 'P28469', 'Q5RBP7', 'P25405', 'P25406', 'P00327', 'P00326', 'O97959', 'P00328', 'P80222', 'P30350', 'P49645', 'P06525', 'P41747', 'Q17334', 'P43067', 'P85440', 'P14219', 'P48814', 'Q70UN9', 'P23991', 'P86883', 'P19631', 'P23236', 'P48586', 'P09370', 'P22246', 'P07...(truncated) | 8,215 | {} | 2023-08-25 19:02:14 | |
| ¶ | pypath.inputs.genecards.genecards_datasheet |
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_soup |
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.genecards.genecards_summaries |
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_desc |
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.get_go_quick | 2023-08-25 19:02:15 | 2023-08-25 19:05:54 | 218.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 937, in get_go_quick
terms[l[5]][l[1]].add(l[4])
KeyError: 'GO ASPECT'
|
{} | 2023-08-22 19:03:59 | |||
| ¶ | pypath.inputs.go.get_goslim | 2023-08-25 19:05:54 | 2023-08-25 19:05:54 | 0.76 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0001618', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003824', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0...(truncated) | 141 | {} | 2023-08-25 19:05:54 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2023-08-25 19:05:54 | 2023-08-25 19:17:19 | 684.65 | dict | {'C': {'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'...(truncated) | 3 | {} | 2023-08-25 19:05:54 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2023-08-25 19:17:19 | 2023-08-25 19:17:19 | 0.05 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 205, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 19:33:26 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2023-08-25 19:17:19 | 2023-08-25 19:17:23 | 3.96 | dict | {'C': {'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016013': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016011': {('GO:0016010', 'part_of'), ('GO:0098797', 'is_a')}, 'GO:0016014': {('GO:0016010', 'part_of'...(truncated) | 3 | {} | 2023-08-25 19:17:19 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2023-08-25 19:17:23 | 2023-08-25 19:17:28 | 4.87 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005615', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H8': {'GO:0005615', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H9': {'GO:0005615', 'GO:0019814', 'GO:0005886'}, 'A0A075B6I0': {'GO:0005615', 'G...(truncated) | 3 | {} | 2023-08-25 19:17:23 | |
| ¶ | pypath.inputs.go.go_annotations_all | 2023-08-25 19:17:28 | 2023-08-25 19:17:34 | 5.76 | dict | {'A0A024RBG1': {GoAnnotation(db='UniProtKB', db_object_id='A0A024RBG1', db_object_symbol='NUDT4B', qualifier='enables', go_id='GO:0008486', reference='PMID:21873635', evidence_code='IBA', with_or_from='FB:FBgn0036111|MGI:MGI:1930957|MGI:MGI:2147931|PANTHER:PTN000290327|SGD:S000005689|UniProtKB:O9598...(truncated) | 19,630 | {} | 2023-08-25 19:17:28 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2023-08-25 19:17:36 | 2023-08-25 19:17:37 | 1.05 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005615', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H8': {'GO:0005615', 'GO:0019814', 'GO:0005886'}, 'A0A075B6H9': {'GO:0005615', 'GO:0019814', 'GO:0005886'}, 'A0A075B6I0': {'GO:0005615', 'G...(truncated) | 3 | {} | 2023-08-25 19:17:36 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2023-08-25 19:17:37 | 2023-08-25 19:17:37 | 0.04 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 852, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 19:33:43 | |||
| ¶ | pypath.inputs.go.go_annotations_solr | 2023-08-25 19:17:37 | 2023-08-25 19:17:38 | 1.44 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 738, in go_annotations_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:33:43 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2023-08-25 19:17:38 | 2023-08-25 19:17:39 | 0.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 61, in go_annotations_uniprot
for x in [x.split('\t') for x in data.split('\n')]
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-07-28 19:33:44 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2023-08-25 19:17:39 | 2023-08-25 19:17:42 | 3.68 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016009', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016013', 'part_of'), ('GO:0016011', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2023-08-25 19:17:39 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2023-08-25 19:17:42 | 2023-08-25 19:17:42 | 0.03 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 283, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 205, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 19:33:49 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2023-08-25 19:17:42 | 2023-08-25 19:17:46 | 3.94 | dict | {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016009', 'is_a'), ('GO:0016006', 'is_a'), ('GO:0016008', 'is_a')}, 'GO:0016010': {('GO:0016013', 'part_of'), ('GO:0016011', 'part_of'), ('GO:0016014', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0043659': {('GO:0043660', 'is_a')}...(truncated) | 3 | {} | 2023-08-25 19:17:42 | |
| ¶ | pypath.inputs.go.go_descendants_to_ancestors |
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2023-08-25 19:17:46 | 2023-08-25 19:17:49 | 3.10 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2023-08-25 19:17:46 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2023-08-25 19:17:49 | 2023-08-25 19:17:49 | 0.04 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 578, in go_terms_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 19:33:56 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2023-08-25 19:17:49 | 2023-08-25 19:17:52 | 2.98 | dict | {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) | 3 | {} | 2023-08-25 19:17:49 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2023-08-25 19:17:52 | 2023-08-25 19:17:53 | 0.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/go.py", line 436, in go_terms_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:34:00 | |||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2023-08-25 19:17:53 | 2023-08-25 19:17:53 | 0.24 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 424 | {} | 2023-08-25 19:17:53 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2023-08-25 19:17:53 | 2023-08-25 19:17:55 | 1.48 | tuple | ({'_background': {'type': 'xdot', 'default': '<none>', 'min': '', 'notes': 'A string in the xdot format specifying an arbitrary background.'}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'Bounding box of drawing in points. \n write only.'}, 'beautify': {'type': 'bool', 'default': 'fal...(truncated) | 3 | {} | 2023-08-25 19:17:53 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2023-08-25 19:17:55 | 2023-08-25 19:17:57 | 2.05 | tuple | ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=('TNFSF9', 9606), target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=False, pubmed_ids=[]), GuideTo...(truncated) | 2 | {} | 2023-08-25 19:17:55 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.gutmgene.gutmgene_annotations | 2023-08-25 19:17:57 | 2023-08-25 19:17:58 | 1.16 | dict | {'A6NDG6': {GutmgeneAnnotation(microbe_taxon='Lactobacillus acidophilus ATCC 4357', microbe_ncbi_tax_id=None, gut_microbiota_id='gm1148', classification='strain', effect='activation', throughput='low-throughput')}, 'P29459': {GutmgeneAnnotation(microbe_taxon='Faecalibacterium prausnitzii', microbe_n...(truncated) | 122 | {} | 2023-08-25 19:17:57 | |
| ¶ | pypath.inputs.gutmgene.gutmgene_raw | 2023-08-25 19:17:58 | 2023-08-25 19:17:58 | 0.00 | list | [GutmgeneRaw(microbe_taxon='Lactobacillus acidophilus ATCC 4357', microbe_ncbi_tax_id=None, gut_microbiota_id='gm1148', classification='strain', genesymbol='PGP', entrez='283871', effect='activation', throughput='low-throughput'), GutmgeneRaw(microbe_taxon='Akkermansia muciniphila', microbe_ncbi_tax...(truncated) | 278 | {} | 2023-08-25 19:17:58 | |
| ¶ | pypath.inputs.havugimana.get_havugimana | 2023-08-25 19:17:58 | 2023-08-25 19:17:58 | 0.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/havugimana.py", line 39, in get_havugimana
path = cell_input.cell_supplementary(supp_url, article_url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:34:06 | |||
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2023-08-25 19:17:58 | 2023-08-25 19:17:58 | 0.09 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/havugimana.py", line 54, in havugimana_complexes
for rec in get_havugimana():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/havugimana.py", line 39, in get_havugimana
path = cell_input.cell_supplementary(supp_url, article_url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:34:06 | |||
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2023-08-25 19:17:58 | 2023-08-25 19:18:01 | 2.91 | dict | {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='Alpha-2-macroglobulin family')}, 'A8K2U0': {HGNCGeneGroupAnnotation(mainclass='Alpha-2...(truncated) | 15,230 | {} | 2023-08-25 19:17:58 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2023-08-25 19:18:01 | 2023-08-25 19:18:28 | 26.89 | list | [HippieInteraction(id_a='Q86V81', id_b='Q96J01', score=0.79, methods=None, references=('15998806', '17190602', '23222130'), sources=None, organisms=None), HippieInteraction(id_a='P05067', id_b='P17096', score=0.78, methods=None, references=('21244100', '28650319'), sources=None, organisms=None), Hip...(truncated) | 102,224 | {} | 2023-08-25 19:18:01 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2023-08-25 19:18:28 | 2023-08-25 19:18:38 | 9.42 | 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 | {'size': 275237, 'type': {'previous': 'NoneType', 'current': 'list'}} | 2023-08-25 19:18:28 | |
| ¶ | pypath.inputs.homologene.homologene_dict |
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.homologene.homologene_uniprot_dict |
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.hpmr.get_hpmr | 2023-08-25 19:18:38 | 2023-08-25 19:18:38 | 0.04 | dict | {'interactions': [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462...(truncated) | 3 | {} | 2023-08-25 19:18:38 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2023-08-25 19:18:38 | 2023-08-25 19:18:38 | 0.00 | dict | {'P26992': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='CICYTR (Cytokine Type 1 receptors)', subsubclass=None)}, 'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P42...(truncated) | 1,141 | {} | 2023-08-25 19:18:38 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2023-08-25 19:18:38 | 2023-08-25 19:18:38 | 0.00 | dict | {} | 0 | {} | 2023-08-25 19:18:38 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2023-08-25 19:18:38 | 2023-08-25 19:18:38 | 0.00 | list | [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462', 'Ligand', 'P26...(truncated) | 619 | {} | 2023-08-25 19:18:38 | |
| ¶ | pypath.inputs.hpo.hpo_annotations | 2023-08-25 19:18:38 | 2023-08-25 19:18:40 | 2.53 | dict | {'P11245': {HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0000007'), HpoAnnotation(entrez_gene_id='10', entrez_gene_symbol='NAT2', hpo_id='HP:0001939')}, 'P49588': {HpoAnnotation(entrez_gene_id='16', entrez_gene_symbol='AARS1', hpo_id='HP:0003202'), HpoAnnotation(entrez_ge...(truncated) | 4,936 | {} | 2023-08-25 19:18:38 | |
| ¶ | pypath.inputs.hpo.hpo_diseases | 2023-08-25 19:18:40 | 2023-08-25 19:18:53 | 12.58 | dict | {'hpo_id': {HpoDisease(omim='database_id', name='disease_name', pmid=None, qualifier='qualifier', evidence='evidence', onset='onset', frequency='frequency', sex='sex', modifier='modifier', aspect='aspect')}, 'HP:0011097': {HpoDisease(omim='OMIM:607872', name='Chromosome 1p36 deletion syndrome', pmid...(truncated) | 10,716 | {} | 2023-08-25 19:18:40 | |
| ¶ | pypath.inputs.hpo.hpo_ontology | 2023-08-25 19:18:54 | 2023-08-25 19:18:56 | 2.42 | dict | {'terms': {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female...(truncated) | 5 | {} | 2023-08-25 19:18:54 | |
| ¶ | pypath.inputs.hpo.hpo_terms | 2023-08-25 19:18:56 | 2023-08-25 19:18:57 | 0.57 | dict | {'HP:0000001': 'All', 'HP:0000002': 'Abnormality of body height', 'HP:0000003': 'Multicystic kidney dysplasia', 'HP:0000005': 'Mode of inheritance', 'HP:0000006': 'Autosomal dominant inheritance', 'HP:0000007': 'Autosomal recessive inheritance', 'HP:0000008': 'Abnormal morphology of female internal ...(truncated) | 17,490 | {} | 2023-08-25 19:18:56 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2023-08-25 19:18:57 | 2023-08-25 19:19:01 | 4.26 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2023-08-25 19:18:57 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2023-08-25 19:19:01 | 2023-08-25 19:19:02 | 1.53 | list | [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) | 4,671 | {} | 2023-08-25 19:19:01 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2023-08-25 19:19:02 | 2023-08-25 19:19:04 | 1.78 | list | [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) | 4,671 | {} | 2023-08-25 19:19:02 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2023-08-25 19:19:04 | 2023-08-25 19:19:06 | 1.41 | list | [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) | 39,241 | {} | 2023-08-25 19:19:04 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2023-08-25 19:19:06 | 2023-08-25 19:19:09 | 3.04 | list | [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) | 18,630 | {} | 2023-08-25 19:19:06 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2023-08-25 19:19:09 | 2023-08-25 19:19:10 | 1.47 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,371 | {} | 2023-08-25 19:19:09 | |
| ¶ | pypath.inputs.humap.humap2_complexes | 2023-08-25 19:19:10 | 2023-08-25 19:19:12 | 1.30 | dict | {'COMPLEX:O95900_Q9BQS8': Complex: COMPLEX:O95900_Q9BQS8, 'COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9': Complex: COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9, 'COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6ZRY4_Q93062_Q96S66_Q9NZC3_Q9UF11_Q9Y6M7': Complex: COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6Z...(truncated) | 6,944 | {} | 2023-08-25 19:19:10 | |
| ¶ | pypath.inputs.humap.humap_complexes | 2023-08-25 19:19:12 | 2023-08-25 19:19:14 | 1.92 | 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) | 4,467 | {} | 2023-08-25 19:19:12 | |
| ¶ | pypath.inputs.humsavar._parse_desc |
Not calling `pypath.inputs.humsavar._parse_desc`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.humsavar.uniprot_variants | 2023-08-25 19:19:14 | 2023-08-25 19:19:18 | 4.39 | dict | {'P04217': {UniprotVariant(genesymbol='A1BG', ftid='VAR_018370', aa_change='p.His395Arg', variant_category='LB/B', dbsnp='rs2241788', disease=None, disease_symbol=None, disease_omim=None), UniprotVariant(genesymbol='A1BG', ftid='VAR_018369', aa_change='p.His52Arg', variant_category='LB/B', dbsnp='rs...(truncated) | 13,047 | {} | 2023-08-25 19:19:14 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2023-08-25 19:19:18 | 2023-08-25 19:19:19 | 1.39 | list | [HuriInteraction(uniprot_a='Q8IY31', uniprot_b='Q9BQD3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='P49902', uniprot_b='P49902', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9BVJ6', uniprot_b='Q8NHQ1', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 5,630 | {} | 2023-08-25 19:19:18 | |
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2023-08-25 19:19:19 | 2023-08-25 19:19:24 | 4.36 | list | [HuriInteraction(uniprot_a='Q9H2A7', uniprot_b='Q6UY14', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q5SY16', uniprot_b='Q09666', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='Q8TAB5', uniprot_b='Q96F24', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 46,706 | {} | 2023-08-25 19:19:19 | |
| ¶ | pypath.inputs.huri.hi_iii_old | 2023-08-25 19:19:24 | 2023-08-25 19:19:24 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/huri.py", line 90, in hi_iii_old
url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
|
{} | 2023-07-28 19:35:50 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2023-08-25 19:19:24 | 2023-08-25 19:19:42 | 17.89 | list | [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) | 229,646 | {} | 2023-08-25 19:19:24 | |
| ¶ | pypath.inputs.huri.huri_interactions | 2023-08-25 19:19:42 | 2023-08-25 19:19:54 | 12.78 | list | [HuriInteraction(uniprot_a='Q68D86', uniprot_b='Q9HD26', isoform_a=1, isoform_b=2, score=0.83445807946), HuriInteraction(uniprot_a='Q13515', uniprot_b='Q9UJW9', isoform_a=1, isoform_b=1, score=0.902943684288), HuriInteraction(uniprot_a='P30049', uniprot_b='Q05519', isoform_a=1, isoform_b=2, score=0....(truncated) | 166,597 | {} | 2023-08-25 19:19:42 | |
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2023-08-25 19:19:54 | 2023-08-25 19:19:55 | 0.90 | list | [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) | 11,045 | {} | 2023-08-25 19:19:54 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2023-08-25 19:19:55 | 2023-08-25 19:19:57 | 1.39 | list | [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) | 48,796 | {} | 2023-08-25 19:19:55 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2023-08-25 19:19:57 | 2023-08-25 19:20:15 | 17.95 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 873, in test_input
size = i + 1
UnboundLocalError: local variable 'i' referenced before assignment
|
{} | 2023-07-28 19:36:46 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2023-08-25 19:20:15 | 2023-08-25 19:20:15 | 0.12 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/huri.py", line 38, in rolland_hi_ii_14
xlsname = cell.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 19:37:15 | |||
| ¶ | pypath.inputs.huri.vidal_hi_iii_old |
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.yang2016_interactions | 2023-08-25 19:20:15 | 2023-08-25 19:20:16 | 0.98 | 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) | 2,811 | {} | 2023-08-25 19:20:15 | |
| ¶ | pypath.inputs.huri.yu2011_interactions | 2023-08-25 19:20:16 | 2023-08-25 19:20:18 | 2.41 | list | [HuriInteraction(uniprot_a='Q5VUM1', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P62166', uniprot_b='Q86UW9', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9NV12', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteractio...(truncated) | 7,326 | {} | 2023-08-25 19:20:16 | |
| ¶ | pypath.inputs.i3d.get_i3d | 2023-08-25 19:20:18 | 2023-08-25 19:20:26 | 7.73 | list | [{'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P02647': {'pfam': None, 'chain': 'A', 'seq': [[68, 265]]}, 'uniprots': ['A0A024RAV5', 'P02647'], 'source': 'I3D', 'pdb': ['2mse'], 'references': []}, {'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P10398': {'pfam': N...(truncated) | 15,984 | {} | 2023-08-25 19:20:18 | |
| ¶ | pypath.inputs.icellnet._icellnet_get_components |
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_entity |
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_references |
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet._icellnet_get_resources |
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.icellnet.icellnet_annotations | 2023-08-25 19:20:26 | 2023-08-25 19:20:26 | 0.26 | dict | {'Q13443': {IcellnetAnnotation(role='ligand', family='ECM', subfamily=None, classification=('Ecm',))}, Complex: COMPLEX:P05556_P56199: {IcellnetAnnotation(role='receptor', family='ECM', subfamily=None, classification=('Ecm',)), IcellnetAnnotation(role='receptor', family='ECM', subfamily=None, classi...(truncated) | 853 | {} | 2023-08-25 19:20:26 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2023-08-25 19:20:26 | 2023-08-25 19:20:26 | 0.03 | dict | {'COMPLEX:P05556_P56199': Complex: COMPLEX:P05556_P56199, 'COMPLEX:P05556_P26006': Complex: COMPLEX:P05556_P26006, 'COMPLEX:P05556_P23229': Complex: COMPLEX:P05556_P23229, 'COMPLEX:P05556_P06756': Complex: COMPLEX:P05556_P06756, 'COMPLEX:P06756_P18084': Complex: COMPLEX:P06756_P18084, 'COMPLEX:Q0477...(truncated) | 131 | {} | 2023-08-25 19:20:26 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2023-08-25 19:20:26 | 2023-08-25 19:20:26 | 0.03 | list | [IcellnetRecord(ligand='Q13443', receptor=Complex: COMPLEX:P05556_P56199, family='ECM', subfamily=None, classification=['Ecm'], resources=None, references=['15361064']), IcellnetRecord(ligand='Q13443', receptor=Complex: COMPLEX:P05556_P26006, family='ECM', subfamily=None, classification=['Ecm'], res...(truncated) | 1,023 | {} | 2023-08-25 19:20:26 | |
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2023-08-25 19:20:26 | 2023-08-25 19:20:27 | 0.97 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/imweb.py", line 72, in _get_imweb
hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-07-28 19:37:29 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2023-08-25 19:20:27 | 2023-08-25 19:20:27 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/imweb.py", line 105, in get_imweb
c0.perform()
pycurl.error: (3, '')
|
{} | 2023-07-28 19:37:31 | |||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2023-08-25 19:20:27 | 2023-08-25 19:20:28 | 0.47 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/imweb.py", line 138, in get_imweb_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.10/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.10/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2023-07-28 19:37:31 | |||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2023-08-25 19:20:28 | 2023-08-25 19:20:30 | 1.81 | list | [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) | 19,036 | {} | 2023-08-25 19:20:28 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2023-08-25 19:20:30 | 2023-08-25 19:20:31 | 1.44 | NoneType | None | 0 | {} | 2023-08-25 19:20:30 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2023-08-25 19:20:31 | 2023-08-25 19:20:32 | 0.41 | NoneType | None | 0 | {} | 2023-08-25 19:20:31 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2023-08-25 19:20:32 | 2023-08-25 19:21:32 | 60.17 | list | [IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, interaction_types={'direct interaction'}, mi_score=0.77, isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', i...(truncated) | 71,496 | {} | 2023-08-25 19:20:32 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2023-08-25 19:21:32 | 2023-08-25 19:21:33 | 0.79 | set | {'P20702', 'P18564', 'Q13349', 'P23229', 'P56199', 'P05556', 'O75578', 'P18084', 'P26006', 'P26010', 'P05106', 'Q9UKX5', 'P08514', 'P08648', 'Q13683', 'P53708', 'P38570', 'P06756', 'P05107', 'P26012', 'Q13797', 'P20701', 'P11215', 'P17301', 'P16144'} | 25 | {} | 2023-08-25 19:21:32 | |
| ¶ | pypath.inputs.interpro.interpro2go_annotations | 2023-08-25 19:21:33 | 2023-08-25 19:21:34 | 1.69 | defaultdict | defaultdict(<class 'set'>, {'IPR000003': {Interpro2GOAnnotation(go_term_id='GO:0005634', go_term_name='nucleus'), Interpro2GOAnnotation(go_term_id='GO:0006355', go_term_name='regulation of DNA-templated transcription'), Interpro2GOAnnotation(go_term_id='GO:0003707', go_term_name='nuclear steroid rec...(truncated) | 14,721 | {} | 2023-08-25 19:21:33 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2023-08-25 19:21:34 | 2023-08-25 19:22:09 | 34.65 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_id='IPR000001', organism='9606', start=302, end=385), InterproAnnotation(interpro_id='IPR013806', organism='9606', start=381, end=477), InterproAnnotation(interpro_id='IPR038178', organism='9606', start=387, end=479), InterproAnnotat...(truncated) | 16,318 | {} | 2023-08-25 19:21:34 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2023-08-25 19:22:09 | 2023-08-25 19:22:30 | 20.56 | list | [InterproEntry(interpro_id='IPR000001', protein_count='18814', name='Kringle', type='Domain', publications=['PUB00000803', 'PUB00001541', 'PUB00001620', 'PUB00002414', 'PUB00003257', 'PUB00003400'], parent_list='', child_list='', member_list={'PFAM': ['PF00051'], 'PROFILE': ['PS50070'], 'SMART': ['S...(truncated) | 39,227 | {} | 2023-08-25 19:22:09 | |
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2023-08-25 19:22:30 | 2023-08-25 19:22:30 | 0.50 | dict | {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) | 483 | {} | 2023-08-25 19:22:30 | |
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2023-08-25 19:22:30 | 2023-08-25 19:22:31 | 0.43 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/ipi.py", line 40, in ipi_uniprot
for row in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 19:51:37 | |||
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2023-08-25 19:22:31 | 2023-08-25 19:30:03 | 452.34 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/iptmnet.py", line 93, in iptmnet_interactions
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-08-10 19:15:18 | |||
| ¶ | pypath.inputs.italk.italk_annotations | 2023-08-25 19:30:03 | 2023-08-25 19:30:06 | 3.11 | dict | {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='other'), ItalkAnnotation(mainclass='receptor', subclass='growth factor')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) | 1,414 | {} | 2023-08-25 19:30:03 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2023-08-25 19:30:06 | 2023-08-25 19:30:06 | 0.02 | list | [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) | 2,706 | {} | 2023-08-25 19:30:06 | |
| ¶ | pypath.inputs.italk.italk_raw | 2023-08-25 19:30:06 | 2023-08-25 19:30:06 | 0.01 | DataFrame | Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) | 2,649 | {} | 2023-08-25 19:30:06 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2023-08-25 19:30:06 | 2023-08-25 19:30:09 | 2.95 | list | [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) | 35,252 | {} | 2023-08-25 19:30:06 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2023-08-25 19:30:09 | 2023-08-25 19:30:10 | 0.18 | list | [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) | 35,252 | {} | 2023-08-25 19:30:09 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2023-08-25 19:30:10 | 2023-08-25 19:34:30 | 260.86 | 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) | 14,576 | {} | 2023-08-25 19:30:10 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2023-08-25 19:34:30 | 2023-08-25 19:34:49 | 18.31 | set | {KeggMedicusRawInteraction(id_a='2525v1', id_b='G01439', name_a='(FUT3*Le) FUT3 Le allele', name_b='III3,IV2Fuca,IV3Gala-nLc4-Cer', effect='stimulation', itype='post_translational', pw_type='reference', type_a='variant', type_b='metabolite', network_id='N01669'), KeggMedicusRawInteraction(id_a='571...(truncated) | 12,808 | {'size': -5} | 2023-08-25 19:34:30 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2023-08-25 19:34:49 | 2023-08-25 19:34:49 | 0.47 | dict | {'COMPLEX:O14521_P21912_P31040_Q99643': Complex: COMPLEX:O14521_P21912_P31040_Q99643, 'COMPLEX:P49768_Q8WW43_Q92542_Q9NZ42': Complex: COMPLEX:P49768_Q8WW43_Q92542_Q9NZ42, 'COMPLEX:P08047_Q13105': Complex: COMPLEX:P08047_Q13105, 'COMPLEX:P59046_Q9ULZ3': Complex: COMPLEX:P59046_Q9ULZ3, 'COMPLEX:P57679...(truncated) | 524 | {'size': 1} | 2023-08-25 19:34:49 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2023-08-25 19:34:49 | 2023-08-25 19:34:50 | 0.73 | list | [KeggMedicusInteraction(id_a='Q8IU85', id_b='Q02930', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='P06400', id_b='Q14209', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) | 9,478 | {'size': 1} | 2023-08-25 19:34:49 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2023-08-25 19:34:50 | 2023-08-25 19:34:55 | 4.69 | dict | {'Q9BQ95': {KeggPathway(pathway='MAPK signaling pathway')}, 'Q16584': {KeggPathway(pathway='MAPK signaling pathway'), KeggPathway(pathway='Non-alcoholic fatty liver disease')}, 'P51452': {KeggPathway(pathway='MAPK signaling pathway')}, 'Q15750': {KeggPathway(pathway='Toll-like receptor signaling pat...(truncated) | 2,587 | {} | 2023-08-25 19:34:50 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2023-08-25 19:34:55 | 2023-08-25 19:34:55 | 0.45 | dict | {'A8K7J7': {KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Fructose and mannose metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPat...(truncated) | 813 | {} | 2023-08-25 19:34:55 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2023-08-25 19:34:55 | 2023-08-25 19:35:00 | 4.68 | tuple | ({'MAPK signaling pathway': {'Q9BQ95', 'Q16584', 'P51452', 'Q15750', 'P0DPQ6', 'P01583', 'Q12988', 'P10398', 'Q8IW41', 'Q9HC77', 'P32248', 'Q7RTX0', 'P15336', 'Q9Y3M2', 'P25445', 'P17980', 'P04792', 'Q15283', 'Q92918', 'Q9NYB0', 'Q9Y4G8', 'O95644', 'P31152', 'O75676', 'O95997', 'P51617', 'P29323', '...(truncated) | 2 | {} | 2023-08-25 19:34:55 | |
| ¶ | pypath.inputs.kegg_api. |
Not calling `pypath.inputs.kegg_api.`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._generate_conv_functions | 2023-08-25 19:35:00 | 2023-08-25 19:35:00 | 0.00 | NoneType | None | 0 | {} | 2023-08-25 19:35:00 | |
| ¶ | pypath.inputs.kegg_api._generate_relation_functions | 2023-08-25 19:35:00 | 2023-08-25 19:35:00 | 0.00 | NoneType | None | 0 | {} | 2023-08-25 19:35:00 | |
| ¶ | pypath.inputs.kegg_api._kegg_conv |
Not calling `pypath.inputs.kegg_api._kegg_conv`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi |
Not calling `pypath.inputs.kegg_api._kegg_ddi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_async |
Not calling `pypath.inputs.kegg_api._kegg_ddi_async`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_ddi_sync |
Not calling `pypath.inputs.kegg_api._kegg_ddi_sync`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general |
Not calling `pypath.inputs.kegg_api._kegg_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_general_async |
Not calling `pypath.inputs.kegg_api._kegg_general_async`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_link |
Not calling `pypath.inputs.kegg_api._kegg_link`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_list |
Not calling `pypath.inputs.kegg_api._kegg_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api._kegg_relations |
Not calling `pypath.inputs.kegg_api._kegg_relations`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_drug |
Not calling `pypath.inputs.kegg_api.disease_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_gene |
Not calling `pypath.inputs.kegg_api.disease_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.disease_to_pathway |
Not calling `pypath.inputs.kegg_api.disease_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_disease |
Not calling `pypath.inputs.kegg_api.drug_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_drug | 2023-08-25 19:35:00 | 2023-08-25 19:35:03 | 2.82 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/kegg_api.py", line 127, in drug_to_drug
entry_dbs = {'drug': _Drug(), 'compound': _Compound()}
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/kegg_api.py", line 445, in __init__
self.load(*args)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/kegg_api.py", line 464, in load
self._data = {
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/kegg_api.py", line 465, in <dictcomp>
self.proc_key(entry[0]): self.proc_value(entry[1])
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/kegg_api.py", line 562, in proc_key
return entry[0].split(':')[1]
IndexError: list index out of range
|
{} | 2023-07-28 20:04:04 | |||
| ¶ | pypath.inputs.kegg_api.drug_to_gene |
Not calling `pypath.inputs.kegg_api.drug_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.drug_to_pathway |
Not calling `pypath.inputs.kegg_api.drug_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_disease |
Not calling `pypath.inputs.kegg_api.gene_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_drug |
Not calling `pypath.inputs.kegg_api.gene_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.gene_to_pathway |
Not calling `pypath.inputs.kegg_api.gene_to_pathway`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_drug_to_chebi |
Not calling `pypath.inputs.kegg_api.kegg_drug_to_chebi`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.kegg_gene_to_uniprot |
Not calling `pypath.inputs.kegg_api.kegg_gene_to_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_disease |
Not calling `pypath.inputs.kegg_api.pathway_to_disease`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_drug |
Not calling `pypath.inputs.kegg_api.pathway_to_drug`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg_api.pathway_to_gene |
Not calling `pypath.inputs.kegg_api.pathway_to_gene`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2023-08-25 19:35:03 | 2023-08-25 19:35:03 | 0.35 | dict | {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) | 504 | {} | 2023-08-25 19:35:03 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2023-08-25 19:35:03 | 2023-08-25 19:35:07 | 3.64 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {} | 2023-08-25 19:35:03 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2023-08-25 19:35:07 | 2023-08-25 19:35:07 | 0.21 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/lambert2018.py", line 99, in lambert2018_annotations
for r in lambert2018_s1_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/lambert2018.py", line 39, in lambert2018_s1_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 20:04:11 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2023-08-25 19:35:07 | 2023-08-25 19:35:07 | 0.07 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/lambert2018.py", line 39, in lambert2018_s1_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 20:04:11 | |||
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2023-08-25 19:35:07 | 2023-08-25 19:35:07 | 0.37 | list | [LaudannaDirection(source_genesymbol='F2R', target_genesymbol='PAWR'), LaudannaDirection(source_genesymbol='PPP1R13B', target_genesymbol='PIK3CB'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CASP9'), LaudannaDirection(source_genesymbol='ATP8A2', target_genesymbol='CAMP'), Lauda...(truncated) | 77,555 | {} | 2023-08-25 19:35:07 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2023-08-25 19:35:07 | 2023-08-25 19:35:08 | 0.77 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2023-08-25 19:35:07 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2023-08-25 19:35:08 | 2023-08-25 19:35:16 | 7.94 | list | [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) | 583 | {} | 2023-08-25 19:35:08 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2023-08-25 19:35:16 | 2023-08-25 19:35:16 | 0.35 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/li2012.py", line 128, in li2012_dmi
se = seq.swissprot_seq(isoforms = True)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/seq.py", line 50, in swissprot_seq
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-07-28 20:04:20 | |||
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2023-08-25 19:35:16 | 2023-08-25 19:35:17 | 0.03 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2023-08-25 19:35:16 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2023-08-25 19:35:17 | 2023-08-25 19:35:17 | 0.03 | list | [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) | 503 | {} | 2023-08-25 19:35:17 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2023-08-25 19:35:17 | 2023-08-25 19:35:21 | 4.25 | dict | {'10001': LincsCompound(lincs='LSM-1001', chembl='CHEMBL14762', chebi='CHEBI:354.22', inchi='InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1', inchi_key='BTIHMVBBUGXLCJ-OAHLLOKOSA-N', smil...(truncated) | 1,320 | {} | 2023-08-25 19:35:17 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2023-08-25 19:35:21 | 2023-08-25 19:35:21 | 0.63 | list | [] | 0 | {} | 2023-08-25 19:35:21 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2023-08-25 19:35:21 | 2023-08-25 19:35:22 | 0.67 | list | [] | 0 | {} | 2023-08-25 19:35:21 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2023-08-25 19:35:22 | 2023-08-25 19:35:22 | 0.38 | list | [] | 0 | {} | 2023-08-25 19:35:22 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2023-08-25 19:35:22 | 2023-08-25 19:35:23 | 0.20 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism='human', pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism='human', pmid='22244333')...(truncated) | 478 | {} | 2023-08-25 19:35:22 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2023-08-25 19:35:23 | 2023-08-25 19:35:23 | 0.66 | list | [] | 0 | {} | 2023-08-25 19:35:23 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2023-08-25 19:35:23 | 2023-08-25 19:36:04 | 40.81 | dict | {'P27824': {LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=None, score=None), LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='type...(truncated) | 9,493 | {} | 2023-08-25 19:35:23 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2023-08-25 19:36:04 | 2023-08-25 19:36:05 | 0.38 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5',), references=('21054788',)), LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', '...(truncated) | 1,536 | {} | 2023-08-25 19:36:04 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2023-08-25 19:36:05 | 2023-08-25 19:36:05 | 0.03 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {} | 2023-08-25 19:36:05 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2023-08-25 19:36:05 | 2023-08-25 19:36:05 | 0.28 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2023-08-25 19:36:05 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2023-08-25 19:36:05 | 2023-08-25 19:36:06 | 0.99 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/matrisome.py", line 86, in __matrisome_annotations_2
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-07-28 20:05:08 | |||
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2023-08-25 19:36:06 | 2023-08-25 19:36:06 | 0.30 | dict | {'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 1,067 | {} | 2023-08-25 19:36:06 | |
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2023-08-25 19:36:06 | 2023-08-25 19:36:09 | 3.12 | dict | {'P51160': {MatrixdbAnnotation(mainclass='membrane')}, 'P59190': {MatrixdbAnnotation(mainclass='membrane')}, 'Q16281': {MatrixdbAnnotation(mainclass='membrane')}, 'Q01959': {MatrixdbAnnotation(mainclass='membrane')}, 'Q96LZ7': {MatrixdbAnnotation(mainclass='membrane')}, 'Q96RP7': {MatrixdbAnnotation...(truncated) | 10,092 | {} | 2023-08-25 19:36:06 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2023-08-25 19:36:09 | 2023-08-25 19:36:09 | 0.01 | set | {'P35247', 'Q96FE5', 'Q8N2E2', 'P39060', 'Q6UXH1', 'P09544', 'O75900', 'Q6PJE2', 'P12110', 'P49747', 'Q01955', 'Q14031', 'Q9UKP4', 'O75445', 'Q9NR99', 'Q9UBX5', 'Q6UXK5', 'P51884', 'Q13201', 'Q9H4F8', 'P56705', 'Q9NZV1', 'Q6WRI0', 'O15230', 'P12644', 'Q8IUX8', 'P02452', 'Q6UXA7', 'Q9UP79', 'O14594',...(truncated) | 483 | {} | 2023-08-25 19:36:09 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2023-08-25 19:36:09 | 2023-08-25 19:36:09 | 0.12 | list | [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) | 425 | {} | 2023-08-25 19:36:09 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2023-08-25 19:36:09 | 2023-08-25 19:36:11 | 1.92 | set | {'P51160', 'P59190', 'Q16281', 'Q01959', 'Q96LZ7', 'Q96RP7', 'Q8NGP9', 'Q9HDB9', 'Q8WZ94', 'Q8N442', 'Q9BUJ0', 'O95672', 'Q96A70', 'Q9Y2C2', 'A6NDH6', 'Q9UNE2', 'Q9NZV8', 'Q9H0D6', 'Q8NGL0', 'P34995', 'Q4G0N8', 'O00499', 'Q9GZT6', 'P40238', 'Q4KMZ8', 'Q96B49', 'P07919', 'P62491', 'Q9NQX7', 'Q8NGK1',...(truncated) | 8,237 | {} | 2023-08-25 19:36:09 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2023-08-25 19:36:11 | 2023-08-25 19:36:12 | 0.32 | set | {'Q9BWW9', 'P0DOX7', 'Q96FE5', 'Q6H9L7', 'Q8N2E2', 'Q9NS98', 'P47929', 'P55145', 'P78380', 'Q8TD46', 'P15018', 'P49747', 'P57764', 'Q01955', 'Q14031', 'P60484', 'Q9UI42', 'P13236', 'Q6WN34', 'P06310', 'Q8TDJ6', 'Q8NEV9', 'P56705', 'Q9NZV1', 'P20648', 'Q14CN2', 'Q6WRI0', 'P36915', 'Q9BQS7', 'O75629',...(truncated) | 2,921 | {} | 2023-08-25 19:36:11 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2023-08-25 19:36:12 | 2023-08-25 19:36:13 | 1.23 | set | {'Q6MZM7', 'Q9NPY3', 'P16671', 'Q9Y624', 'Q49MI3', 'Q08174', 'P01732', 'Q05084', 'Q9BX67', 'P50895', 'P18827', 'Q86UP0', 'Q8TEW0', 'Q13477', 'P42081', 'Q9UQS6', 'Q86WK6', 'P53708', 'P35443', 'P11215', 'Q96GP6', 'Q12860', 'Q9Y4C0', 'O60759', 'Q86SJ6', 'Q6UWL6', 'Q99418', 'P08F94', 'O94856', 'O95471',...(truncated) | 103 | {} | 2023-08-25 19:36:12 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2023-08-25 19:36:13 | 2023-08-25 19:36:35 | 22.09 | list | [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) | 2,384 | {} | 2023-08-25 19:36:13 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2023-08-25 19:36:35 | 2023-08-25 19:36:35 | 0.14 | dict | {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) | 4 | {} | 2023-08-25 19:36:35 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2023-08-25 19:36:35 | 2023-08-25 19:36:37 | 2.04 | list | [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) | 17,030 | {} | 2023-08-25 19:36:35 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2023-08-25 19:36:37 | 2023-08-25 19:36:38 | 0.56 | list | [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) | 17,030 | {} | 2023-08-25 19:36:37 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2023-08-25 19:36:38 | 2023-08-25 19:36:38 | 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 | {} | 2023-08-25 19:36:38 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2023-08-25 19:36:38 | 2023-08-25 19:36:38 | 0.17 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2023-08-25 19:36:38 | 2023-08-25 19:36:38 | 0.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2023-08-25 19:36:38 | 2023-08-25 19:36:39 | 0.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 76, in mirbase_mature
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2023-08-25 19:36:39 | 2023-08-25 19:36:39 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 167, in mirbase_mature_all
return [i[0] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 167, in <listcomp>
return [i[0] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:52 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2023-08-25 19:36:39 | 2023-08-25 19:36:39 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 89, in mirbase_precursor
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:53 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2023-08-25 19:36:39 | 2023-08-25 19:36:39 | 0.14 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 172, in mirbase_precursor_all
return [i[1] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 172, in <listcomp>
return [i[1] for i in mirbase_ids(organism = organism)]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:53 | |||
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2023-08-25 19:36:39 | 2023-08-25 19:36:39 | 0.16 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 108, in mirbase_precursor_to_mature
for mmat, mpre in ids:
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 140, in mirbase_ids
mat, mir = get_mirbase_aliases(organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirbase.py", line 56, in get_mirbase_aliases
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:05:53 | |||
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2023-08-25 19:36:39 | 2023-08-25 19:36:39 | 0.20 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2023-08-25 19:36:39 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2023-08-25 19:36:39 | 2023-08-25 19:36:40 | 0.43 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism='Homo sapiens', target_organism='Homo sapiens', pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organ...(truncated) | 3,106 | {} | 2023-08-25 19:36:39 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2023-08-25 19:36:40 | 2023-08-25 19:36:45 | 5.45 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirtarbase.py", line 39, in mirtarbase_interactions
result.extend(_mirtarbase_interactions('curated'))
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/mirtarbase.py", line 74, in _mirtarbase_interactions
tbl = inputs_common.read_xls(c.fileobj.name)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-07-28 20:05:54 | |||
| ¶ | pypath.inputs.mitab.mitab_field_list |
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mitab.mitab_field_uniprot |
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mppi.mppi_interactions | 2023-08-25 19:36:45 | 2023-08-25 19:36:46 | 0.53 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {} | 2023-08-25 19:36:45 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2023-08-25 19:36:46 | 2023-08-25 19:37:39 | 52.78 | dict | {'O14625': {MsigdbAnnotation(collection='immunesigdb', geneset='GSE22140_GERMFREE_VS_SPF_ARTHRITIC_MOUSE_CD4_TCELL_UP'), MsigdbAnnotation(collection='chemical_and_genetic_perturbations', geneset='DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP'), MsigdbAnnotation(collection='cancer_modules', geneset='MOD...(truncated) | 20,099 | {} | 2023-08-25 19:36:46 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2023-08-25 19:37:40 | 2023-08-25 19:37:50 | 9.33 | dict | {'chr1p11': {'PPIAL4A', 'NBPF26', 'FAM72B', 'NOTCH2NLR', 'SRGAP2C', 'H2BP1', 'LINC01691', 'RNVU1-19', 'PDE4DIPP2', 'PDE4DIPP4', 'RPL22P6', 'H3P4', 'MTIF2P1', 'LINC00623', 'NBPF8', 'EMBP1', 'SRGAP2-AS1', 'PFN1P2', 'FCGR1BP', 'RNVU1-4', 'LINC02798'}, 'chr1p12': {'ENSG00000226172', 'LINC00622', 'U1', '...(truncated) | 33,591 | {} | 2023-08-25 19:37:40 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2023-08-25 19:37:50 | 2023-08-25 19:37:51 | 0.41 | dict | {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'EFNA1', 'LITAF', 'TNFAIP3', 'RIPK2', 'IL15RA', 'LDLR', 'HES1', 'SOCS3', 'SERPINB2', 'CXCL1', 'CXCL3', 'EGR2', 'DUSP1', 'IL6', 'PMEPA1', 'TGIF1', 'RELB', 'CXCL11', 'DUSP5', 'TSC22D1', 'SLC16A6', 'CXCL2', 'PLAU', 'TNFAIP6', 'SERPINB8', 'EH...(truncated) | 18 | {} | 2023-08-25 19:37:50 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2023-08-25 19:37:51 | 2023-08-25 19:37:51 | 0.35 | list | [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) | 7,305 | {} | 2023-08-25 19:37:51 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2023-08-25 19:37:51 | 2023-08-25 19:38:21 | 30.01 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/negatome.py", line 49, in negatome_interactions
for l in f:
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 20:07:16 | |||
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2023-08-25 19:38:21 | 2023-08-25 19:38:21 | 0.13 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2023-08-25 19:38:21 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2023-08-25 19:38:21 | 2023-08-25 19:38:22 | 0.12 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {} | 2023-08-25 19:38:21 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2023-08-25 19:38:22 | 2023-08-25 19:38:24 | 2.42 | list | [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) | 7,555 | {} | 2023-08-25 19:38:22 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2023-08-25 19:38:24 | 2023-08-25 19:38:24 | 0.01 | dict | {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) | 35 | {} | 2023-08-25 19:38:24 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2023-08-25 19:38:24 | 2023-08-25 19:38:39 | 14.73 | dict | {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Interleukin-9 (IL-...(truncated) | 1,870 | {} | 2023-08-25 19:38:24 | |
| ¶ | pypath.inputs.offsides._sides_base |
Not calling `pypath.inputs.offsides._sides_base`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.offsides.offsides_side_effects | 2023-08-25 19:38:39 | 2023-08-25 19:38:58 | 19.05 | list | [OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002034', prr='1299', prr_error='2.85714', mean_reporting_frequency='0.45382'), OffsideSideEffect(drug_rxnorn='4024', drug='ergoloid mesylates', condition_meddra='USP', condition='10002965', prr='13...(truncated) | 3,206,558 | {} | 2023-08-25 19:38:39 | |
| ¶ | pypath.inputs.oma.oma_orthologs |
Not calling `pypath.inputs.oma.oma_orthologs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ontology.listof_ontologies | 2023-08-25 19:38:58 | 2023-08-25 19:38:58 | 0.66 | dict | {'sbo': 'Systems Biology Ontology', 'rs': 'Rat Strain Ontology', 'tgma': 'Mosquito gross anatomy ontology', 'uberon': 'Uber-anatomy ontology', 'tto': 'Teleost taxonomy ontology', 'txpo': 'TOXic Process Ontology (TXPO)', 'spd': 'Spider Ontology', 'taxrank': 'Taxonomic rank vocabulary', 'xao': 'Xenopu...(truncated) | 280 | {} | 2023-08-25 19:38:58 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets._opentargets_general |
Not calling `pypath.inputs.opentargets._opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_adverse_reactions | 2023-08-25 19:38:58 | 2023-08-25 19:39:25 | 26.58 | list | [{'chembl_id': 'CHEMBL1200632', 'event': 'acute generalised exanthematous pustulosis', 'count': 17, 'llr': 34.164839700408265, 'critval': 13.880781728509543, 'meddraCode': '10048799'}, {'chembl_id': 'CHEMBL1200632', 'event': 'anal ulcer', 'count': 5, 'llr': 16.745304158079307, 'critval': 13.88078172...(truncated) | 112,928 | {} | 2023-08-25 19:38:58 | |
| ¶ | pypath.inputs.opentargets.opentargets_baseline_expression | 2023-08-25 19:39:25 | 2023-08-25 19:48:49 | 564.27 | list | [{'id': 'ENSG00000020219', 'tissues': [{'efo_code': 'UBERON_0012249', 'label': 'ectocervix', 'organs': ['reproductive organ', 'reproductive structure'], 'anatomical_systems': ['reproductive system'], 'rna': {'value': 2.0, 'zscore': -1, 'level': -1, 'unit': 'TPM'}, 'protein': {'reliability': False, '...(truncated) | 43,791 | {} | 2023-08-25 19:39:25 | |
| ¶ | pypath.inputs.opentargets.opentargets_direct_score | 2023-08-25 19:48:49 | 2023-08-25 19:50:46 | 116.61 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006128', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000006210', 'score': 0.0022174791281082103, 'evidenceCount': 1}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000007952', 'score': 0...(truncated) | 2,146,271 | {} | 2023-08-25 19:48:49 | |
| ¶ | pypath.inputs.opentargets.opentargets_general |
Not calling `pypath.inputs.opentargets.opentargets_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opentargets.opentargets_indirect_score | 2023-08-25 19:50:46 | 2023-08-25 19:56:20 | 334.39 | list | [{'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001617', 'score': 0.05099149718673741, 'evidenceCount': 4}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000001626', 'score': 0.00792543466157194, 'evidenceCount': 3}, {'diseaseId': 'DOID_0050890', 'targetId': 'ENSG00000002330', 'score': 0.003...(truncated) | 6,960,486 | {} | 2023-08-25 19:50:46 | |
| ¶ | pypath.inputs.opm.opm_annotations | 2023-08-25 19:56:20 | 2023-08-25 19:56:41 | 20.99 | dict | {'O00168': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P26678': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Calcium ATPase regulators', tran...(truncated) | 87 | {} | 2023-08-25 19:56:20 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2023-08-25 19:56:41 | 2023-08-25 19:57:11 | 30.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/oreganno.py", line 72, in oreganno_interactions
for l in oreganno_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-07-28 20:26:47 | |||
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2023-08-25 19:57:11 | 2023-08-25 19:57:41 | 30.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/oreganno.py", line 39, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{} | 2023-07-28 20:27:17 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2023-08-25 19:57:41 | 2023-08-25 19:58:54 | 72.90 | defaultdict | defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=True, cell_type='Acinar cells', organ='Pancreas', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=1.0, mouse_sensitivity=0.957143, human_specificity=0.000628931, mouse_specificit...(truncated) | 4,792 | {} | 2023-08-25 19:57:41 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2023-08-25 19:58:54 | 2023-08-25 19:58:54 | 0.04 | list | [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) | 8,286 | {} | 2023-08-25 19:58:54 | |
| ¶ | pypath.inputs.pathophenodb.disease_pathogen_interactions | 2023-08-25 19:58:54 | 2023-08-25 19:58:54 | 0.00 | list | [] | 0 | {} | 2023-08-25 19:58:54 | |
| ¶ | pypath.inputs.pathwaycommons._create_single_resource_method |
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons.pathwaycommons_interactions | 2023-08-25 19:58:54 | 2023-08-25 19:59:11 | 16.38 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ABCC6', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ANXA7', resource='BioGRID'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='C...(truncated) | 1,261,865 | {} | 2023-08-25 19:58:54 | |
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pathwaycommons._pc_single_resource |
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pazar.pazar_interactions | 2023-08-25 19:59:12 | 2023-08-25 19:59:12 | 0.27 | list | [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) | 16,386 | {} | 2023-08-25 19:59:12 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2023-08-25 19:59:12 | 2023-08-25 19:59:22 | 10.36 | tuple | ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) | 2 | {} | 2023-08-25 19:59:12 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2023-08-25 19:59:25 | 2023-08-25 19:59:34 | 8.36 | 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) | 43,467 | {} | 2023-08-25 19:59:25 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2023-08-25 19:59:34 | 2023-08-25 20:00:10 | 36.89 | tuple | ({'P02185': {('1h1x', 'X-ray', 1.4), ('1n9f', 'X-ray', 1.8), ('6m8f', 'X-ray', 1.1), ('2eku', 'X-ray', 1.4), ('1vxe', 'X-ray', 1.7), ('2mya', 'X-ray', 1.8), ('7ylk', 'X-ray', 1.63), ('5ut9', 'X-ray', 1.85), ('7cez', 'X-ray', 1.57), ('5ilp', 'X-ray', 1.88), ('1moa', 'X-ray', 1.9), ('1ltw', 'X-ray', 1...(truncated) | 2 | {} | 2023-08-25 19:59:34 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2023-08-25 20:00:11 | 2023-08-25 20:00:12 | 0.95 | list | [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) | 339 | {} | 2023-08-25 20:00:11 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2023-08-25 20:00:12 | 2023-08-25 20:12:00 | 707.66 | list | [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) | 5,590 | {} | 2023-08-25 20:00:12 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2023-08-25 20:12:00 | 2023-08-25 20:12:01 | 1.15 | tuple | ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'Phage_lysozyme': {'PF00959'}, 'GST_N': {'PF02798'}, 'GST_C_3': {'PF14497'}, 'DNA_methylase': {'PF00145'}, 'Pyrophosphatase': {'PF00719'}, 'AsnA': {'PF03590'}, 'RnaseA': {'PF00074'}, 'Ras': {'PF00071'}, 'Carb_anhydrase': {'PF00194'}, 'Lys': {...(truncated) | 2 | {} | 2023-08-25 20:12:00 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2023-08-25 20:12:01 | 2023-08-25 20:12:04 | 3.74 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': PfamDomain(chain='A', star...(truncated) | 2 | {} | 2023-08-25 20:12:01 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2023-08-25 20:12:05 | 2023-08-25 20:17:01 | 295.57 | tuple | ({}, {}) | 2 | {} | 2023-08-25 20:12:05 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2023-08-25 20:17:01 | 2023-08-25 20:17:01 | 0.60 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/pfam.py", line 94, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-07-28 20:47:35 | |||
| ¶ | pypath.inputs.pharos._create_query_functions | 2023-08-25 20:17:01 | 2023-08-25 20:17:01 | 0.00 | NoneType | None | 0 | {} | 2023-08-25 20:17:01 | |
| ¶ | pypath.inputs.pharos.pharos_diseases | 2023-08-25 20:17:01 | 2023-08-25 20:18:12 | 71.18 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'fixed': True} | 2023-08-25 20:17:01 | |
| ¶ | pypath.inputs.pharos.pharos_expression | 2023-08-25 20:18:14 | 2023-08-25 20:18:17 | 3.18 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'fixed': True} | 2023-08-25 20:18:14 | |
| ¶ | pypath.inputs.pharos.pharos_general |
Not calling `pypath.inputs.pharos.pharos_general`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pharos.pharos_gtex | 2023-08-25 20:18:18 | 2023-08-25 20:18:21 | 3.05 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'fixed': True} | 2023-08-25 20:18:18 | |
| ¶ | pypath.inputs.pharos.pharos_ligands | 2023-08-25 20:18:22 | 2023-08-25 20:18:26 | 3.23 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'fixed': True} | 2023-08-25 20:18:22 | |
| ¶ | pypath.inputs.pharos.pharos_orthologs | 2023-08-25 20:18:27 | 2023-08-25 20:18:30 | 3.13 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'fixed': True} | 2023-08-25 20:18:27 | |
| ¶ | pypath.inputs.pharos.pharos_targets | 2023-08-25 20:18:31 | 2023-08-25 20:19:08 | 36.28 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2'}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34'}, {'name': 'Keratin-associated protein 19-4', 'sym': 'KRTAP19-4', 'uniprot': 'Q3LI73'}, {'name': 'Keratin-associated protein 20-3',...(truncated) | 20,412 | {} | 2023-08-25 20:18:31 | |
| ¶ | pypath.inputs.pharos.pharos_xrefs | 2023-08-25 20:19:08 | 2023-08-25 20:19:11 | 3.44 | list | [{'name': 'Keratin-associated protein 9-6', 'sym': 'KRTAP9-6', 'uniprot': 'A8MVA2', 'diseases': []}, {'name': 'Keratin-associated protein 29-1', 'sym': 'KRTAP29-1', 'uniprot': 'A8MX34', 'diseases': [{'name': 'psoriasis', 'mondoID': 'MONDO:0005083', 'dids': [{'id': 'DOID:8893', 'dataSources': ['Expre...(truncated) | 20,412 | {'fixed': True} | 2023-08-25 20:19:08 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2023-08-25 20:19:12 | 2023-08-25 20:19:13 | 0.58 | dict | {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) | 20,350 | {} | 2023-08-25 20:19:12 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2023-08-25 20:19:13 | 2023-08-25 20:19:13 | 0.19 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/phosphatome.py", line 48, in phosphatome_annotations
path = science_input.science_download(url = url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 21:24:25 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2023-08-25 20:19:13 | 2023-08-25 20:19:15 | 1.46 | list | [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) | 2,426 | {} | 2023-08-25 20:19:13 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2023-08-25 20:19:15 | 2023-08-25 20:19:15 | 0.67 | list | [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) | 2,426 | {} | 2023-08-25 20:19:15 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2023-08-25 20:19:15 | 2023-08-25 20:19:15 | 0.12 | dict | {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) | 247 | {} | 2023-08-25 20:19:15 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2023-08-25 20:19:15 | 2023-08-25 20:19:17 | 1.44 | list | [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) | 4,417 | {} | 2023-08-25 20:19:15 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2023-08-25 20:19:17 | 2023-08-25 20:19:17 | 0.02 | list | [['PBK', 'MTA1'], ['STK16', 'RUVBL2'], ['PRKCA', 'NFATC4'], ['NEK9', 'MDM2'], ['MAPK3', 'MAPK8'], ['BUB1', 'C21orf66'], ['MAPK10', 'HLCS'], ['PRKCD', 'NPM1'], ['AURKB', 'RACGAP1'], ['WEE1', 'CAMKK1'], ['PRKCD', 'PRKD1'], ['ULK3', 'ZYX'], ['MAPK1', 'MED1'], ['MAP2K2', 'MAPK3'], ['MAPK1', 'RPS6KA5'], ...(truncated) | 1,821 | {} | 2023-08-25 20:19:17 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2023-08-25 20:19:17 | 2023-08-25 20:19:17 | 0.25 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2023-08-25 20:19:17 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2023-08-25 20:19:17 | 2023-08-25 20:19:17 | 0.01 | list | [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) | 9,269 | {} | 2023-08-25 20:19:17 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2023-08-25 20:19:17 | 2023-08-25 20:19:17 | 0.18 | list | [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P45984', 'P46937'], ['P06493', 'Q9GZV5'], ['P11309', 'P52907'], ['O14757', 'Q...(truncated) | 8,971 | {} | 2023-08-25 20:19:17 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2023-08-25 20:19:17 | 2023-08-25 20:19:18 | 0.36 | list | [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) | 13,459 | {} | 2023-08-25 20:19:17 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2023-08-25 20:19:18 | 2023-08-25 20:19:18 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) | 2 | {} | 2023-08-25 20:19:18 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2023-08-25 20:19:18 | 2023-08-25 20:19:18 | 0.08 | list | [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) | 9,041 | {} | 2023-08-25 20:19:18 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2023-08-25 20:19:18 | 2023-08-25 20:19:18 | 0.00 | list | [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) | 4,309 | {} | 2023-08-25 20:19:18 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2023-08-25 20:19:18 | 2023-08-25 20:19:18 | 0.00 | tuple | ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) | 2 | {} | 2023-08-25 20:19:18 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2023-08-25 20:19:18 | 2023-08-25 20:19:18 | 0.00 | list | [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'AB;WB;MA'...(truncated) | 4,732 | {} | 2023-08-25 20:19:18 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2023-08-25 20:19:18 | 2023-08-25 20:19:24 | 5.72 | dict | {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'S', 6, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'S', 6, 9606,...(truncated) | 198,635 | {} | 2023-08-25 20:19:18 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2023-08-25 20:19:24 | 2023-08-25 20:19:39 | 14.71 | list | [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) | 239,789 | {} | 2023-08-25 20:19:24 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2023-08-25 20:19:39 | 2023-08-25 20:19:40 | 0.55 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'phosphorylation', 'protein degradation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {} | 2023-08-25 20:19:39 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2023-08-25 20:19:40 | 2023-08-25 20:21:35 | 114.97 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'21148409', '21209006', '28052875', '24876223'}, 'isoforms': {1}, 'process': {''}, 'function': {'protein stabilization', 'protein degradation', 'intracellular localization', 'phosphorylation', 'ubiquitination'}...(truncated) | 3,618 | {} | 2023-08-25 20:19:40 | |
| ¶ | pypath.inputs.phosphosite.regsites_tab |
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_bonds |
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pisa.pisa_interfaces |
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pro.get_pro | 2023-08-25 20:21:35 | 2023-08-25 20:27:35 | 360.01 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2023-08-25 20:21:35 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2023-08-25 20:27:35 | 2023-08-25 20:28:42 | 67.43 | list | [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) | 320,143 | {} | 2023-08-25 20:27:35 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2023-08-25 20:28:43 | 2023-08-25 20:28:48 | 5.69 | dict | {'P35250': {ProgenyAnnotation(pathway='NFkB', weight=-0.4099507693295503, p_value=0.37172804911595947), ProgenyAnnotation(pathway='Hypoxia', weight=-2.049501418649251, p_value=0.0007040310639538167), ProgenyAnnotation(pathway='Estrogen', weight=2.40982404059, p_value=0.0238138596584), ProgenyAnnotat...(truncated) | 18,590 | {} | 2023-08-25 20:28:43 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2023-08-25 20:28:49 | 2023-08-25 20:28:51 | 2.03 | DataFrame | gene pathway weight p.value 1 RFC2 EGFR 1.470647 0.001655 2 ESRRA EGFR 0.178590 0.211838 3 HNRNPK EGFR 0.306699 0.084560 4 CBX6 EGFR -0.675507 0.017641 5 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2023-08-25 20:28:49 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2023-08-25 20:28:51 | 2023-08-25 20:28:57 | 6.46 | dict | {'normal': {'adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detected', 'Approved'...(truncated) | 2 | {} | 2023-08-25 20:28:51 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2023-08-25 20:28:59 | 2023-08-25 20:29:13 | 14.17 | dict | {'O43657': {ProtainatlasAnnotation(organ='skin 1', tissue='fibroblasts', level='Not detected', status='Approved', n_not_detected=None, n_low=None, n_medium=None, n_high=None, prognostic=False, favourable=False, score=None, pathology=False), ProtainatlasAnnotation(organ='endometrium 2', tissue='cells...(truncated) | 19,462 | {} | 2023-08-25 20:28:59 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2023-08-25 20:29:15 | 2023-08-25 20:29:15 | 0.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/proteinatlas.py", line 247, in proteinatlas_secretome_annotations
path = science.science_download(url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 21:35:20 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2023-08-25 20:29:15 | 2023-08-25 20:29:16 | 0.34 | dict | {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Golgi apparatus', status='Supported'), ProteinatlasSubcellularAnnotation(location='Cytosol', status='Supported')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellularAnno...(truncated) | 6,981 | {} | 2023-08-25 20:29:15 | |
| ¶ | pypath.inputs.proteins.variants | 2023-08-25 20:29:16 | 2023-08-25 20:40:21 | 665.18 | list | [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) | 48,722 | {} | 2023-08-25 20:29:16 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2023-08-25 20:40:22 | 2023-08-25 20:40:26 | 4.67 | tuple | ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) | 2 | {} | 2023-08-25 20:40:22 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2023-08-25 20:40:27 | 2023-08-25 20:40:27 | 0.73 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'22304920', '24727247', '25545367', '25728676', '24357804'}, 'substrate': 'P15336', 'databases': {'REACH', 'SIGNOR', 'PhosphoSite', 'Sparser'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'24727247', '23708658'}, ...(truncated) | 22,139 | {} | 2023-08-25 20:40:27 | |
| ¶ | pypath.inputs.protmapper.protmapper_interactions |
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubchem.pubchem_mapping |
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pmid |
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.get_pubmeds |
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.only_pmids |
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.open_pubmed |
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_dict |
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pubmed.pmids_list |
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramilowski2015.ramilowski_interactions | 2023-08-25 20:40:27 | 2023-08-25 20:40:28 | 0.53 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2023-08-25 20:40:27 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2023-08-25 20:40:28 | 2023-08-25 20:40:32 | 4.18 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), Rami...(truncated) | 18,852 | {} | 2023-08-25 20:40:28 | |
| ¶ | pypath.inputs.ramp._ramp_sqldump | 2023-08-25 20:40:32 | 2023-08-25 20:40:37 | 4.91 | TextIOWrapper | <_io.TextIOWrapper name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/cache/2ac9fe4b32649e946c59f28f74943748-38534654' encoding='utf-8'> | 0 | {} | 2023-08-25 20:40:32 | |
| ¶ | pypath.inputs.ramp.ramp_id_types | 2023-08-25 20:40:37 | 2023-08-25 20:48:46 | 488.62 | set | {'CAS', 'kegg_glycan', 'uniprot', 'ensembl', 'EN', 'kegg', 'chemspider', 'lipidbank', 'hmdb', 'entrez', 'plantfa', 'LIPIDMAPS', 'swisslipids', 'pubchem', 'chebi', 'gene_symbol', 'ncbiprotein', 'brenda', 'wikidata'} | 19 | {} | 2023-08-25 20:40:37 | |
| ¶ | pypath.inputs.ramp.ramp_id_types_2 | 2023-08-25 20:48:46 | 2023-08-25 20:48:53 | 7.72 | set | {'CAS', 'kegg_glycan', 'uniprot', 'ensembl', 'EN', 'kegg', 'chemspider', 'lipidbank', 'hmdb', 'entrez', 'plantfa', 'LIPIDMAPS', 'swisslipids', 'pubchem', 'chebi', 'gene_symbol', 'ncbiprotein', 'brenda', 'wikidata'} | 19 | {} | 2023-08-25 20:48:46 | |
| ¶ | pypath.inputs.ramp.ramp_list_tables | 2023-08-25 20:48:53 | 2023-08-25 20:48:56 | 2.46 | dict | {'analyte': ['rampId', 'type'], 'analytehasontology': ['rampCompoundId', 'rampOntologyId'], 'analytehaspathway': ['rampId', 'pathwayRampId', 'pathwaySource'], 'analytesynonym': ['Synonym', 'rampId', 'geneOrCompound', 'source'], 'catalyzed': ['rampCompoundId', 'rampGeneId'], 'chem_props': ['ramp_id',...(truncated) | 13 | {} | 2023-08-25 20:48:53 | |
| ¶ | pypath.inputs.ramp.ramp_mapping |
Not calling `pypath.inputs.ramp.ramp_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_raw |
Not calling `pypath.inputs.ramp.ramp_raw`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ramp.ramp_show_tables | 2023-08-25 20:48:56 | 2023-08-25 20:48:58 | 2.46 | NoneType | None | 0 | {} | 2023-08-25 20:48:56 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2023-08-25 20:48:58 | 2023-08-25 20:48:58 | 0.00 | NoneType | None | 0 | {} | 2023-08-25 20:48:58 | |
| ¶ | pypath.inputs.rdata._rdata_data_frame_get_rownames |
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.rdata._rdata_list_get_names |
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._bp_collect_resources |
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._process_controls |
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_resources |
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_collect_species |
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_compartment |
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_id |
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_extract_res |
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_id |
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reaction |
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_reactions | 2023-08-25 20:48:58 | 2023-08-25 20:48:58 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 966, in _reactome_reactions
for pw, soup in soups:
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 134, in reactome_bs
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-07-28 21:56:04 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2023-08-25 20:48:58 | 2023-08-25 20:48:58 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 1032, in _reactome_reactions_et
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-07-28 21:56:04 | |||
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2023-08-25 20:48:58 | 2023-08-25 20:48:59 | 0.91 | list | ['<?xml version="1.0" encoding="UTF-8"?>\n', '<rdf:RDF\n', ' xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n', ' xmlns:owl="http://www.w3.org/2002/07/owl#"\n', ' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n', ' xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"\n', ' xml:base="...(truncated) | 190,854 | {} | 2023-08-25 20:48:58 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2023-08-25 20:48:59 | 2023-08-25 20:48:59 | 0.09 | list | [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) | 37,288 | {} | 2023-08-25 20:48:59 | |
| ¶ | pypath.inputs.reaction.get_controls |
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_interactions |
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_reactions | 2023-08-25 20:48:59 | 2023-08-25 20:49:02 | 2.51 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 1182, in get_reactions
rea.load_all()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/pyreact.py", line 1295, in load_all
self.load_wikipathways()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/pyreact.py", line 1188, in load_wikipathways
self.add_dataset(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/pyreact.py", line 1309, in add_dataset
self.merge()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/pyreact.py", line 1345, in merge
self.merge_modifications()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/pyreact.py", line 1577, in merge_modifications
self.load_sequences()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/pyreact.py", line 2328, in load_sequences
self.seq = seq.swissprot_seq(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/utils/seq.py", line 50, in swissprot_seq
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-07-28 21:56:06 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2023-08-25 20:49:02 | 2023-08-25 20:49:07 | 5.61 | dict | {'BioPAX/Fructose_galactose_metabolism.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/B_cell_activation.owl': <ExFileObject name='/mnt/disk0/build/omnipath-build/pypath_inputs_status__202...(truncated) | 178 | {} | 2023-08-25 20:49:02 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2023-08-25 20:49:07 | 2023-08-25 20:49:09 | 1.89 | NoneType | None | 0 | {} | 2023-08-25 20:49:07 | |
| ¶ | pypath.inputs.reaction.pid_interactions |
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_complex |
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_controls |
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.process_reactions |
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactions_biopax |
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_biopax | 2023-08-25 20:49:09 | 2023-08-25 20:49:09 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 79, in reactome_biopax
url = urls.urls['reactome']['biopax_l3']
KeyError: 'biopax_l3'
|
{} | 2023-07-28 21:56:16 | |||
| ¶ | pypath.inputs.reaction.reactome_bs | 2023-08-25 20:49:09 | 2023-08-25 20:49:09 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 134, in reactome_bs
sbml = reactome_sbml()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-07-28 21:56:16 | |||
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2023-08-25 20:49:09 | 2023-08-25 20:49:09 | 0.00 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reaction.py", line 57, in reactome_sbml
url = urls.urls['reactome']['sbml']
KeyError: 'sbml'
|
{} | 2023-07-28 21:56:16 | |||
| ¶ | pypath.inputs.reactome._reactome_data |
Not calling `pypath.inputs.reactome._reactome_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome._reactome_data_gen |
Not calling `pypath.inputs.reactome._reactome_data_gen`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reactome.reactome_chebis | 2023-08-25 20:49:09 | 2023-08-25 20:49:15 | 5.23 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-07-28 21:56:16 | |||
| ¶ | pypath.inputs.reactome.reactome_pathway_relations | 2023-08-25 20:49:15 | 2023-08-25 20:49:15 | 0.83 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-07-28 21:56:29 | |||
| ¶ | pypath.inputs.reactome.reactome_pathways | 2023-08-25 20:49:15 | 2023-08-25 20:49:16 | 0.93 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-07-28 21:56:37 | |||
| ¶ | pypath.inputs.reactome.reactome_uniprots | 2023-08-25 20:49:16 | 2023-08-25 20:49:37 | 20.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 867, in test_input
for i, rec in enumerate(value_gen):
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/reactome.py", line 107, in _reactome_data_gen
record = collections.namedtuple('Reactome', fields)
NameError: name 'fields' is not defined
|
{} | 2023-07-28 21:56:44 | |||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2023-08-25 20:49:37 | 2023-08-25 20:49:40 | 2.61 | dict | {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human'), ScconnectAnnota...(truncated) | 3,286 | {} | 2023-08-25 20:49:37 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2023-08-25 20:49:40 | 2023-08-25 20:49:40 | 0.03 | set | {Complex: COMPLEX:P01215_P01229, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P01215_P01225, Complex: COMPLEX:P05111_P08476, Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:P29460_Q9NPF7, Complex: COMPLEX:P01562, Complex: COMPLEX:P05496_P48201_Q06055, Complex: COMPLEX:O15263, Complex: CO...(truncated) | 17 | {} | 2023-08-25 20:49:40 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2023-08-25 20:49:40 | 2023-08-25 20:56:15 | 395.67 | list | [ScconnectInteraction(ligand_id='P41273', target_id='Q07011', ligand_organism=9606, target_organism=9606, ligand_type='protein', target_type='protein', effect='None', references=''), ScconnectInteraction(ligand_id='P20292', target_id='P09917', ligand_organism=9606, target_organism=9606, ligand_type=...(truncated) | 1,766 | {} | 2023-08-25 20:49:40 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.sider.sider_drug_names | 2023-08-25 20:56:15 | 2023-08-25 20:56:15 | 0.12 | dict | {'CID100012536': {SiderDrug(name='desonide', atc='D07AB08'), SiderDrug(name='desonide', atc='S01BA11')}, 'CID100104799': {SiderDrug(name='fotemustine', atc='L01AD05')}, 'CID100005253': {SiderDrug(name='sotalol', atc='C07AA07')}, 'CID100208902': {SiderDrug(name='ramelteon', atc='N05CH02')}, 'CID10000...(truncated) | 1,430 | {} | 2023-08-25 20:56:15 | |
| ¶ | pypath.inputs.sider.sider_meddra_side_effects | 2023-08-25 20:56:15 | 2023-08-25 20:56:16 | 0.34 | list | [SiderSideeffectMeddra(cid='C0334203', meddra_id='10068735', side_effect_name='Decidual cast'), SiderSideeffectMeddra(cid='C0001193', meddra_id='10002943', side_effect_name="Apert's syndrome"), SiderSideeffectMeddra(cid='C0853845', meddra_id='10037415', side_effect_name='Pulmonary interstitial emphy...(truncated) | 20,307 | {} | 2023-08-25 20:56:15 | |
| ¶ | pypath.inputs.sider.sider_side_effect_frequencies | 2023-08-25 20:56:16 | 2023-08-25 20:56:17 | 1.51 | dict | {'CID100000085': {SiderSideeffetFrequency(umls_concept_on_label='C0042963', umls_concept_in_meddra='C0042963', side_effect='Vomiting', frequency='16%'), SiderSideeffetFrequency(umls_concept_on_label='C0030554', umls_concept_in_meddra='C0030554', side_effect='Paraesthesia', frequency='5%'), SiderSide...(truncated) | 968 | {} | 2023-08-25 20:56:16 | |
| ¶ | pypath.inputs.sider.sider_side_effects | 2023-08-25 20:56:17 | 2023-08-25 20:56:19 | 1.51 | dict | {'CID100000085': {SiderSideeffect(umls_concept_on_label='C0152020', umls_concept_in_meddra='C0152020', side_effect='Gastric atony'), SiderSideeffect(umls_concept_on_label='C0033774', umls_concept_in_meddra='C0033774', side_effect='Pruritus'), SiderSideeffect(umls_concept_on_label='C0085595', umls_co...(truncated) | 1,430 | {} | 2023-08-25 20:56:17 | |
| ¶ | pypath.inputs.signalink.signalink_annotations | 2023-08-25 20:56:19 | 2023-08-25 20:56:21 | 1.52 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway...(truncated) | 2 | {} | 2023-08-25 20:56:19 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2023-08-25 20:56:21 | 2023-08-25 20:56:22 | 0.94 | dict | {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Co-factor')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 783 | {} | 2023-08-25 20:56:21 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2023-08-25 20:56:22 | 2023-08-25 20:56:22 | 0.45 | list | [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) | 1,939 | {} | 2023-08-25 20:56:22 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2023-08-25 20:56:22 | 2023-08-25 20:56:23 | 0.47 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='To...(truncated) | 835 | {} | 2023-08-25 20:56:22 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2023-08-25 20:56:23 | 2023-08-25 20:56:23 | 0.61 | dict | {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4...(truncated) | 4,868 | {} | 2023-08-25 20:56:23 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2023-08-25 20:56:23 | 2023-08-25 20:56:26 | 2.56 | list | [{'typ': 'phosphorylation', 'resnum': 214, 'instance': 'SRSGLYRSPSMPENL', 'substrate': 'P30307', 'start': 207, 'end': 221, 'kinase': 'P06493', 'resaa': 'S', 'motif': 'SRSGLYRSPSMPENL', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'10864927'}}, {'typ': 'methylation', 'resnum': 5,...(truncated) | 10,339 | {} | 2023-08-25 20:56:23 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2023-08-25 20:56:26 | 2023-08-25 20:56:26 | 0.53 | list | [SignorInteraction(source='P48436', target='P32243', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='up-regulates activity', mechanism='binding', ncbi_tax_id='10090', pubmeds='20530484', direct=True, ptm_type='binding', ptm_residue='', ptm_motif=''), S...(truncated) | 90,412 | {} | 2023-08-25 20:56:26 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2023-08-25 20:56:26 | 2023-08-25 20:56:42 | 15.96 | dict | {'Q76L83': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P29375': {SignorPathway(pathway='Acute Myeloid Leukemia')}, 'P40763': {SignorPathway(pathway='Acute Myeloid Leukemia'), SignorPathway(pathway='IL6 Signaling'), SignorPathway(pathway='Leptin Signaling'), SignorPathway(pathway='EBV infecti...(truncated) | 672 | {} | 2023-08-25 20:56:26 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2023-08-25 20:56:42 | 2023-08-25 20:56:42 | 0.00 | dict | {'SIGNOR-PF1': ['P27361', 'P28482'], 'SIGNOR-PF2': ['Q92633', 'Q9HBW0', 'Q9UBY5'], 'SIGNOR-PF3': ['O14610', 'O60262', 'P50150', 'P50151', 'P59768', 'P61952', 'P63211', 'P63215', 'P63218', 'Q9P2W3', 'Q9UBI6', 'Q9UK08'], 'SIGNOR-PF4': ['O14775', 'P16520', 'P62873', 'P62879', 'Q9HAV0'], 'SIGNOR-PF5': [...(truncated) | 90 | {} | 2023-08-25 20:56:42 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2023-08-25 20:56:42 | 2023-08-25 20:56:54 | 11.81 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/spike.py", line 187, in spike_complexes
interactions = spike_interactions(min_confidence = min_confidence)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/spike.py", line 101, in spike_interactions
if all(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/spike.py", line 103, in <genexpr>
genes[m][0].type != 'complex'
IndexError: list index out of range
|
{} | 2023-07-28 22:05:50 | |||
| ¶ | pypath.inputs.spike.spike_interactions | 2023-08-25 20:56:54 | 2023-08-25 20:56:57 | 2.33 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/spike.py", line 101, in spike_interactions
if all(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/spike.py", line 103, in <genexpr>
genes[m][0].type != 'complex'
IndexError: list index out of range
|
{} | 2023-07-28 22:06:00 | |||
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2023-08-25 20:56:57 | 2023-08-25 20:58:15 | 78.76 | list | [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) | 21,773,491 | {} | 2023-08-25 20:56:57 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2023-08-25 20:58:15 | 2023-08-25 20:59:49 | 93.35 | list | [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) | 150,645 | {} | 2023-08-25 20:58:15 | |
| ¶ | pypath.inputs.string.string_effects | 2023-08-25 20:59:49 | 2023-08-25 20:59:57 | 8.59 | list | [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) | 2,250,122 | {} | 2023-08-25 20:59:49 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2023-08-25 20:59:59 | 2023-08-25 21:00:29 | 30.49 | list | [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000440005', neighborhood_score=0, fusion=0, cooccurence=50, coexpression=99, experimental=679, database=900, textmining=59, combined_score=969, physical_combined_score=740), StringLinksInteraction(protein_a='ENSP00000000233', prot...(truncated) | 247,200 | {} | 2023-08-25 20:59:59 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2023-08-25 21:00:29 | 2023-08-25 21:00:31 | 1.79 | list | [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000221957', experimental=483, database=600, textmining=821, combined_score=959), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=932, database=0, textmining=0, combined_score=932...(truncated) | 83,896 | {} | 2023-08-25 21:00:29 | |
| ¶ | pypath.inputs.string.string_species | 2023-08-25 21:00:31 | 2023-08-25 21:00:31 | 0.11 | dict | {'23': 'Shewanella colwelliana', '48': 'Archangium gephyra', '52': 'Chondromyces crocatus', '54': 'Nannocystis exedens', '69': 'Lysobacter enzymogenes', '140': 'Borrelia hermsii', '162': 'Treponema phagedenis', '163': 'Treponema bryantii', '183': 'Leptonema illini', '192': 'Azospirillum brasilense',...(truncated) | 14,094 | {} | 2023-08-25 21:00:31 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2023-08-25 21:00:31 | 2023-08-25 21:00:34 | 2.59 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/surfaceome.py", line 37, in surfaceome_annotations
raw = inputs_common.read_xls(xlsname, 'in silico surfaceome only')[2:]
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 143, in read_xls
table = [
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 144, in <listcomp>
[
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/common.py", line 148, in <listcomp>
cell.value
AttributeError: 'int' object has no attribute 'value'
|
{} | 2023-07-28 22:09:41 | |||
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2023-08-25 21:00:34 | 2023-08-25 21:00:39 | 5.18 | list | [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) | 839 | {} | 2023-08-25 21:00:34 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2023-08-25 21:00:39 | 2023-08-25 21:00:40 | 0.72 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False)}, 'Q16613': {Talklr...(truncated) | 1,344 | {} | 2023-08-25 21:00:39 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2023-08-25 21:00:40 | 2023-08-25 21:00:40 | 0.04 | list | [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) | 2,422 | {} | 2023-08-25 21:00:40 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2023-08-25 21:00:40 | 2023-08-25 21:00:40 | 0.03 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2023-08-25 21:00:40 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2023-08-25 21:00:40 | 2023-08-25 21:00:45 | 5.65 | dict | {'P60201': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2'), TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.4')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(fam...(truncated) | 2,275 | {} | 2023-08-25 21:00:40 | |
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2023-08-25 21:00:45 | 2023-08-25 21:00:46 | 0.52 | dict | {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) | 23,269 | {} | 2023-08-25 21:00:45 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2023-08-25 21:00:46 | 2023-08-25 21:00:46 | 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) | 1,864 | {'size': 1} | 2023-08-25 21:00:46 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2023-08-25 21:00:46 | 2023-08-25 21:00:46 | 0.20 | dict | {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) | 1,490 | {} | 2023-08-25 21:00:46 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2023-08-25 21:00:46 | 2023-08-25 21:00:51 | 5.12 | dict | {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) | 174,325 | {} | 2023-08-25 21:00:46 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2023-08-25 21:00:51 | 2023-08-25 21:01:17 | 25.49 | set | {ThreedcomplexContact(pdb='2w9l_1', uniprot_1='Q65914', uniprot_2='P78310', chain_1='N', chain_2='Y', n_residues=15.0, length_1=182, length_2=119, domain_s1=('49835',), domain_p1=('PF00541.12',), domain_s2=('48726',), domain_p2=('PF07686.12',), ident=False, homo=False), ThreedcomplexContact(pdb='3ud...(truncated) | 259,798 | {} | 2023-08-25 21:00:51 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2023-08-25 21:01:18 | 2023-08-25 21:04:01 | 162.67 | list | [<pypath.internals.intera.DomainDomain object at 0x7fbca9127df0>, <pypath.internals.intera.DomainDomain object at 0x7fbca9127f40>, <pypath.internals.intera.DomainDomain object at 0x7fbca9127fd0>, <pypath.internals.intera.DomainDomain object at 0x7fbd1de0c130>, <pypath.internals.intera.DomainDomain o...(truncated) | 524,436 | {} | 2023-08-25 21:01:18 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2023-08-25 21:04:01 | 2023-08-25 21:04:10 | 9.23 | dict | {'2w9l_1': {('P78310', 'Q65914'): 14.5, ('Q65914', 'Q65914'): 25.5, ('P78310', 'P78310'): 1.0}, '3udg_1': {('Q9RY51', 'Q9RY51'): 24.5}, '1dqa_1': {('P04035', 'P04035'): 98.5}, '3abk_1': {('P00396', 'P10175'): 20.5, ('P00396', 'P00430'): 35.0, ('P00396', 'P13183'): 8.0, ('P00415', 'P07470'): 27.0, ('...(truncated) | 81,192 | {} | 2023-08-25 21:04:01 | |
| ¶ | pypath.inputs.threedid.get_3did | 2023-08-25 21:04:11 | 2023-08-25 21:39:01 | 2,089.88 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7fbe2e93f8e0>, <pypath.internals.intera.DomainDomain object at 0x7fbe2e93c070>, <pypath.internals.intera.DomainDomain object at 0x7fbe2e93dff0>, <pypath.internals.intera.DomainDomain object at 0x7fbe2e93c280>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2023-08-25 21:04:11 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2023-08-25 21:39:01 | 2023-08-25 21:39:03 | 2.61 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/threedid.py", line 54, in get_3did_ddi
u_pfam, pfam_u = pfam_input.pfam_uniprot(organism = organism)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/pfam.py", line 94, in pfam_uniprot
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 2023-07-28 22:44:56 | |||
| ¶ | pypath.inputs.topdb.topdb_annotations | 2023-08-25 21:39:03 | 2023-08-25 21:39:07 | 4.00 | dict | {'P05067': {TopdbAnnotation(membrane='Extracellular', topology='Outside', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplasm', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Plasma membrane', topology='Inside', score=89, tmregions=1), TopdbAnnotation(membrane='Extrac...(truncated) | 1,248 | {} | 2023-08-25 21:39:03 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2023-08-25 21:39:07 | 2023-08-25 21:39:08 | 0.68 | list | [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) | 2,678 | {} | 2023-08-25 21:39:07 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2023-08-25 21:39:08 | 2023-08-25 21:39:08 | 0.01 | dict | {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) | 5 | {} | 2023-08-25 21:39:08 | |
| ¶ | pypath.inputs.trip.trip_find_uniprot |
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_get_uniprot |
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trip.trip_interactions | 2023-08-25 21:39:08 | 2023-08-25 21:39:08 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11983166;12601176;11290752', 'Fluorescence probe labeling;Fusion protein-pull down assay;Calciu...(truncated) | 359 | {} | 2023-08-25 21:39:08 | |
| ¶ | pypath.inputs.trip.trip_process | 2023-08-25 21:39:08 | 2023-08-25 21:39:08 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Porcine coronary artery', 'Rat aortic vascular smooth muscle cell', 'HEK293', 'Rat vascular smooth muscle cell'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2023-08-25 21:39:08 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.trrust.trrust_human | 2023-08-25 21:39:08 | 2023-08-25 21:39:12 | 3.50 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2023-08-25 21:39:08 | |
| ¶ | pypath.inputs.trrust.trrust_interactions | 2023-08-25 21:39:12 | 2023-08-25 21:39:12 | 0.01 | list | [TrrustInteraction(source_genesymbol='AATF', target_genesymbol='BAX', effect='Repression', references=('22909821',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='CDKN1A', effect='Unknown', references=('17157788',)), TrrustInteraction(source_genesymbol='AATF', target_genesymbol='KL...(truncated) | 9,396 | {} | 2023-08-25 21:39:12 | |
| ¶ | pypath.inputs.trrust.trrust_mouse | 2023-08-25 21:39:12 | 2023-08-25 21:39:14 | 2.85 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/trrust.py", line 91, in trrust_mouse
return trrust_interactions('mouse')
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/trrust.py", line 80, in trrust_interactions
interactions = [TrrustInteraction(line) for line in c.result]
TypeError: 'NoneType' object is not iterable
|
{} | 2023-07-28 22:45:07 | |||
| ¶ | pypath.inputs.twosides.twosides_interactions | 2023-08-25 21:39:14 | 2023-08-25 21:42:42 | 207.36 | list | [TwosidesInteraction(drug1_rxnorm='10355', drug1='Temazepam', drug2_rxnorm='136411', drug2='sildenafil', condition_meddra='10003239', condition='Arthralgia', prr='2.91667', pee_error='0.421275', mean_reporting_frequency='0.0448718'), TwosidesInteraction(drug1_rxnorm='1808', drug1='Bumetanide', drug2...(truncated) | 42,920,391 | {} | 2023-08-25 21:39:14 | |
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2023-08-25 21:42:42 | 2023-08-25 21:42:42 | 0.03 | list | [UnichemSource(number='1', label='chembl', name='ChEMBL', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) | 41 | {} | 2023-08-25 21:42:42 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2023-08-25 21:42:42 | 2023-08-25 21:42:42 | 0.02 | dict | {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma', '22': 'pubc...(truncated) | 41 | {} | 2023-08-25 21:42:42 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2023-08-25 21:42:42 | 2023-08-25 21:42:42 | 0.05 | set | {'H0YMB5', 'F6IQF2', 'K7ESM3', 'E9PPA4', 'A0A2R8Y5R1', 'A0A5C2FUL3', 'A0A5C2G4L9', 'H0YC45', 'A0A5H2UDC9', 'Q9TQP2', 'B5A927', 'I3L385', 'A0A087WYU3', 'F2X5X3', 'A0A024R6C2', 'A0A0A7C6Y1', 'F2X620', 'H3BLU5', 'J3QKS7', 'D6REM0', 'Q96PQ5', 'A0A7I2V3V9', 'J9PVN8', 'Q9GJ16', 'A0A8I5KWE1', 'Q8NBV5', 'A0...(truncated) | 207,892 | {} | 2023-08-25 21:42:42 | |
| ¶ | pypath.inputs.uniprot._cleanup | 2023-08-25 21:42:42 | 2023-08-25 21:42:42 | 0.00 | NoneType | None | 0 | {} | 2023-08-25 21:42:42 | |
| ¶ | pypath.inputs.uniprot._protein_datasheet |
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot._remove |
Not calling `pypath.inputs.uniprot._remove`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot._swissprot_param |
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.all_swissprots | 2023-08-25 21:42:42 | 2023-08-25 21:42:42 | 0.00 | set | {'P59190', 'O60829', 'Q96RP7', 'P23490', 'Q8WXI3', 'Q6PJE2', 'Q9HDB9', 'Q96PQ5', 'B7ZBB8', 'P57076', 'Q8IXS2', 'Q9HBL8', 'O75629', 'Q96JP2', 'Q9H0H9', 'Q9P2D7', 'P53367', 'P98170', 'Q9NS18', 'Q69YL0', 'Q8WU10', 'Q9Y5C1', 'Q96EI5', 'Q8NGK1', 'Q8NGG7', 'Q9Y224', 'Q9UII2', 'Q86UV7', 'Q86WZ6', 'Q86W26',...(truncated) | 20,423 | {} | 2023-08-25 21:42:42 | |
| ¶ | pypath.inputs.uniprot.all_trembls | 2023-08-25 21:42:42 | 2023-08-25 21:43:33 | 50.82 | set | {'H0YMB5', 'F6IQF2', 'K7ESM3', 'E9PPA4', 'A0A2R8Y5R1', 'A0A5C2FUL3', 'A0A5C2G4L9', 'H0YC45', 'A0A5H2UDC9', 'Q9TQP2', 'B5A927', 'I3L385', 'A0A087WYU3', 'F2X5X3', 'A0A024R6C2', 'A0A0A7C6Y1', 'F2X620', 'H3BLU5', 'J3QKS7', 'D6REM0', 'A0A7I2V3V9', 'J9PVN8', 'Q9GJ16', 'A0A8I5KWE1', 'Q8NBV5', 'A0A126GW85',...(truncated) | 187,469 | {} | 2023-08-25 21:42:42 | |
| ¶ | pypath.inputs.uniprot.all_uniprots | 2023-08-25 21:43:33 | 2023-08-25 21:43:33 | 0.00 | set | {'H0YMB5', 'F6IQF2', 'K7ESM3', 'E9PPA4', 'A0A2R8Y5R1', 'A0A5C2FUL3', 'A0A5C2G4L9', 'H0YC45', 'A0A5H2UDC9', 'Q9TQP2', 'B5A927', 'I3L385', 'A0A087WYU3', 'F2X5X3', 'A0A024R6C2', 'A0A0A7C6Y1', 'F2X620', 'H3BLU5', 'J3QKS7', 'D6REM0', 'Q96PQ5', 'A0A7I2V3V9', 'J9PVN8', 'Q9GJ16', 'A0A8I5KWE1', 'Q8NBV5', 'A0...(truncated) | 207,892 | {} | 2023-08-25 21:43:33 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_db | 2023-08-25 21:43:33 | 2023-08-25 21:43:33 | 0.00 | set | {'H0YMB5', 'F6IQF2', 'K7ESM3', 'E9PPA4', 'A0A2R8Y5R1', 'A0A5C2FUL3', 'A0A5C2G4L9', 'H0YC45', 'A0A5H2UDC9', 'Q9TQP2', 'B5A927', 'I3L385', 'A0A087WYU3', 'F2X5X3', 'A0A024R6C2', 'A0A0A7C6Y1', 'F2X620', 'H3BLU5', 'J3QKS7', 'D6REM0', 'Q96PQ5', 'A0A7I2V3V9', 'J9PVN8', 'Q9GJ16', 'A0A8I5KWE1', 'Q8NBV5', 'A0...(truncated) | 207,892 | {} | 2023-08-25 21:43:33 | |
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2023-08-25 21:43:33 | 2023-08-25 21:43:34 | 0.83 | list | [['A0A023HHK9', 'Q8NFU7'], ['A0A023HHL0', 'Q8NFU7'], ['A0A023IN41', 'H0Y5F6'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZR6', 'Q9UII6'], ['A0A024R056', 'A0A140VJJ8'], ['A0A024R072', 'Q96S94'], ['A0A024R...(truncated) | 72,064 | {} | 2023-08-25 21:43:33 | |
| ¶ | pypath.inputs.uniprot.init_db | 2023-08-25 21:43:34 | 2023-08-25 21:43:34 | 0.06 | NoneType | None | 0 | {} | 2023-08-25 21:43:34 | |
| ¶ | pypath.inputs.uniprot.is_swissprot |
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.is_trembl |
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.is_uniprot |
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.protein_datasheet |
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_data |
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_families | 2023-08-25 21:43:34 | 2023-08-25 21:43:51 | 17.33 | dict | {'A0A087X1C5': {UniprotFamily(family='Cytochrome P450', subfamily=None)}, 'A0A0B4J2F2': {UniprotFamily(family='Protein kinase superfamily, CAMK Ser/Thr protein kinase', subfamily='AMPK')}, 'A0A0K2S4Q6': {UniprotFamily(family='CD300', subfamily=None)}, 'A0A1B0GTW7': {UniprotFamily(family='Peptidase M...(truncated) | 14,429 | {} | 2023-08-25 21:43:34 | |
| ¶ | pypath.inputs.uniprot.uniprot_history |
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_history_recent_datasheet |
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_keywords | 2023-08-25 21:43:51 | 2023-08-25 21:44:07 | 16.10 | dict | {'A0A087X1C5': {UniprotKeyword(keyword='Transmembrane'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Cytoplasm'), UniprotKeyword(keyword='Iron'), UniprotKeyword(keyword='Oxidoreductase'), UniprotKeyword(keyword='Mitochondrion'), UniprotKeyword(keyword='Monooxygenase'), UniprotKe...(truncated) | 20,423 | {} | 2023-08-25 21:43:51 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2023-08-25 21:44:07 | 2023-08-25 21:44:25 | 18.01 | dict | {'A0A087X1C5': {UniprotLocation(location='Mitochondrion', features=None), UniprotLocation(location='Membrane', features=('Multi-pass membrane protein',)), UniprotLocation(location='Cytoplasm', features=None)}, 'A0A0B4J2F0': {UniprotLocation(location='Mitochondrion outer membrane', features=('Single-...(truncated) | 17,055 | {} | 2023-08-25 21:44:07 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2023-08-25 21:44:25 | 2023-08-25 21:44:25 | 0.09 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,347 | {} | 2023-08-25 21:44:25 | |
| ¶ | pypath.inputs.uniprot.uniprot_preprocess |
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_recent_version |
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.uniprot_taxonomy | 2023-08-25 21:44:25 | 2023-08-25 21:44:28 | 2.13 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Pinus balsamea', 'Balsam fir', 'Abies balsamea'}, 'H8ZM71': {'Pinus balsamea', 'Balsam fir', 'Abies balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Pinus grandis', 'Abies grandis', '...(truncated) | 555,337 | {} | 2023-08-25 21:44:25 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2023-08-25 21:44:28 | 2023-08-25 21:44:45 | 17.28 | dict | {'A0A087X1C5': {UniprotTissue(tissue='Brain cortex', level='undefined')}, 'A0A0C5B5G6': {UniprotTissue(tissue='Plasma', level='undefined'), UniprotTissue(tissue='Skeletal muscle', level='undefined')}, 'A0A0K2S4Q6': {UniprotTissue(tissue='Myeloid dendritic cells', level='undefined'), UniprotTissue(ti...(truncated) | 10,052 | {} | 2023-08-25 21:44:28 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2023-08-25 21:44:45 | 2023-08-25 21:45:58 | 72.89 | dict | {'A0A087X1C5': {UniprotTopology(topology='Extracellular', start=1, end=2), UniprotTopology(topology='Cytoplasmic', start=24, end=301), UniprotTopology(topology='Extracellular', start=323, end=515), UniprotTopology(topology='Transmembrane', start=302, end=322), UniprotTopology(topology='Transmembrane...(truncated) | 5,240 | {} | 2023-08-25 21:44:45 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang._wang_process |
Not calling `pypath.inputs.wang._wang_process`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang.cui_interactions | 2023-08-25 21:45:58 | 2023-08-25 21:45:58 | 0.15 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/wang.py", line 139, in cui_interactions
raw = embo.embopress_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/embopress.py", line 96, in embopress_supplementary
fname = c.fname
AttributeError: 'Curl' object has no attribute 'fname'
|
{} | 2023-08-23 21:43:49 | |||
| ¶ | pypath.inputs.wang.hsn_interactions | 2023-08-25 21:45:58 | 2023-08-25 21:45:59 | 0.47 | list | [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) | 62,937 | {} | 2023-08-25 21:45:58 | |
| ¶ | pypath.inputs.wang.wang_annotations | 2023-08-25 21:45:59 | 2023-08-25 21:45:59 | 0.20 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/wang.py", line 262, in wang_annotations
data = func()
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/ca1.py", line 53, in ca1_interactions
path = science_input.science_download(url = url)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/science.py", line 102, in science_download
c_main.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 22:52:23 | |||
| ¶ | pypath.inputs.wang.wang_interactions | 2023-08-25 21:45:59 | 2023-08-25 21:46:00 | 0.55 | list | [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) | 62,937 | {} | 2023-08-25 21:45:59 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2023-08-25 21:46:00 | 2023-08-25 21:46:00 | 0.12 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/wojtowicz2020.py", line 79, in wojtowicz2020_interactions
for rec in wojtowicz2020_raw():
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/wojtowicz2020.py", line 37, in wojtowicz2020_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 22:52:24 | |||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2023-08-25 21:46:00 | 2023-08-25 21:46:00 | 0.08 |
Traceback (most recent call last):
File "/mnt/disk0/build/omnipath-build/status-report.py", line 847, in test_input
value = fun(*_args, **_kwargs)
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/wojtowicz2020.py", line 37, in wojtowicz2020_raw
path = cell_input.cell_supplementary(
File "/mnt/disk0/build/omnipath-build/pypath_inputs_status__20230825-182601/pypath_git/pypath/inputs/cell.py", line 128, in cell_supplementary
c_table.fileobj.close()
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2023-07-28 22:52:25 | |||
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2023-08-25 21:46:00 | 2023-08-25 21:46:01 | 1.03 | dict | {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM')}, 'Q12864': {Zhong2015Ann...(truncated) | 466 | {} | 2023-08-25 21:46:00 |
The OmniPath Team • Saez Lab • 2023-08-25