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 2022-09-16 17:34:43 and 2022-09-16 20:51:40; pypath version: 0.14.16 (from installed by poetry; b42c274 )
| Modules collected: | 153 |
|---|---|
| Modules failed to import: | 7 |
| Functions collected: | 481 |
| Functions run without error: | 320 |
| Functions returned empty value: | 13 |
| Functions skipped due to lack of arguments: | 121 |
| Functions run with error: | 40 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2022-09-16 17:34:44 | 2022-09-16 17:34:44 | 0.32 | 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 | {} | 2022-09-16 17:34:44 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2022-09-16 17:34:44 | 2022-09-16 17:34:45 | 0.47 | 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 | {} | 2022-09-16 17:34:44 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2022-09-16 17:34:45 | 2022-09-16 17:34:45 | 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 | {} | 2022-09-16 17:34:45 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2022-09-16 17:34:45 | 2022-09-16 17:36:53 | 127.25 | dict | {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) | 239 | {} | 2022-09-16 17:34:45 | |
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2022-09-16 17:36:53 | 2022-09-16 17:36:53 | 0.18 | 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 | {} | 2022-09-16 17:36:53 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2022-09-16 17:36:53 | 2022-09-16 17:36:55 | 1.85 | dict | {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) | 4,825 | {'size': -1} | 2022-09-16 17:36:53 | |
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2022-09-16 17:36:55 | 2022-09-16 17:40:37 | 222.07 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 196, in baccin2019_annotations
ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 137, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 84, in raw_to_uniprots
itertools.product(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 85, in <genexpr>
*(id_translate(comp) for comp in components)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 66, in id_translate
itertools.chain(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 67, in <genexpr>
homology_mod.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 1187, in translate
return manager.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 258, in translate
table = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 172, in which_table
self.load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 203, in load
self.tables[key] = self._load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 213, in _load
return ProteinHomology(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 485, in __init__
self.load(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 505, in load
self.load_ensembl(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 741, in load_ensembl
source_uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3314, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1735, in map_name
mapped_names = self._map_ensp(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2232, in _map_ensp
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 00:50:39 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2022-09-16 17:40:37 | 2022-09-16 17:40:44 | 6.88 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 137, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 84, in raw_to_uniprots
itertools.product(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 85, in <genexpr>
*(id_translate(comp) for comp in components)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 66, in id_translate
itertools.chain(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/baccin2019.py", line 67, in <genexpr>
homology_mod.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 1187, in translate
return manager.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 258, in translate
table = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 172, in which_table
self.load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 203, in load
self.tables[key] = self._load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 213, in _load
return ProteinHomology(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 485, in __init__
self.load(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 505, in load
self.load_ensembl(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 741, in load_ensembl
source_uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3314, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1735, in map_name
mapped_names = self._map_ensp(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2232, in _map_ensp
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:01:56 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2022-09-16 17:40:44 | 2022-09-16 17:40:44 | 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 | {} | 2022-09-16 17:40:44 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2022-09-16 17:40:44 | 2022-09-16 17:41:19 | 35.06 | 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 | {} | 2022-09-16 17:40:44 | |
| ¶ | pypath.inputs.biogrid.biogrid_all_interactions | 2022-09-16 17:41:19 | 2022-09-16 17:42:12 | 52.39 | 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) | 8,056 | {'size': 158} | 2022-09-16 17:41:19 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2022-09-16 17:42:12 | 2022-09-16 17:42:13 | 1.02 | 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) | 6,817 | {'size': 119} | 2022-09-16 17:42:12 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2022-09-16 17:42:13 | 2022-09-16 17:43:04 | 51.56 | 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) | 179,928 | {'size': 3255} | 2022-09-16 17:42:13 | |
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2022-09-16 17:43:05 | 2022-09-16 17:43:07 | 1.95 | list | [{'format': 'EXPRESSION', 'array': 'OneArray', 'description': None, 'vendor': 'PHALANX', 'type': 'OLIGO', 'label': 'PHALANX OneArray'}, {'format': 'EXPRESSION', 'array': 'CODELINK', 'description': None, 'vendor': 'CODELINK', 'type': 'OLIGO', 'label': 'CODELINK CODELINK'}, {'description': None, 'arra...(truncated) | 40 | {'size': 1} | 2022-09-16 17:43:05 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2022-09-16 17:43:07 | 2022-09-16 17:43:09 | 2.75 | list | [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) | 1,788 | {} | 2022-09-16 17:43:07 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2022-09-16 17:43:09 | 2022-09-16 17:43:11 | 1.85 | 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 | {} | 2022-09-16 17:43:09 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2022-09-16 17:43:11 | 2022-09-16 17:43:20 | 9.15 | 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 | {'fixed': True} | 2022-09-16 17:43:11 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2022-09-16 17:43:20 | 2022-09-16 17:43:20 | 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) | 287 | {'size': 3} | 2022-09-16 17:43:20 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2022-09-16 17:43:20 | 2022-09-16 17:43:21 | 0.14 | list | [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='P51532', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) | 2,306 | {'fixed': True} | 2022-09-16 17:43:20 | |
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2022-09-16 17:43:21 | 2022-09-16 17:43:23 | 2.40 | dict | {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) | 1,247 | {} | 2022-09-16 17:43:21 | |
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2022-09-16 17:43:23 | 2022-09-16 17:43:26 | 3.30 | dict | {'Q9Y4X3': {CellcallAnnotation(role='ligand')}, 'P51677': {CellcallAnnotation(role='receptor')}, 'Q9H1J7': {CellcallAnnotation(role='ligand')}, 'Q9NPG1': {CellcallAnnotation(role='receptor')}, 'Q8IZJ0': {CellcallAnnotation(role='ligand')}, 'Q8IU57': {CellcallAnnotation(role='receptor')}, 'P01133': {...(truncated) | 460 | {} | 2022-09-16 17:43:23 | |
| ¶ | pypath.inputs.cellcall.cellcall_download | 2022-09-16 17:43:26 | 2022-09-16 17:43:26 | 0.05 | list | [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) | 19,144 | {} | 2022-09-16 17:43:26 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2022-09-16 17:43:26 | 2022-09-16 17:43:28 | 1.41 | 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 | {} | 2022-09-16 17:43:26 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2022-09-16 17:43:28 | 2022-09-16 17:43:30 | 1.74 | list | [CellcallInteraction(ligand_uniprot='Q9Y4X3', receptor_uniprot='P51677', core=True), CellcallInteraction(ligand_uniprot='Q9H1J7', receptor_uniprot='Q9NPG1', core=True), CellcallInteraction(ligand_uniprot='Q8IZJ0', receptor_uniprot='Q8IU57', core=True), CellcallInteraction(ligand_uniprot='P01133', re...(truncated) | 797 | {} | 2022-09-16 17:43:28 | |
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2022-09-16 17:43:30 | 2022-09-16 17:43:31 | 0.93 | dict | {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='Receptor')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='ECM'), CellcellinteractionsAnnotation(mainclass='Ligand'), Cellcellinteractions...(truncated) | 3,425 | {} | 2022-09-16 17:43:30 | |
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2022-09-16 17:43:31 | 2022-09-16 17:43:31 | 0.00 | int | 9606 | 0 | {} | 2022-09-16 17:43:31 | |
| ¶ | 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 | 2022-09-16 17:43:31 | 2022-09-16 17:43:38 | 7.80 | 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='NODAL', category...(truncated) | 1,067 | {} | 2022-09-16 17:43:31 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2022-09-16 17:43:38 | 2022-09-16 17:43:44 | 5.58 | dict | {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'P41271', 'O75610', 'O00292', 'P12645', 'Q9H772', 'Q9H2X0', 'Q13253', 'O60565'}, 'BMP inhibition receptor': {'Q13145'...(truncated) | 31 | {} | 2022-09-16 17:43:38 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2022-09-16 17:43:44 | 2022-09-16 17:43:49 | 4.87 | 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 | {} | 2022-09-16 17:43:44 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2022-09-16 17:43:49 | 2022-09-16 17:43:54 | 4.80 | 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 | {} | 2022-09-16 17:43:49 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2022-09-16 17:43:54 | 2022-09-16 17:43:59 | 5.63 | 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 | {} | 2022-09-16 17:43:54 | |
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2022-09-16 17:43:59 | 2022-09-16 17:44:00 | 0.30 | 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 | {} | 2022-09-16 17:43:59 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2022-09-16 17:44:00 | 2022-09-16 17:44:00 | 0.78 | dict | {'P04141': {CellinkerAnnotation(role='ligand', location='Secreted', type='Cytokine-cytokine receptor interaction')}, 'Q99062': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor in...(truncated) | 1,921 | {} | 2022-09-16 17:44:00 | |
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2022-09-16 17:44:00 | 2022-09-16 17:44:01 | 0.69 | dict | {Complex: COMPLEX:O60353_O75581: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, Complex: COMPLEX:O14786_Q9HCM2: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotat...(truncated) | 134 | {} | 2022-09-16 17:44:00 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2022-09-16 17:44:01 | 2022-09-16 17:44:01 | 0.03 | 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 | {} | 2022-09-16 17:44:01 | |
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2022-09-16 17:44:01 | 2022-09-16 17:44:01 | 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 | {} | 2022-09-16 17:44:01 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2022-09-16 17:44:01 | 2022-09-16 17:44:02 | 0.69 | set | {CellinkerInteraction(ligand='P04141', receptor='Q99062', ligand_location='Secreted', receptor_location='Membrane', resources='HPMR', pmids='11091218;16720384', type='Cytokine-cytokine receptor interaction'), CellinkerInteraction(ligand='Q9BXY4', receptor='Q9HBX8', ligand_location='Secreted', recept...(truncated) | 3,812 | {} | 2022-09-16 17:44:01 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2022-09-16 17:44:02 | 2022-09-16 17:44:02 | 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 | {} | 2022-09-16 17:44:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2022-09-16 17:44:02 | 2022-09-16 17:44:03 | 0.70 | dict | {'P04141': {CellinkerAnnotation(role='ligand', location='Secreted', type='Cytokine-cytokine receptor interaction')}, 'Q99062': {CellinkerAnnotation(role='ligand', location='Membrane', type='Cell adhesion'), CellinkerAnnotation(role='receptor', location='Membrane', type='Cytokine-cytokine receptor in...(truncated) | 1,787 | {} | 2022-09-16 17:44:02 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2022-09-16 17:44:03 | 2022-09-16 17:44:03 | 0.18 | set | {CellinkerInteraction(ligand='60961', receptor='P29275', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='15822182;7746802;14662005', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='5957', receptor='Q99572', ligand_location=None, receptor_location=...(truncated) | 314 | {} | 2022-09-16 17:44:03 | |
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2022-09-16 17:44:03 | 2022-09-16 17:44:03 | 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 | {} | 2022-09-16 17:44:03 | |
| ¶ | 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 | 2022-09-16 17:44:03 | 2022-09-16 17:44:03 | 0.22 | dict | {Complex 12oxoLeukotrieneB4_byPTGR1: COMPLEX:Q14914: CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('chebi:27814',), transmembrane=False, integrin=False), Complex 22Hydroxycholesterol_byCYP11A1: COMPLEX:P05108: CellPhoneDBAnnotation(receptor...(truncated) | 256 | {'size': 144} | 2022-09-16 17:44:03 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2022-09-16 17:44:03 | 2022-09-16 17:44:03 | 0.02 | dict | {'COMPLEX:Q14914': Complex 12oxoLeukotrieneB4_byPTGR1: COMPLEX:Q14914, 'COMPLEX:P05108': Complex 22Hydroxycholesterol_byCYP11A1: COMPLEX:P05108, 'COMPLEX:P08684': Complex 22Hydroxycholesterol_byCYP3A4: COMPLEX:P08684, 'COMPLEX:Q9Y4D2': Complex 2arachidonoylglycerol_byDAGLA: COMPLEX:Q9Y4D2, 'COMPLEX:...(truncated) | 256 | {'size': 144} | 2022-09-16 17:44:03 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2022-09-16 17:44:03 | 2022-09-16 17:44:04 | 0.56 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/cellphonedb.py", line 298, in cellphonedb_interactions
_partner_a = _cellphonedb_get_entity(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/cellphonedb.py", line 243, in _cellphonedb_get_entity
name = _cellphonedb_hla(name)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/cellphonedb.py", line 182, in _cellphonedb_hla
if uniprot.startswith('HLA') and '-' not in uniprot:
AttributeError: 'NoneType' object has no attribute 'startswith'
|
{'broke': True} | 2022-05-21 01:19:46 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2022-09-16 17:44:04 | 2022-09-16 17:44:04 | 0.10 | tuple | ({Complex FZD4_LRP6: COMPLEX:O75581_Q9ULV1, 'P12034', Complex LeukotrieneE4_byDPEP3: COMPLEX:Q9H4B8, 'Q969E3', 'Q16661', 'P58166', 'P23582', 'Q9NTN9', 'Q9BZZ2', 'P47992', 'P15248', Complex glyco_Lutropin: COMPLEX:P01215_P01229, 'P20396', 'Q4G0M1', 'Q9Y6F9', 'P78423', 'Q12860', 'P06850', Complex inte...(truncated) | 2 | {} | 2022-09-16 17:44:04 | |
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2022-09-16 17:44:04 | 2022-09-16 17:44:04 | 0.07 | dict | {'A4D1S0': CellPhoneDBAnnotation(receptor=True, receptor_class=('klr',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), 'A5X5Y0': CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), transme...(truncated) | 1,279 | {'size': 301} | 2022-09-16 17:44:04 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2022-09-16 17:44:04 | 2022-09-16 17:46:04 | 120.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltalkdb.py", line 184, in celltalkdb_annotations
for rec in celltalkdb_download(organism = ncbi_tax_id):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltalkdb.py", line 90, in celltalkdb_download
soup = bs4.BeautifulSoup(c_init.fileobj, 'html.parser')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:19:46 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2022-09-16 17:46:04 | 2022-09-16 17:46:14 | 10.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltalkdb.py", line 90, in celltalkdb_download
soup = bs4.BeautifulSoup(c_init.fileobj, 'html.parser')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:19:54 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2022-09-16 17:46:14 | 2022-09-16 17:46:24 | 10.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltalkdb.py", line 148, in celltalkdb_interactions
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltalkdb.py", line 148, in <listcomp>
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltalkdb.py", line 90, in celltalkdb_download
soup = bs4.BeautifulSoup(c_init.fileobj, 'html.parser')
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:19:54 | |||
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2022-09-16 17:46:24 | 2022-09-16 17:46:24 | 0.22 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/celltypist.py", line 64, in celltypist_annotations
xls = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:19:54 | |||
| ¶ | pypath.inputs.compleat.compleat_complexes | 2022-09-16 17:46:24 | 2022-09-16 17:46:29 | 4.74 | 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 | {} | 2022-09-16 17:46:24 | |
| ¶ | pypath.inputs.compleat.compleat_raw | 2022-09-16 17:46:29 | 2022-09-16 17:46:29 | 0.05 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2022-09-16 17:46:29 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2022-09-16 17:46:29 | 2022-09-16 17:47:25 | 55.98 | dict | {'COMPLEX:P84022_Q13485_Q15796': Complex SMAD2-SMAD3-SMAD4 complex: COMPLEX:P84022_Q13485_Q15796, 'COMPLEX:P16220_P18848': Complex bZIP transcription factor complex, ATF4-CREB1: COMPLEX:P16220_P18848, 'COMPLEX:P18846_P18848': Complex bZIP transcription factor complex, ATF1-ATF4: COMPLEX:P18846_P1884...(truncated) | 1,364 | {'size': 103} | 2022-09-16 17:46:29 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2022-09-16 17:47:25 | 2022-09-16 17:48:29 | 64.19 | 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) | 590,678 | {'size': -400} | 2022-09-16 17:47:25 | |
| ¶ | pypath.inputs.comppi.comppi_locations | 2022-09-16 17:48:29 | 2022-09-16 17:49:37 | 67.80 | dict | {'Q8TES7': {ComppiLocation(location='nucleus', score=0.7), ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='nucleus', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation(l...(truncated) | 18,214 | {'size': 5} | 2022-09-16 17:48:29 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2022-09-16 17:49:37 | 2022-09-16 17:49:38 | 0.51 | 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 | {} | 2022-09-16 17:49:37 | |
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2022-09-16 17:49:38 | 2022-09-16 17:49:38 | 0.02 | list | [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) | 2,293 | {} | 2022-09-16 17:49:38 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2022-09-16 17:49:38 | 2022-09-16 17:49:38 | 0.43 | 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 | {'fixed': True} | 2022-09-16 17:49:38 | |
| ¶ | pypath.inputs.cpad.cpad_annotations | 2022-09-16 17:49:38 | 2022-09-16 17:49:43 | 5.26 | dict | {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'MIMAT0000431'...(truncated) | 1,038 | {} | 2022-09-16 17:49:38 | |
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2022-09-16 17:49:43 | 2022-09-16 17:49:43 | 0.05 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='TGF-beta signaling pathway', cancer='Glioma', pathway_category='TGF-beta signaling pathway', effect_on_cancer='Activating', effect_on_cancer_outcome='regulate glioma invasion'), CpadPathwayCancer(pathway='AMPK signaling pathway', cancer='Glioma', pathway_categ...(truncated) | 2 | {} | 2022-09-16 17:49:43 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2022-09-16 17:49:43 | 2022-09-16 17:49:43 | 0.04 | list | [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) | 4,709 | {} | 2022-09-16 17:49:43 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2022-09-16 17:49:43 | 2022-09-16 17:49:47 | 3.77 | 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 | {} | 2022-09-16 17:49:43 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2022-09-16 17:49:47 | 2022-09-16 17:49:51 | 3.09 | 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 | {} | 2022-09-16 17:49:47 | |
| ¶ | pypath.inputs.cspa.cspa_annotations | 2022-09-16 17:49:51 | 2022-09-16 17:49:52 | 0.72 | dict | {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) | 1,446 | {} | 2022-09-16 17:49:51 | |
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2022-09-16 17:49:52 | 2022-09-16 17:49:52 | 0.73 | dict | {'A1A5B4': {CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='ZL55', valu...(truncated) | 1,407 | {} | 2022-09-16 17:49:52 | |
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2022-09-16 17:49:52 | 2022-09-16 17:49:53 | 0.53 | dict | {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.11804, 'A8MVW0': None, 'A8MVW5': None, 'A8MWY0': None, 'A8TX70': None, 'O00116': None, 'O00206': 15.9843,...(truncated) | 47 | {} | 2022-09-16 17:49:52 | |
| ¶ | pypath.inputs.cytosig.cytosig_annotations | 2022-09-16 17:49:53 | 2022-09-16 17:50:13 | 20.19 | dict | {'Q9NPC4': {CytosigAnnotation(cytokine='P12643', score=-0.0185015764811096), CytosigAnnotation(cytokine='P48061', score=0.0046073476872248), CytosigAnnotation(cytokine='P05231', score=0.0084669266516721), CytosigAnnotation(cytokine='P01137', score=-0.0123877715497178), CytosigAnnotation(cytokine='P3...(truncated) | 4,890 | {'size': 1} | 2022-09-16 17:49:53 | |
| ¶ | pypath.inputs.cytosig.cytosig_df | 2022-09-16 17:50:13 | 2022-09-16 17:50:13 | 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 | {} | 2022-09-16 17:50:13 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2022-09-16 17:50:13 | 2022-09-16 17:50:16 | 2.45 | 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 | {} | 2022-09-16 17:50:13 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2022-09-16 17:50:16 | 2022-09-16 17:50:21 | 4.25 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/dbptm.py", line 102, in dbptm_enzyme_substrate_old
for k, data in iteritems(extra):
File "/home/omnipath/.cache/pypoetry/virtualenvs/pypath-omnipath-Z-uUCylT-py3.8/lib/python3.8/site-packages/future/utils/__init__.py", line 311, in iteritems
func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2022-01-07 23:35:25 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2022-09-16 17:50:21 | 2022-09-16 17:50:22 | 1.38 | 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 | {} | 2022-09-16 17:50:21 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2022-09-16 17:50:22 | 2022-09-16 17:50:23 | 0.92 | list | [] | 0 | {} | 2022-09-16 17:50:22 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2022-09-16 17:50:23 | 2022-09-16 17:50:23 | 0.14 | 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 | {} | 2022-09-16 17:50:23 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2022-09-16 17:50:23 | 2022-09-16 17:50:23 | 0.10 | 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 | {} | 2022-09-16 17:50:23 | |
| ¶ | pypath.inputs.depod.depod_interactions | 2022-09-16 17:50:23 | 2022-09-16 17:50:23 | 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 | {} | 2022-09-16 17:50:23 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2022-09-16 17:50:23 | 2022-09-16 17:50:26 | 3.07 | 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) | 10,495 | {'size': 2} | 2022-09-16 17:50:23 | |
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2022-09-16 17:50:26 | 2022-09-16 17:51:30 | 63.65 | set | {'Q02161', 'Q8NGI4', 'Q969E3', 'O14980', 'Q9H2J7', 'Q6IF63', 'Q9Y5R2', 'Q9H6B4', 'Q9NY61', 'P42772', 'Q6DJT9', 'P59796', 'O15455', 'Q8NH57', 'Q8N697', 'P51617', 'Q9NYG8', 'Q5K4L6', 'Q9H3S3', 'Q8NGK6', 'O75746', 'Q9BTN0', 'P63127', 'Q8TCT9', 'P18283', 'O43908', 'O75871', 'P49662', 'Q8TBK2', 'O00213',...(truncated) | 5,906 | {'size': 6} | 2022-09-16 17:50:26 | |
| ¶ | pypath.inputs.dip.dip_interactions | 2022-09-16 17:51:30 | 2022-09-16 17:51:30 | 0.26 | list | [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) | 2,283 | {} | 2022-09-16 17:51:30 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.disgenet.disgenet_annotations | 2022-09-16 17:51:30 | 2022-09-16 17:51:36 | 5.42 | dict | {'P04217': {DisGeNetAnnotation(disease='Hepatomegaly', type='phenotype', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',)), DisGeNetAnnotation(disease='Schizophrenia', type='disease', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',))}, 'P0102...(truncated) | 9,206 | {'size': 3} | 2022-09-16 17:51:30 | |
| ¶ | pypath.inputs.domino.domino_ddi | 2022-09-16 17:51:36 | 2022-09-16 17:51:42 | 6.52 | list | [<pypath.internals.intera.DomainDomain object at 0x7f6d7bf86040>, <pypath.internals.intera.DomainDomain object at 0x7f6d7bf866a0>, <pypath.internals.intera.DomainDomain object at 0x7f6d7bf86070>, <pypath.internals.intera.DomainDomain object at 0x7f6d44a27070>, <pypath.internals.intera.DomainDomain o...(truncated) | 1,294 | {} | 2022-09-16 17:51:36 | |
| ¶ | pypath.inputs.domino.domino_enzsub | 2022-09-16 17:51:42 | 2022-09-16 17:51:43 | 0.96 | dict | {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f6d5d2b3970>, <pypath.internals.intera.DomainDomain object at 0x7f6d5d2b3df0>, <pypath.internals.intera.DomainDomain object at 0x7f6d5d304910>, <pypath.internals.intera.DomainDomain object at 0x7f6d4446c6d0>, <pypath.internals.intera.Domain...(truncated) | 2 | {} | 2022-09-16 17:51:42 | |
| ¶ | pypath.inputs.domino.domino_interactions | 2022-09-16 17:51:43 | 2022-09-16 17:51:44 | 0.37 | 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 | {} | 2022-09-16 17:51:43 | |
| ¶ | pypath.inputs.domino.get_domino | 2022-09-16 17:51:44 | 2022-09-16 17:51:44 | 0.35 | 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 | {} | 2022-09-16 17:51:44 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2022-09-16 17:51:44 | 2022-09-16 17:51:52 | 7.72 | 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 | {} | 2022-09-16 17:51:44 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2022-09-16 17:51:52 | 2022-09-16 17:52:05 | 12.58 | 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 | {} | 2022-09-16 17:51:52 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2022-09-16 17:52:05 | 2022-09-16 17:52:05 | 0.55 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2022-01-07 23:37:25 | |||
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2022-09-16 17:52:05 | 2022-09-16 17:52:05 | 0.12 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2022-01-07 23:37:25 | |||
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2022-09-16 17:52:05 | 2022-09-16 17:52:07 | 1.69 | 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 | {} | 2022-09-16 17:52:05 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2022-09-16 17:52:07 | 2022-09-16 17:52:07 | 0.33 | 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 | {} | 2022-09-16 17:52:07 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2022-09-16 17:52:07 | 2022-09-16 17:52:08 | 1.14 | 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 | {} | 2022-09-16 17:52:07 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2022-09-16 17:52:08 | 2022-09-16 17:52:21 | 12.82 | 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 | {} | 2022-09-16 17:52:08 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2022-09-16 17:52:21 | 2022-09-16 17:52:21 | 0.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
|
{} | 2022-01-07 23:37:25 | |||
| ¶ | pypath.inputs.ebi.ebi_rest |
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.elm.elm_classes | 2022-09-16 17:52:21 | 2022-09-16 17:52:21 | 0.07 | dict | {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) | 317 | {} | 2022-09-16 17:52:21 | |
| ¶ | pypath.inputs.elm.elm_domains | 2022-09-16 17:52:21 | 2022-09-16 17:52:22 | 0.50 | 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 | {'size': 602} | 2022-09-16 17:52:21 | |
| ¶ | pypath.inputs.elm.elm_instances | 2022-09-16 17:52:22 | 2022-09-16 17:52:22 | 0.23 | list | [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) | 3,934 | {} | 2022-09-16 17:52:22 | |
| ¶ | pypath.inputs.elm.elm_interactions | 2022-09-16 17:52:22 | 2022-09-16 17:52:22 | 0.12 | list | [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) | 2,394 | {} | 2022-09-16 17:52:22 | |
| ¶ | 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 | 2022-09-16 17:52:22 | 2022-09-16 17:52:31 | 8.32 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 163, in embrace_annotations
for rec in embrace_translated(organism = organism):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 93, in embrace_translated
ligands = _embrace_id_translation(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 72, in _embrace_id_translation
uniprots = homology.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 1187, in translate
return manager.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 258, in translate
table = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 172, in which_table
self.load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 203, in load
self.tables[key] = self._load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 213, in _load
return ProteinHomology(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 485, in __init__
self.load(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 505, in load
self.load_ensembl(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 741, in load_ensembl
source_uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3314, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1735, in map_name
mapped_names = self._map_ensp(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2232, in _map_ensp
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:28:49 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2022-09-16 17:52:31 | 2022-09-16 17:52:37 | 6.35 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 129, in embrace_interactions
for rec in embrace_translated(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 93, in embrace_translated
ligands = _embrace_id_translation(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 72, in _embrace_id_translation
uniprots = homology.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 1187, in translate
return manager.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 258, in translate
table = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 172, in which_table
self.load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 203, in load
self.tables[key] = self._load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 213, in _load
return ProteinHomology(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 485, in __init__
self.load(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 505, in load
self.load_ensembl(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 741, in load_ensembl
source_uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3314, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1735, in map_name
mapped_names = self._map_ensp(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2232, in _map_ensp
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:28:51 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2022-09-16 17:52:37 | 2022-09-16 17:52:37 | 0.30 | list | [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) | 1,710 | {} | 2022-09-16 17:52:37 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2022-09-16 17:52:37 | 2022-09-16 17:52:44 | 6.47 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 93, in embrace_translated
ligands = _embrace_id_translation(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embrace.py", line 72, in _embrace_id_translation
uniprots = homology.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 1187, in translate
return manager.translate(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 258, in translate
table = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 172, in which_table
self.load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 203, in load
self.tables[key] = self._load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 213, in _load
return ProteinHomology(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 485, in __init__
self.load(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 505, in load
self.load_ensembl(source)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/homology.py", line 741, in load_ensembl
source_uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3314, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1735, in map_name
mapped_names = self._map_ensp(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2232, in _map_ensp
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 01:28:51 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2022-09-16 17:52:44 | 2022-09-16 17:52:45 | 0.74 | 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 | {} | 2022-09-16 17:52:44 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2022-09-16 17:52:45 | 2022-09-16 17:52:45 | 0.69 | list | [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) | 314 | {'size': 3} | 2022-09-16 17:52:45 | |
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2022-09-16 17:52:45 | 2022-09-16 17:52:55 | 9.28 | 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 | {} | 2022-09-16 17:52:45 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2022-09-16 17:52:55 | 2022-09-16 17:52:55 | 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 | {} | 2022-09-16 17:52:55 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2022-09-16 17:52:55 | 2022-09-16 17:53:48 | 53.07 | 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 | {} | 2022-09-16 17:52:55 | |
| ¶ | 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 | 2022-09-16 17:53:48 | 2022-09-16 17:57:12 | 204.04 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 884, in get_go_quick
terms[l[5]][l[1]].add(l[4])
KeyError: 'GO ASPECT'
|
{'broke': True} | 2022-05-21 01:29:58 | |||
| ¶ | pypath.inputs.go.get_goslim | 2022-09-16 17:57:12 | 2022-09-16 17:57:12 | 0.77 | 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) | 144 | {'size': -1} | 2022-09-16 17:57:12 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2022-09-16 17:57:12 | 2022-09-16 18:15:17 | 1,084.52 | dict | {'C': {'GO:1990040': {('GO:1990039', 'is_a')}, 'GO:0030992': {('GO:0030990', 'part_of'), ('GO:0032991', 'is_a')}, 'GO:0030991': {('GO:0030990', 'part_of'), ('GO:0032991', 'is_a')}, 'GO:1990176': {('GO:0098797', 'is_a'), ('GO:1990060', 'part_of')}, 'GO:0097566': {('GO:0042995', 'part_of'), ('GO:01101...(truncated) | 3 | {} | 2022-09-16 17:57:12 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2022-09-16 18:15:17 | 2022-09-16 18:15:21 | 4.06 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 152, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2022-01-07 23:57:44 | |||
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2022-09-16 18:15:21 | 2022-09-16 18:15:25 | 3.66 | dict | {'C': {'GO:1990040': {('GO:1990039', 'is_a')}, 'GO:0030992': {('GO:0030990', 'part_of'), ('GO:0032991', 'is_a')}, 'GO:0030991': {('GO:0030990', 'part_of'), ('GO:0032991', 'is_a')}, 'GO:1990176': {('GO:0098797', 'is_a'), ('GO:1990060', 'part_of')}, 'GO:0097566': {('GO:0042995', 'part_of'), ('GO:01101...(truncated) | 3 | {} | 2022-09-16 18:15:21 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2022-09-16 18:15:25 | 2022-09-16 18:15:27 | 2.31 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2022-09-16 18:15:25 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2022-09-16 18:15:27 | 2022-09-16 18:15:28 | 1.06 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H8': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6H9': {'GO:0005886', 'GO:0019814', 'GO:0005615'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) | 3 | {} | 2022-09-16 18:15:27 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2022-09-16 18:15:28 | 2022-09-16 18:15:32 | 3.37 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 799, in go_annotations_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2022-01-07 23:57:55 | |||
| ¶ | pypath.inputs.go.go_annotations_solr | 2022-09-16 18:15:32 | 2022-09-16 18:15:33 | 0.94 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 685, in go_annotations_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2022-01-07 23:57:58 | |||
| ¶ | pypath.inputs.go.go_annotations_uniprot | 2022-09-16 18:15:33 | 2022-09-16 18:15:39 | 6.48 | dict | {'Entry': ['Gene ontology IDs'], 'P0DP02': ['GO:0003823', 'GO:0006910', 'GO:0006911', 'GO:0006958', 'GO:0009897', 'GO:0034987', 'GO:0042571', 'GO:0042742', 'GO:0045087', 'GO:0050853', 'GO:0050871'], 'Q9H293': ['GO:0002437', 'GO:0005125', 'GO:0005576', 'GO:0005615', 'GO:0009620', 'GO:0009624', 'GO:00...(truncated) | 20,399 | {'size': 22} | 2022-09-16 18:15:33 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2022-09-16 18:15:39 | 2022-09-16 18:15:43 | 3.57 | dict | {'C': defaultdict(<class 'set'>, {'GO:1990039': {('GO:1990040', 'is_a')}, 'GO:0030990': {('GO:0030992', 'part_of'), ('GO:0030991', 'part_of')}, 'GO:1990060': {('GO:1990176', 'part_of')}, 'GO:0042995': {('GO:0097566', 'part_of'), ('GO:0097589', 'is_a'), ('GO:0097564', 'part_of'), ('GO:0009289', 'is_a...(truncated) | 3 | {} | 2022-09-16 18:15:39 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2022-09-16 18:15:43 | 2022-09-16 18:15:46 | 3.39 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 230, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 152, in go_ancestors_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2022-01-07 23:58:11 | |||
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2022-09-16 18:15:46 | 2022-09-16 18:15:50 | 3.56 | dict | {'C': defaultdict(<class 'set'>, {'GO:1990039': {('GO:1990040', 'is_a')}, 'GO:0030990': {('GO:0030992', 'part_of'), ('GO:0030991', 'part_of')}, 'GO:1990060': {('GO:1990176', 'part_of')}, 'GO:0042995': {('GO:0097566', 'part_of'), ('GO:0097589', 'is_a'), ('GO:0097564', 'part_of'), ('GO:0009289', 'is_a...(truncated) | 3 | {} | 2022-09-16 18:15:46 | |
| ¶ | 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 | 2022-09-16 18:15:50 | 2022-09-16 18:15:53 | 2.88 | dict | {'C': {'GO:1990027': 'S bouton', 'GO:1990040': 'sub-surface cisterna', 'GO:0030998': 'linear element', 'GO:1990037': 'Lewy body core', 'GO:1990038': 'Lewy body corona', 'GO:1990039': 'hypolemmal cisterna', 'GO:0030990': 'intraciliary transport particle', 'GO:0030992': 'intraciliary transport particl...(truncated) | 3 | {} | 2022-09-16 18:15:50 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2022-09-16 18:15:53 | 2022-09-16 18:15:56 | 3.36 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 525, in go_terms_goose
for l in c.result:
TypeError: 'NoneType' object is not iterable
|
{} | 2022-01-07 23:58:20 | |||
| ¶ | pypath.inputs.go.go_terms_quickgo | 2022-09-16 18:15:56 | 2022-09-16 18:15:59 | 2.88 | dict | {'C': {'GO:1990027': 'S bouton', 'GO:1990040': 'sub-surface cisterna', 'GO:0030998': 'linear element', 'GO:1990037': 'Lewy body core', 'GO:1990038': 'Lewy body corona', 'GO:1990039': 'hypolemmal cisterna', 'GO:0030990': 'intraciliary transport particle', 'GO:0030992': 'intraciliary transport particl...(truncated) | 3 | {} | 2022-09-16 18:15:56 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2022-09-16 18:15:59 | 2022-09-16 18:16:00 | 0.60 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/go.py", line 383, in go_terms_solr
parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2022-01-07 23:58:26 | |||
| ¶ | pypath.inputs.gpcrdb.gpcrdb_annotations | 2022-09-16 18:16:00 | 2022-09-16 18:16:00 | 0.33 | 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 | {'size': 22} | 2022-09-16 18:16:00 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2022-09-16 18:16:00 | 2022-09-16 18:16:01 | 1.07 | tuple | ({'_background': {'type': 'string', '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.'}, 'bgcolor': {'type': 'colorcolorList', 'def...(truncated) | 3 | {} | 2022-09-16 18:16:00 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2022-09-16 18:16:01 | 2022-09-16 18:16:03 | 1.75 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/guide2pharma.py", line 115, in guide2pharma_download
data = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/guide2pharma.py", line 118, in <listcomp>
get_taxid(d['target_species']) == organism and
KeyError: 'target_species'
|
{'broke': True} | 2022-05-21 01:47:30 | |||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.havugimana.get_havugimana | 2022-09-16 18:16:03 | 2022-09-16 18:16:05 | 1.99 | list | [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) | 622 | {} | 2022-09-16 18:16:03 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2022-09-16 18:16:05 | 2022-09-16 18:16:05 | 0.03 | dict | {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) | 622 | {} | 2022-09-16 18:16:05 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2022-09-16 18:16:05 | 2022-09-16 18:16:10 | 5.23 | 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) | 15,041 | {'size': 23} | 2022-09-16 18:16:05 | |
| ¶ | pypath.inputs.hippie.hippie_interactions | 2022-09-16 18:16:10 | 2022-09-16 18:16:38 | 28.34 | list | [HippieInteraction(id_a='Q8IXM3', id_b='Q9H9J2', score=0.87, methods=None, references=('22939629', '28514442', '33961781'), sources=None, organisms=None), HippieInteraction(id_a='O95905', id_b='Q9UHR6', score=0.87, methods=None, references=('28514442', '28561026', '33961781'), sources=None, organism...(truncated) | 102,255 | {'size': -1} | 2022-09-16 18:16:10 | |
| ¶ | pypath.inputs.homologene.get_homologene | 2022-09-16 18:16:39 | 2022-09-16 18:16:39 | 0.04 | list | ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) | 275,237 | {} | 2022-09-16 18:16:39 | |
| ¶ | 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 | 2022-09-16 18:16:39 | 2022-09-16 18:16:39 | 0.02 | 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 | {} | 2022-09-16 18:16:39 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2022-09-16 18:16:39 | 2022-09-16 18:16:39 | 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 | {} | 2022-09-16 18:16:39 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2022-09-16 18:16:39 | 2022-09-16 18:16:39 | 0.00 | dict | {} | 0 | {} | 2022-09-16 18:16:39 | |
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2022-09-16 18:16:39 | 2022-09-16 18:16:39 | 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 | {} | 2022-09-16 18:16:39 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2022-09-16 18:16:39 | 2022-09-16 18:16:42 | 3.32 | 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 | {} | 2022-09-16 18:16:39 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2022-09-16 18:16:42 | 2022-09-16 18:16:44 | 1.54 | 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 | {} | 2022-09-16 18:16:42 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2022-09-16 18:16:44 | 2022-09-16 18:16:45 | 1.53 | 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 | {} | 2022-09-16 18:16:44 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2022-09-16 18:16:45 | 2022-09-16 18:16:47 | 1.29 | 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 | {} | 2022-09-16 18:16:45 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2022-09-16 18:16:47 | 2022-09-16 18:16:49 | 2.65 | 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 | {} | 2022-09-16 18:16:47 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2022-09-16 18:16:49 | 2022-09-16 18:16:51 | 1.58 | dict | {'Q9NRG9': {HumancellmapAnnotation(localization='peroxisome', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) | 4,371 | {} | 2022-09-16 18:16:49 | |
| ¶ | pypath.inputs.humap.humap2_complexes | 2022-09-16 18:16:51 | 2022-09-16 18:16:53 | 2.50 | 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) | 6,942 | {} | 2022-09-16 18:16:51 | |
| ¶ | pypath.inputs.humap.humap_complexes | 2022-09-16 18:16:53 | 2022-09-16 18:16:55 | 1.67 | 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) | 4,499 | {} | 2022-09-16 18:16:53 | |
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2022-09-16 18:16:55 | 2022-09-16 18:17:03 | 8.45 | 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) | 5,632 | {'size': -44} | 2022-09-16 18:16:55 | |
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2022-09-16 18:17:03 | 2022-09-16 18:17:17 | 13.59 | 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) | 46,730 | {'size': -168} | 2022-09-16 18:17:03 | |
| ¶ | pypath.inputs.huri.hi_iii_old | 2022-09-16 18:17:17 | 2022-09-16 18:17:17 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/huri.py", line 95, in hi_iii_old
url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
|
{} | 2022-01-08 00:02:33 | |||
| ¶ | pypath.inputs.huri.hi_union_interactions | 2022-09-16 18:17:17 | 2022-09-16 18:17:58 | 40.46 | 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) | 229,780 | {'size': -1224} | 2022-09-16 18:17:17 | |
| ¶ | pypath.inputs.huri.huri_interactions | 2022-09-16 18:17:58 | 2022-09-16 18:18:26 | 28.77 | 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) | 166,693 | {'size': -945} | 2022-09-16 18:17:58 | |
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2022-09-16 18:18:26 | 2022-09-16 18:18:27 | 0.93 | 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 | {} | 2022-09-16 18:18:26 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2022-09-16 18:18:27 | 2022-09-16 18:18:29 | 1.30 | 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 | {} | 2022-09-16 18:18:27 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2022-09-16 18:18:29 | 2022-09-16 18:18:31 | 2.62 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/huri.py", line 265, in lit_bm_interactions
uniprots_a = mapping.map_name(row[0], 'ensembl', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3314, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1777, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 02:06:00 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2022-09-16 18:18:31 | 2022-09-16 18:18:34 | 2.73 | list | [['14', '6293', 'AAMP', 'VPS52', '1'], ['14', '8553', 'AAMP', 'BHLHE40', '1'], ['14', '64782', 'AAMP', 'AEN', '2'], ['15', '4188', 'AANAT', 'MDFI', '1'], ['15', '8553', 'AANAT', 'BHLHE40', '1'], ['28', '65983', 'ABO', 'GRAMD3', '2'], ['28', '84283', 'ABO', 'TMEM79', '1'], ['39', '39', 'ACAT2', 'ACAT...(truncated) | 13,944 | {} | 2022-09-16 18:18:31 | |
| ¶ | 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 | 2022-09-16 18:18:34 | 2022-09-16 18:18:36 | 2.25 | list | [HuriInteraction(uniprot_a='P07196', uniprot_b='Q9BQQ3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='O94989', uniprot_b='Q53EZ4', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q8NHQ1', uniprot_b='Q9H7H0', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) | 2,823 | {'size': -6} | 2022-09-16 18:18:34 | |
| ¶ | pypath.inputs.huri.yu2011_interactions | 2022-09-16 18:18:36 | 2022-09-16 18:18:38 | 2.08 | 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 | {'size': -55} | 2022-09-16 18:18:36 | |
| ¶ | pypath.inputs.i3d.get_i3d | 2022-09-16 18:18:38 | 2022-09-16 18:18:44 | 6.25 | 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 | {} | 2022-09-16 18:18:38 | |
| ¶ | 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 | 2022-09-16 18:18:45 | 2022-09-16 18:18:45 | 0.42 | 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=None, subfamily=None, classif...(truncated) | 853 | {'size': 165} | 2022-09-16 18:18:45 | |
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2022-09-16 18:18:45 | 2022-09-16 18:18:45 | 0.15 | 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 | {'size': 14} | 2022-09-16 18:18:45 | |
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2022-09-16 18:18:45 | 2022-09-16 18:18:45 | 0.15 | 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 | {'size': 280} | 2022-09-16 18:18:45 | |
| ¶ | 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 | 2022-09-16 18:18:45 | 2022-09-16 18:18:47 | 1.57 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/imweb.py", line 77, in _get_imweb
hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
File "/usr/lib/python3.8/json/__init__.py", line 341, in loads
raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not NoneType
|
{} | 2022-05-16 17:24:43 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2022-09-16 18:18:47 | 2022-09-16 18:18:47 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/imweb.py", line 110, in get_imweb
c0.perform()
pycurl.error: (3, '')
|
{} | 2022-05-16 17:24:45 | |||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2022-09-16 18:18:47 | 2022-09-16 18:18:47 | 0.57 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/imweb.py", line 143, in get_imweb_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.8/json/__init__.py", line 357, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.8/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)
|
{} | 2022-05-16 17:24:45 | |||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2022-09-16 18:18:47 | 2022-09-16 18:18:49 | 2.01 | 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 | {} | 2022-09-16 18:18:47 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2022-09-16 18:18:50 | 2022-09-16 18:18:50 | 0.62 | NoneType | None | 0 | {'size': -11470, 'type': {'previous': 'list', 'current': 'NoneType'}} | 2022-09-16 18:18:50 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2022-09-16 18:18:50 | 2022-09-16 18:18:51 | 0.41 | NoneType | None | 0 | {'size': -11620, 'type': {'previous': 'dict', 'current': 'NoneType'}} | 2022-09-16 18:18:50 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2022-09-16 18:18:51 | 2022-09-16 18:19:38 | 47.41 | 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) | 71,286 | {'size': 324} | 2022-09-16 18:18:51 | |
| ¶ | pypath.inputs.integrins.get_integrins | 2022-09-16 18:19:38 | 2022-09-16 18:19:39 | 1.19 | set | {'Q13683', 'Q13349', 'Q13797', 'P56199', 'P05106', 'P38570', 'P53708', 'P05107', 'P08514', 'P18564', 'P26006', 'O75578', 'P08648', 'P16144', 'P17301', 'P26010', 'P20701', 'P11215', 'Q9UKX5', 'P26012', 'P23229', 'P06756', 'P18084', 'P05556', 'P20702'} | 25 | {} | 2022-09-16 18:19:38 | |
| ¶ | pypath.inputs.interpro.interpro_annotations | 2022-09-16 18:19:39 | 2022-09-16 18:20:36 | 56.13 | defaultdict | defaultdict(<class 'set'>, {'P14210': {InterproAnnotation(interpro_acc='IPR013806', organism='9606', locations=('115-208', '210-293', '302-386', '381-477')), InterproAnnotation(interpro_acc='IPR018056', organism='9606', locations=('176-189', '259-271', '353-365', '439-452')), InterproAnnotation(inte...(truncated) | 16,879 | {'first': True} | 2022-09-16 18:19:39 | |
| ¶ | pypath.inputs.interpro.interpro_entries | 2022-09-16 18:20:36 | 2022-09-16 18:20:36 | 0.18 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/interpro.py", line 70, in interpro_entries
path = curl.Curl(
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'first': True} | 2022-09-16 18:20:36 | |||
| ¶ | pypath.inputs.interpro.interpro_xrefs |
Not calling `pypath.inputs.interpro.interpro_xrefs`, not enough arguments. |
{'first': True} | never | ||||||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2022-09-16 18:20:36 | 2022-09-16 18:20:49 | 12.88 | 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) | 482 | {'size': 2} | 2022-09-16 18:20:36 | |
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2022-09-16 18:20:49 | 2022-09-16 18:20:49 | 0.28 | dict | {'IPI00807623': {'A0A183'}, 'IPI00396341': {'A0AUZ9'}, 'IPI00884975': {'A0AUZ9'}, 'IPI00884987': {'A0AUZ9'}, 'IPI00885003': {'A0AUZ9'}, 'IPI00855723': {'A0AV02'}, 'IPI00867607': {'A0AV02'}, 'IPI00793608': {'A0AV02'}, 'IPI00867726': {'A0AV02'}, 'IPI00867740': {'A0AV02'}, 'IPI00169342': {'A0AV96'}, 'I...(truncated) | 51,106 | {} | 2022-09-16 18:20:49 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2022-09-16 18:20:49 | 2022-09-16 18:21:08 | 19.11 | list | [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['19955365']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetyl...(truncated) | 16,686 | {} | 2022-09-16 18:20:49 | |
| ¶ | pypath.inputs.italk.italk_annotations | 2022-09-16 18:21:08 | 2022-09-16 18:21:09 | 0.88 | 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 | {} | 2022-09-16 18:21:08 | |
| ¶ | pypath.inputs.italk.italk_interactions | 2022-09-16 18:21:09 | 2022-09-16 18:21:09 | 0.25 | 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 | {} | 2022-09-16 18:21:09 | |
| ¶ | pypath.inputs.italk.italk_raw | 2022-09-16 18:21:09 | 2022-09-16 18:21:09 | 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 | {} | 2022-09-16 18:21:09 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2022-09-16 18:21:09 | 2022-09-16 18:21:15 | 5.45 | 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 | {'size': 56} | 2022-09-16 18:21:09 | |
| ¶ | pypath.inputs.kea.kea_interactions | 2022-09-16 18:21:15 | 2022-09-16 18:21:18 | 3.25 | 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 | {'size': 56} | 2022-09-16 18:21:15 | |
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2022-09-16 18:21:18 | 2022-09-16 18:25:33 | 254.55 | 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) | 14,413 | {'size': -6} | 2022-09-16 18:21:18 | |
| ¶ | pypath.inputs.kegg.kegg_medicus | 2022-09-16 18:25:33 | 2022-09-16 18:25:46 | 13.14 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 557, in kegg_medicus
set(get_interactions(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 422, in get_interactions
itype, effect = i_code[connections[i + 1]]
KeyError: '=='
|
{'broke': True} | 2022-05-21 02:20:14 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2022-09-16 18:25:46 | 2022-09-16 18:25:46 | 0.35 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 681, in kegg_medicus_complexes
cplexes = kegg_medicus_interactions(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 645, in kegg_medicus_interactions
for rec in kegg_medicus(max_entity_variations = max_entity_variations):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 557, in kegg_medicus
set(get_interactions(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 422, in get_interactions
itype, effect = i_code[connections[i + 1]]
KeyError: '=='
|
{'broke': True} | 2022-05-21 02:20:27 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2022-09-16 18:25:46 | 2022-09-16 18:25:46 | 0.12 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 645, in kegg_medicus_interactions
for rec in kegg_medicus(max_entity_variations = max_entity_variations):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 557, in kegg_medicus
set(get_interactions(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kegg.py", line 422, in get_interactions
itype, effect = i_code[connections[i + 1]]
KeyError: '=='
|
{'broke': True} | 2022-05-21 02:20:29 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2022-09-16 18:25:46 | 2022-09-16 18:25:54 | 7.26 | dict | {'P21333': {KeggPathway(pathway='Proteoglycans in cancer'), KeggPathway(pathway='MAPK signaling pathway')}, 'Q9Y243': {KeggPathway(pathway='Phospholipase D signaling pathway'), KeggPathway(pathway='Apoptosis'), KeggPathway(pathway='JAK-STAT signaling pathway'), KeggPathway(pathway='Estrogen signalin...(truncated) | 2,576 | {'size': 1} | 2022-09-16 18:25:46 | |
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2022-09-16 18:25:54 | 2022-09-16 18:25:54 | 0.51 | dict | {'A8K7J7': {KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPathway(pathway='Metabolic pathways'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathwa...(truncated) | 813 | {} | 2022-09-16 18:25:54 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2022-09-16 18:25:54 | 2022-09-16 18:26:01 | 7.23 | tuple | ({'MAPK signaling pathway': {'P21333', 'Q9Y243', 'Q07889', 'O95257', 'P01106', 'P62993', 'P04049', 'P17252', 'O75608', 'P25445', 'Q9NYL2', 'P51617', 'P45983', 'Q9HBH9', 'P35638', 'P10398', 'P15056', 'Q12933', 'P16949', 'P52564', 'Q12968', 'O60359', 'P11831', 'P61244', 'P08571', 'O00622', 'Q9UHA4', '...(truncated) | 2 | {} | 2022-09-16 18:25:54 | |
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2022-09-16 18:26:01 | 2022-09-16 18:26:02 | 0.43 | 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 | {'size': 1} | 2022-09-16 18:26:01 | |
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2022-09-16 18:26:02 | 2022-09-16 18:26:02 | 0.48 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/kirouac2010.py", line 92, in kirouac2010_interactions
tbl = embo.embopress_supplementary(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embopress.py", line 99, in embopress_supplementary
fname = c.fname
AttributeError: 'Curl' object has no attribute 'fname'
|
{'broke': True} | 2022-05-21 02:20:47 | |||
| ¶ | pypath.inputs.lambert2018.lambert2018_annotations | 2022-09-16 18:26:02 | 2022-09-16 18:26:07 | 4.70 | dict | {'P05549': {Lambert2018Annotation(ensg='ENSG00000137203', genesymbol='TFAP2A', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', binding_domain='AP-2', tf_disagree=False, binding_disagree=False, binding1='1 Monomer or homomultimer', binding2='1 Monomer or homomultime...(truncated) | 2,760 | {'size': 3} | 2022-09-16 18:26:02 | |
| ¶ | pypath.inputs.lambert2018.lambert2018_s1_raw | 2022-09-16 18:26:07 | 2022-09-16 18:26:09 | 2.53 | list | [Lambert2018Raw(id='ENSG00000137203', name='TFAP2A', dbd='AP-2', is_tf=True, tf_assessment='Known motif', binding_mode='1 Monomer or homomultimer', motif_status='High-throughput in vitro', notes=None, comments=None, committee_notes=None, mtw_notes=None, trh_notes=None, sl_notes=None, aj_notes=None, ...(truncated) | 2,765 | {} | 2022-09-16 18:26:07 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2022-09-16 18:26:10 | 2022-09-16 18:26:10 | 0.34 | 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 | {} | 2022-09-16 18:26:10 | |
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2022-09-16 18:26:10 | 2022-09-16 18:26:10 | 0.31 | list | [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) | 63,438 | {} | 2022-09-16 18:26:10 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2022-09-16 18:26:10 | 2022-09-16 18:26:21 | 10.75 | 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 | {} | 2022-09-16 18:26:10 | |
| ¶ | pypath.inputs.li2012.li2012_dmi | 2022-09-16 18:26:21 | 2022-09-16 18:26:33 | 11.60 | list | [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) | 593 | {} | 2022-09-16 18:26:21 | |
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2022-09-16 18:26:33 | 2022-09-16 18:26:33 | 0.03 | list | [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) | 349 | {} | 2022-09-16 18:26:33 | |
| ¶ | pypath.inputs.li2012.li2012_interactions | 2022-09-16 18:26:33 | 2022-09-16 18:26:33 | 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 | {} | 2022-09-16 18:26:33 | |
| ¶ | pypath.inputs.lincs.lincs_compounds | 2022-09-16 18:26:33 | 2022-09-16 18:26:36 | 3.78 | 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 | {} | 2022-09-16 18:26:33 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2022-09-16 18:26:36 | 2022-09-16 18:26:38 | 1.04 | list | [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) | 1,170 | {} | 2022-09-16 18:26:36 | |
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2022-09-16 18:26:38 | 2022-09-16 18:26:38 | 0.76 | list | [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) | 1,170 | {} | 2022-09-16 18:26:38 | |
| ¶ | pypath.inputs.lmpid.load_lmpid | 2022-09-16 18:26:38 | 2022-09-16 18:26:39 | 0.77 | list | [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) | 1,170 | {} | 2022-09-16 18:26:38 | |
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2022-09-16 18:26:39 | 2022-09-16 18:26:39 | 0.18 | 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 | {} | 2022-09-16 18:26:39 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2022-09-16 18:26:39 | 2022-09-16 18:26:40 | 0.41 | list | [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism='Paramecium tetraurelia', pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism='Loris tardigradus', pmid='17175535'), LncrnadbInteraction(lncrna='G22'...(truncated) | 773 | {} | 2022-09-16 18:26:39 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2022-09-16 18:26:40 | 2022-09-16 18:27:17 | 37.39 | dict | {'P27824': {LocateAnnotation(source='UniProt/SPTrEMBL', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='endoplasmic reticulum', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='plasma membrane', cls='typeI...(truncated) | 9,494 | {'size': -2} | 2022-09-16 18:26:40 | |
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2022-09-16 18:27:17 | 2022-09-16 18:27:18 | 0.72 | dict | {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPRD', 'Reactome'), references=('11421580',)), LrdbAnnotation(role='receptor', cell_type=None, so...(truncated) | 1,536 | {} | 2022-09-16 18:27:17 | |
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2022-09-16 18:27:18 | 2022-09-16 18:27:18 | 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 | {} | 2022-09-16 18:27:18 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2022-09-16 18:27:18 | 2022-09-16 18:27:18 | 0.26 | 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 | {} | 2022-09-16 18:27:18 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2022-09-16 18:27:18 | 2022-09-16 18:27:35 | 16.52 | set | {'Col6a3', 'C1QC', 'Lgals4', 'C1qtnf7', 'Sftpa1', 'ANXA6', 'P4ha2', 'Gldn', 'Col5a1', 'CSTA', 'COL21A1', 'CBLN1', 'HSPG2', 'PLXNA1', 'SFTPD', 'LAMA4', 'ITLN2', 'Lamb2', 'ST14', 'Dmbt1', 'Lman1', 'LOXL3', 'COL4A4', 'Lgals3', 'Plod1', 'FGF2', 'COL27A1', 'Thbs1', 'SPON1', 'ANXA13', 'MMP12', 'Emid1', 'L...(truncated) | 744 | {} | 2022-09-16 18:27:18 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2022-09-16 18:27:35 | 2022-09-16 18:27:35 | 0.79 | dict | {'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) | 1,065 | {'size': 1} | 2022-09-16 18:27:35 | |
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2022-09-16 18:27:35 | 2022-09-16 18:27:41 | 5.43 | dict | {'O94777': {MatrixdbAnnotation(mainclass='membrane')}, 'Q8NGI4': {MatrixdbAnnotation(mainclass='membrane')}, 'O14980': {MatrixdbAnnotation(mainclass='membrane')}, 'Q5BJH2': {MatrixdbAnnotation(mainclass='membrane')}, 'P58753': {MatrixdbAnnotation(mainclass='membrane')}, 'Q6IF63': {MatrixdbAnnotation...(truncated) | 10,096 | {'size': -1} | 2022-09-16 18:27:35 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2022-09-16 18:27:41 | 2022-09-16 18:27:41 | 0.08 | set | {'Q9Y6C2', 'P24347', 'P23352', 'Q8N0V4', 'Q9Y5R2', 'Q6AZY7', 'Q08380', 'O15455', 'P49747', 'Q02509', 'Q9Y6F9', 'Q92832', 'Q7Z5L7', 'Q5GFL6', 'Q96SY0', 'Q9UBV4', 'P56703', 'Q15113', 'P02462', 'Q96JA1', 'Q12836', 'P21754', 'Q9BXN1', 'P07478', 'Q3B7J2', 'Q8N119', 'Q5K4E3', 'P10124', 'Q8WX77', 'O94769',...(truncated) | 483 | {} | 2022-09-16 18:27:41 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2022-09-16 18:27:41 | 2022-09-16 18:27:41 | 0.14 | 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 | {} | 2022-09-16 18:27:41 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2022-09-16 18:27:41 | 2022-09-16 18:27:45 | 4.23 | set | {'O94777', 'Q8NGI4', 'O14980', 'Q5BJH2', 'P58753', 'Q6IF63', 'A2RU67', 'Q9Y5R2', 'Q96CM4', 'Q14699', 'Q8N697', 'Q99795', 'Q6IEE8', 'Q9NTI2', 'Q5K4L6', 'Q8NGK6', 'O75746', 'P46940', 'Q9NRJ1', 'Q9BTN0', 'Q8TCT9', 'O43908', 'Q71RS6', 'P49662', 'P54710', 'Q7Z444', 'Q96NU0', 'Q96RV3', 'Q92765', 'P02538',...(truncated) | 8,239 | {'size': -1} | 2022-09-16 18:27:41 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2022-09-16 18:27:45 | 2022-09-16 18:27:46 | 0.42 | set | {'A0A0C4DH41', 'P33763', 'Q969E3', 'Q5T655', 'Q9Y5R2', 'Q9NRI6', 'Q9Y5Z4', 'P59796', 'O15455', 'P0DOX7', 'Q5EBL8', 'P68871', 'P15309', 'P78325', 'Q16553', 'O95352', 'P02745', 'O15496', 'Q6UWW8', 'Q9H7B7', 'Q5T742', 'P02814', 'Q8WUM4', 'P27352', 'Q96PB7', 'P49662', 'Q8NB37', 'Q8NES8', 'P04085', 'Q151...(truncated) | 2,923 | {} | 2022-09-16 18:27:45 | |
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2022-09-16 18:27:46 | 2022-09-16 18:27:50 | 4.12 | set | {'Q13797', 'Q6UWL6', 'Q9Y624', 'P08575', 'Q92729', 'Q9NPY3', 'P78325', 'Q9BYD3', 'Q12860', 'Q8TEW0', 'Q13449', 'Q9UQS6', 'P05107', 'O43854', 'Q9Y5B2', 'Q15223', 'O00548', 'Q8TD84', 'Q8WWQ8', 'P13612', 'P20702', 'P50895', 'O95500', 'Q9Y4C0', 'P18827', 'P53708', 'P43121', 'P28827', 'Q6MZK0', 'Q9BRX2',...(truncated) | 103 | {} | 2022-09-16 18:27:46 | |
| ¶ | pypath.inputs.membranome.membranome_annotations | 2022-09-16 18:27:50 | 2022-09-16 18:28:29 | 39.37 | 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) | 2,385 | {} | 2022-09-16 18:27:50 | |
| ¶ | pypath.inputs.mimp.get_kinase_class | 2022-09-16 18:28:29 | 2022-09-16 18:28:30 | 0.12 | 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 | {} | 2022-09-16 18:28:29 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2022-09-16 18:28:30 | 2022-09-16 18:28:33 | 3.76 | 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 | {'size': -2885} | 2022-09-16 18:28:30 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2022-09-16 18:28:33 | 2022-09-16 18:28:34 | 0.47 | 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 | {'size': -2885} | 2022-09-16 18:28:33 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.16 | 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 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.08 | tuple | ({'MIMAT0000062': {'hsa-let-7a', 'hsa-let-7a-5p'}, 'MIMAT0000063': {'hsa-let-7b', 'hsa-let-7b-5p'}, 'MIMAT0000064': {'hsa-let-7c-5p', 'hsa-let-7c'}, 'MIMAT0000065': {'hsa-let-7d-5p', 'hsa-let-7d'}, 'MIMAT0000066': {'hsa-let-7e', 'hsa-let-7e-5p'}, 'MIMAT0000067': {'hsa-let-7f-5p', 'hsa-let-7f'}, 'MIM...(truncated) | 2 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.08 | list | [('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000068', 'MI...(truncated) | 3,027 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.06 | list | [('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000064', 'hsa-let-7c-5p'), ('MIMAT0000064', 'hsa-let-7c'), ('MIMAT0000065', 'hsa-let-7d-5p'), ('MIMAT0000065', 'hsa-let-7d'), ('MIMAT0000066', 'hsa-let-7e'),...(truncated) | 3,487 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.08 | list | ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) | 3,027 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.06 | list | [('MI0000060', 'hsa-let-7a-1L'), ('MI0000060', 'hsa-let-7a-1'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,173 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2022-09-16 18:28:34 | 2022-09-16 18:28:34 | 0.08 | list | ['MI0000060', 'MI0000061', 'MI0000062', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000068', 'MI0000067', 'MI0000069', 'MI0000115', 'MI0000070', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000074', 'MI0000075', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000080', ...(truncated) | 3,027 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2022-09-16 18:28:34 | 2022-09-16 18:28:35 | 0.14 | list | [('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT0010195'), ('hsa-let-7a-2L', 'MIMAT...(truncated) | 3,361 | {} | 2022-09-16 18:28:34 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2022-09-16 18:28:35 | 2022-09-16 18:28:35 | 0.30 | 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 | {} | 2022-09-16 18:28:35 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2022-09-16 18:28:35 | 2022-09-16 18:34:35 | 360.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/mirecords.py", line 53, in mirecords_interactions
tbl = inputs_common.read_xls(c.fileobj.name)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 02:29:59 | |||
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2022-09-16 18:34:35 | 2022-09-16 18:34:38 | 3.02 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/mirtarbase.py", line 44, in mirtarbase_interactions
result.extend(_mirtarbase_interactions('curated'))
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/mirtarbase.py", line 79, in _mirtarbase_interactions
tbl = inputs_common.read_xls(c.fileobj.name)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 02:30:03 | |||
| ¶ | 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 | 2022-09-16 18:34:38 | 2022-09-16 18:34:38 | 0.25 | list | [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) | 777 | {'fixed': True} | 2022-09-16 18:34:38 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2022-09-16 18:34:38 | 2022-09-16 18:34:58 | 19.39 | dict | {} | 0 | {} | 2022-09-16 18:34:38 | |
| ¶ | pypath.inputs.msigdb.msigdb_download | 2022-09-16 18:34:58 | 2022-09-16 18:34:59 | 1.07 | dict | {} | 0 | {} | 2022-09-16 18:34:58 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2022-09-16 18:34:59 | 2022-09-16 18:35:18 | 19.31 | dict | {('hallmark', 'h.all'): {}, ('positional', 'c1.all'): {}, ('chemical_and_genetic_perturbations', 'c2.cgp'): {}, ('biocarta_pathways', 'c2.cp.biocarta'): {}, ('kegg_pathways', 'c2.cp.kegg'): {}, ('pid_pathways', 'c2.cp.pid'): {}, ('reactome_pathways', 'c2.cp.reactome'): {}, ('wikipathways', 'c2.cp.wi...(truncated) | 18 | {} | 2022-09-16 18:34:59 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2022-09-16 18:35:18 | 2022-09-16 18:35:18 | 0.34 | 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 | {} | 2022-09-16 18:35:18 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2022-09-16 18:35:18 | 2022-09-16 18:35:18 | 0.07 | list | [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) | 2,171 | {'fixed': True} | 2022-09-16 18:35:18 | |
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2022-09-16 18:35:18 | 2022-09-16 18:35:19 | 0.12 | 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 | {} | 2022-09-16 18:35:18 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2022-09-16 18:35:19 | 2022-09-16 18:35:19 | 0.11 | 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 | {} | 2022-09-16 18:35:19 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2022-09-16 18:35:19 | 2022-09-16 18:35:20 | 1.65 | 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 | {} | 2022-09-16 18:35:19 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2022-09-16 18:35:20 | 2022-09-16 18:35:20 | 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 | {} | 2022-09-16 18:35:20 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2022-09-16 18:35:20 | 2022-09-16 18:35:49 | 28.52 | 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='Androgen receptor ...(truncated) | 1,870 | {'size': 1} | 2022-09-16 18:35:20 | |
| ¶ | pypath.inputs.ontology.listof_ontologies | 2022-09-16 18:35:49 | 2022-09-16 18:35:50 | 0.87 | dict | {'so': 'Sequence types and features ontology', 'snomed': 'SNOMED CT (International Edition)', 'zeco': 'Zebrafish Experimental Conditions Ontology', 'ado': "Alzheimer's Disease Ontology (ADO)", 'tgma': 'Mosquito gross anatomy ontology', 'swo': 'SWO (The Software Ontology)', 'zp': 'Zebrafish Phenotype...(truncated) | 277 | {'size': 2} | 2022-09-16 18:35:49 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opm.opm_annotations | 2022-09-16 18:35:50 | 2022-09-16 18:36:02 | 12.38 | dict | {'O14745': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P59666': {OpmAnnotation(membrane='Secreted', family='Vertebrate defensin', transmembrane=False)},...(truncated) | 405 | {} | 2022-09-16 18:35:50 | |
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2022-09-16 18:36:02 | 2022-09-16 18:37:56 | 113.38 | list | [OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='ESR1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', target='MACROD1', pmid='15691879'), OregannoInteraction(tf='SP1', ta...(truncated) | 5,903 | {'fixed': True} | 2022-09-16 18:36:02 | |
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2022-09-16 18:37:56 | 2022-09-16 18:38:07 | 11.91 | list | [('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493', 'NCBI', 'N/A', 'N/A', 'N/A', 'rs3087243', '12724780', 'N/A', 'hg18', '1', 'chr2', '204447164', '204447164'), ('OREG0000000', 'Homo sapiens', 'POSITIVE OUTCOME', 'REGULATORY POLYMORPHISM', 'CTLA4', '1493'...(truncated) | 5,688,970 | {'fixed': True} | 2022-09-16 18:37:56 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2022-09-16 18:38:07 | 2022-09-16 18:38:12 | 4.96 | 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) | 4,808 | {'size': 1} | 2022-09-16 18:38:07 | |
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2022-09-16 18:38:12 | 2022-09-16 18:38:13 | 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 | {} | 2022-09-16 18:38:12 | |
| ¶ | 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 | 2022-09-16 18:38:13 | 2022-09-16 18:38:28 | 15.62 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ACE2', resource='BIND'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ADAM10', resource='BIND'), PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='ADAM17'...(truncated) | 1,261,865 | {} | 2022-09-16 18:38:13 | |
| ¶ | 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 | 2022-09-16 18:38:29 | 2022-09-16 18:38:29 | 0.26 | 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 | {} | 2022-09-16 18:38:29 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2022-09-16 18:38:29 | 2022-09-16 18:38:35 | 5.99 | 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 | {} | 2022-09-16 18:38:29 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2022-09-16 18:38:38 | 2022-09-16 18:38:44 | 6.65 | 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) | 40,839 | {'size': 811} | 2022-09-16 18:38:38 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2022-09-16 18:38:44 | 2022-09-16 18:38:50 | 5.27 | tuple | ({'P02185': {('6f19', 'X-ray', 1.9), ('5yce', 'X-ray', 0.77), ('5ut7', 'X-ray', 1.85), ('1vxh', 'X-ray', 1.7), ('1iop', 'X-ray', 1.9), ('1mcy', 'X-ray', 1.7), ('6f17', 'X-ray', 1.45), ('7cen', 'X-ray', 2.35), ('109m', 'X-ray', 1.83), ('3e4n', 'X-ray', 1.21), ('2myc', 'X-ray', 1.8), ('2zss', 'X-ray',...(truncated) | 2 | {} | 2022-09-16 18:38:44 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2022-09-16 18:38:50 | 2022-09-16 18:38:51 | 0.78 | 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 | {} | 2022-09-16 18:38:50 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2022-09-16 18:38:51 | 2022-09-16 18:49:46 | 655.74 | 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 | {} | 2022-09-16 18:38:51 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2022-09-16 18:49:46 | 2022-09-16 18:49:47 | 0.89 | 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 | {} | 2022-09-16 18:49:46 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2022-09-16 18:49:47 | 2022-09-16 18:49:50 | 2.64 | 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 | {} | 2022-09-16 18:49:47 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2022-09-16 18:49:50 | 2022-09-16 18:54:42 | 291.14 | tuple | ({}, {}) | 2 | {} | 2022-09-16 18:49:50 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2022-09-16 18:54:42 | 2022-09-16 18:58:53 | 250.87 | tuple | ({'Q16322': {'PF02214', 'PF00520'}, 'Q9NUP9': {'PF02828', 'PF00595'}, 'Q96GW9': {'PF19303', 'PF09334'}, 'Q9NYW1': {'PF05296'}, 'Q14525': {'PF00038'}, 'Q8N7U9': set(), 'Q9H461': {'PF01392', 'PF01534'}, 'A0A1B0GVH7': set(), 'Q93099': {'PF04209'}, 'P08217': {'PF00089'}, 'Q9UQV4': {'PF01299'}, 'Q8N3J3':...(truncated) | 2 | {} | 2022-09-16 18:54:42 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2022-09-16 18:58:53 | 2022-09-16 18:58:53 | 0.34 | 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 | {} | 2022-09-16 18:58:53 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2022-09-16 18:58:53 | 2022-09-16 18:58:59 | 5.65 | dict | {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) | 264 | {} | 2022-09-16 18:58:53 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2022-09-16 18:58:59 | 2022-09-16 18:59:01 | 2.05 | 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 | {} | 2022-09-16 18:58:59 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2022-09-16 18:59:01 | 2022-09-16 18:59:01 | 0.49 | 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 | {} | 2022-09-16 18:59:01 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2022-09-16 18:59:01 | 2022-09-16 18:59:01 | 0.22 | 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 | {} | 2022-09-16 18:59:01 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2022-09-16 18:59:01 | 2022-09-16 18:59:03 | 1.39 | 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 | {} | 2022-09-16 18:59:01 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 0.02 | list | [['MAPK3', 'DUSP1'], ['NEK4', 'POGZ'], ['TBK1', 'IRF3'], ['VRK3', 'EZH1'], ['PRKACA', 'HLCS'], ['CSK', 'YES1'], ['CSNK2A1', 'EIF2B5'], ['PIM1', 'HLCS'], ['TGFBR2', 'PRMT8'], ['PTK2B', 'TGFB1I1'], ['STK3', 'EIF4ENIF1'], ['AKT1', 'ZRANB2'], ['PRKCA', 'EP300'], ['SIK1', 'DDEF2'], ['CAMK2D', 'CTTN'], ['...(truncated) | 1,821 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 0.23 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 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 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 0.02 | 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 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 0.37 | 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 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 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 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2022-09-16 18:59:03 | 2022-09-16 18:59:03 | 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) | 9,041 | {} | 2022-09-16 18:59:03 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2022-09-16 18:59:04 | 2022-09-16 18:59:04 | 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 | {} | 2022-09-16 18:59:04 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2022-09-16 18:59:04 | 2022-09-16 18:59:04 | 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 | {} | 2022-09-16 18:59:04 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2022-09-16 18:59:04 | 2022-09-16 18:59:04 | 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 | {} | 2022-09-16 18:59:04 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2022-09-16 18:59:04 | 2022-09-16 18:59:09 | 5.07 | 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 | {} | 2022-09-16 18:59:04 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2022-09-16 18:59:09 | 2022-09-16 18:59:36 | 26.52 | 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 | {} | 2022-09-16 18:59:09 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2022-09-16 18:59:36 | 2022-09-16 18:59:37 | 0.52 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'phosphorylation', 'protein degradation', 'intracellular localization'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,435 | {} | 2022-09-16 18:59:36 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2022-09-16 18:59:37 | 2022-09-16 19:01:56 | 139.70 | dict | {'P41181': {('K', 270, 'ubiquitination'): {'induces': set(), 'disrupts': set(), 'pmids': {'24876223', '21148409', '21209006', '28052875'}, 'isoforms': {1}, 'process': {''}, 'function': {'phosphorylation', 'protein degradation', 'intracellular localization', 'ubiquitination', 'protein stabilization'}...(truncated) | 3,619 | {} | 2022-09-16 18:59:37 | |
| ¶ | 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 | 2022-09-16 19:01:56 | 2022-09-16 19:02:39 | 42.63 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | 0 | {} | 2022-09-16 19:01:56 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2022-09-16 19:02:39 | 2022-09-16 19:02:39 | 0.39 | 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) | 319,792 | {'size': 439} | 2022-09-16 19:02:39 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2022-09-16 19:02:40 | 2022-09-16 19:02:55 | 15.63 | dict | {'P35250': {ProgenyAnnotation(pathway='Hypoxia', weight=-2.049501418649251, p_value=0.0007040310639538167), ProgenyAnnotation(pathway='TGFb', weight=-0.430508102546081, p_value=0.6304595613186617), ProgenyAnnotation(pathway='Trail', weight=-0.8006773132589663, p_value=0.6240861307828072), ProgenyAnn...(truncated) | 18,601 | {'size': 3} | 2022-09-16 19:02:40 | |
| ¶ | pypath.inputs.progeny.progeny_raw | 2022-09-16 19:02:56 | 2022-09-16 19:02:57 | 1.69 | 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 | {} | 2022-09-16 19:02:56 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2022-09-16 19:02:57 | 2022-09-16 19:04:13 | 75.26 | 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 | {} | 2022-09-16 19:02:57 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2022-09-16 19:04:14 | 2022-09-16 19:06:40 | 145.63 | dict | {'O43657': {ProtainatlasAnnotation(organ='adipose tissue', tissue='adipocytes', 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='cerebral cortex', tiss...(truncated) | 19,391 | {'size': 18} | 2022-09-16 19:04:14 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2022-09-16 19:06:42 | 2022-09-16 19:06:44 | 2.47 | dict | {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) | 2,591 | {} | 2022-09-16 19:06:42 | |
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2022-09-16 19:06:44 | 2022-09-16 19:06:45 | 0.97 | dict | {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Nuclear bodies', status='Uncertain'), ProteinatlasSubcellularAnnotation(location='Microtubules', status='Uncertain')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellular...(truncated) | 6,823 | {'size': 2} | 2022-09-16 19:06:44 | |
| ¶ | pypath.inputs.proteins.variants | 2022-09-16 19:06:45 | 2022-09-16 19:24:40 | 1,074.92 | 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) | 45,429 | {'size': 262} | 2022-09-16 19:06:45 | |
| ¶ | pypath.inputs.protmapper.get_protmapper | 2022-09-16 19:24:41 | 2022-09-16 19:24:45 | 4.78 | 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 | {} | 2022-09-16 19:24:41 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2022-09-16 19:24:46 | 2022-09-16 19:24:46 | 0.61 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'25545367', '24357804', '24727247', '25728676', '22304920'}, 'substrate': 'P15336', 'databases': {'SIGNOR', 'REACH', 'Sparser', 'PhosphoSite'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'24727247', '23708658'}, ...(truncated) | 22,139 | {} | 2022-09-16 19:24:46 | |
| ¶ | 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 | 2022-09-16 19:24:47 | 2022-09-16 19:24:47 | 0.51 | 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 | {} | 2022-09-16 19:24:47 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2022-09-16 19:24:47 | 2022-09-16 19:24:56 | 9.04 | dict | {'P04217': {RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='LocTree3', tmh=0, note=None, long_note=None), Ramilo...(truncated) | 18,860 | {'size': -1} | 2022-09-16 19:24:47 | |
| ¶ | pypath.inputs.rdata._patch_rdata | 2022-09-16 19:24:56 | 2022-09-16 19:24:56 | 0.00 | NoneType | None | 0 | {} | 2022-09-16 19:24:56 | |
| ¶ | 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 | 2022-09-16 19:24:56 | 2022-09-16 19:25:12 | 15.69 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/reaction.py", line 986, in _reactome_reactions
for i in sp.find('bqbiol:haspart').find_all('rdf:li'):
AttributeError: 'NoneType' object has no attribute 'find_all'
|
{} | 2022-01-08 00:48:01 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2022-09-16 19:25:12 | 2022-09-16 19:25:14 | 2.04 | tuple | ({}, {}, {}) | 3 | {} | 2022-09-16 19:25:12 | |
| ¶ | 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 | 2022-09-16 19:25:14 | 2022-09-16 19:25:16 | 2.29 | 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 | {} | 2022-09-16 19:25:14 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2022-09-16 19:25:16 | 2022-09-16 19:25:16 | 0.20 | 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 | {} | 2022-09-16 19:25:16 | |
| ¶ | 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 | 2022-09-16 19:25:16 | 2022-09-16 19:27:36 | 139.81 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 859, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/reaction.py", line 1187, in get_reactions
rea.load_all()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/pyreact.py", line 1304, in load_all
self.load_pid()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/pyreact.py", line 1159, in load_pid
parser.process()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/pyreact.py", line 251, in process
self.open_biopax()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/pyreact.py", line 295, in open_biopax
self.opener = curl.FileOpener(self.biopax, **opener_args)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/share/curl.py", line 585, in __init__
if type(file_param) in common.char_types else file_param.name
AttributeError: 'NoneType' object has no attribute 'name'
|
{} | 2022-01-08 00:48:07 | |||
| ¶ | pypath.inputs.reaction.get_soup |
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.panther_biopax | 2022-09-16 19:27:36 | 2022-09-16 19:27:36 | 0.18 | dict | {'BioPAX/Fructose_galactose_metabolism.owl': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/B_cell_activation.owl': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_s...(truncated) | 178 | {} | 2022-09-16 19:27:36 | |
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2022-09-16 19:27:36 | 2022-09-16 19:27:38 | 1.67 | NoneType | None | 0 | {} | 2022-09-16 19:27:36 | |
| ¶ | 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 | 2022-09-16 19:27:38 | 2022-09-16 19:28:16 | 37.81 | TextIOWrapper | <_io.TextIOWrapper name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/cache/reactome_biopax_Homo_sapiens.owl' mode='r' encoding='UTF-8'> | 0 | {'fixed': True} | 2022-09-16 19:27:38 | |
| ¶ | pypath.inputs.reaction.reactome_bs | 2022-09-16 19:28:16 | 2022-09-16 19:34:56 | 399.61 | list | [('R-HSA-1059683', <?xml version='1.0' encoding='utf-8' standalone='no'?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 81 on 6/9/22, 8:40 PM using JSBML version 1.5...(truncated) | 2,585 | {'size': 5} | 2022-09-16 19:28:16 | |
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2022-09-16 19:35:13 | 2022-09-16 19:35:15 | 2.03 | dict | {'R-HSA-1059683.sbml': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-17340...(truncated) | 2,585 | {'size': 5} | 2022-09-16 19:35:13 | |
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2022-09-16 19:35:15 | 2022-09-16 19:35:16 | 1.02 | 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 | {'size': 1} | 2022-09-16 19:35:15 | |
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2022-09-16 19:35:16 | 2022-09-16 19:35:16 | 0.19 | set | {Complex: COMPLEX:P01374_Q06643, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:P01215_P01229, Complex: COMPLEX:P01215_P0DN86, Complex: COMPLEX:P05111_P08476, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:P01215_P01222, Complex: COMPLEX:P01215_P01225, Comp...(truncated) | 17 | {} | 2022-09-16 19:35:16 | |
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2022-09-16 19:35:16 | 2022-09-16 19:59:31 | 1,455.25 | list | [ScconnectInteraction(ligand_id='ML355', target_id='P18054', ligand_organism=None, target_organism=9606, ligand_type='small_molecule', target_type='protein', effect='Inhibition', references='24393039'), ScconnectInteraction(ligand_id='PKUMDL_MH_1001', target_id='P16050', ligand_organism=None, target...(truncated) | 20,434 | {} | 2022-09-16 19:35:16 | |
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signalink.signalink_annotations | 2022-09-16 19:59:31 | 2022-09-16 19:59:33 | 1.67 | dict | {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathw...(truncated) | 2 | {} | 2022-09-16 19:59:31 | |
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2022-09-16 19:59:33 | 2022-09-16 19:59:34 | 0.83 | dict | {'P43403': {SignalinkFunction(function='Mediator'), SignalinkFunction(function='Scaffold')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) | 783 | {'size': -1} | 2022-09-16 19:59:33 | |
| ¶ | pypath.inputs.signalink.signalink_interactions | 2022-09-16 19:59:34 | 2022-09-16 19:59:34 | 0.40 | 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 | {} | 2022-09-16 19:59:34 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2022-09-16 19:59:34 | 2022-09-16 19:59:35 | 0.82 | dict | {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(pathway='JAK/STAT'), SignalinkPathway(pathway='Innate i...(truncated) | 835 | {'size': -1} | 2022-09-16 19:59:34 | |
| ¶ | pypath.inputs.signor.signor_complexes | 2022-09-16 19:59:35 | 2022-09-16 19:59:35 | 0.37 | 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) | 3,244 | {'size': 26} | 2022-09-16 19:59:35 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2022-09-16 19:59:35 | 2022-09-16 19:59:37 | 1.89 | list | [{'typ': 'methylation', 'resnum': 5, 'instance': 'KQTARKST', 'substrate': 'P68431', 'start': -2, 'end': 12, 'kinase': Complex MLL2 complex: COMPLEX:O14686_O15047_P61964_Q15291_Q9C005_Q9UBL3_Q9UPS6, 'resaa': 'K', 'motif': 'KQTARKST', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'...(truncated) | 10,120 | {'size': 116} | 2022-09-16 19:59:35 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2022-09-16 19:59:37 | 2022-09-16 19:59:38 | 0.41 | list | [SignorInteraction(source='CHEBI:33216', target='P03372', source_isoform=None, target_isoform=None, source_type='chemical', target_type='protein', effect='up-regulates activity', mechanism='chemical activation', ncbi_tax_id='-1', pubmeds='31995776', direct=True, ptm_type='chemical activation', ptm_r...(truncated) | 37,790 | {'size': 868} | 2022-09-16 19:59:37 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2022-09-16 19:59:38 | 2022-09-16 19:59:55 | 17.38 | dict | {'Q07889': {SignorPathway(pathway='Hepatocellular Tumor'), SignorPathway(pathway='Colorectal Carcinoma'), SignorPathway(pathway='Rhabdomyosarcoma'), SignorPathway(pathway='T cell activation'), SignorPathway(pathway='PI3K/AKT Signaling'), SignorPathway(pathway='SARS-CoV MAPK PERTURBATION'), SignorPat...(truncated) | 671 | {'size': 60} | 2022-09-16 19:59:38 | |
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2022-09-16 19:59:55 | 2022-09-16 19:59:55 | 0.00 | dict | {'SIGNOR-PF1': ['P28482', 'P27361'], 'SIGNOR-PF2': ['Q9HBW0', 'Q9UBY5', 'Q92633'], 'SIGNOR-PF3': ['O14610', 'O60262', 'Q9P2W3', 'P63215', 'P63211', 'P50150', 'P59768', 'P63218', 'P61952', 'Q9UK08', 'Q9UBI6', 'P50151'], 'SIGNOR-PF4': ['O14775', 'Q9HAV0', 'P62873', 'P62879', 'P16520'], 'SIGNOR-PF5': [...(truncated) | 97 | {'size': 1} | 2022-09-16 19:59:55 | |
| ¶ | pypath.inputs.spike.spike_complexes | 2022-09-16 19:59:55 | 2022-09-16 20:00:08 | 12.37 | dict | {'COMPLEX:P67775_Q15172_Q15257': Complex PP2A: COMPLEX:P67775_Q15172_Q15257, 'COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478': Complex AMPK: COMPLEX:O43741_P54619_P54646_Q13131_Q9UGI9_Q9UGJ0_Q9Y478, 'COMPLEX:P67870_P68400': Complex CK2: COMPLEX:P67870_P68400, 'COMPLEX:P05412_P15336': Compl...(truncated) | 154 | {} | 2022-09-16 19:59:55 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2022-09-16 20:00:08 | 2022-09-16 20:00:10 | 2.81 | list | [SpikeInteraction(entrez_a='554210', genesymbol_a='MIR429', entrez_b='55914', genesymbol_b='ERBB2IP', directed='1', pmids='20005803', integrity='2', effect='2', assay='', data_source='Published research', description='Luciferase activity assay', mechanism='N/A', regulation=True), SpikeInteraction(en...(truncated) | 8,903 | {} | 2022-09-16 20:00:08 | |
| ¶ | pypath.inputs.stitch.stitch_actions_interactions | 2022-09-16 20:00:10 | 2022-09-16 20:01:24 | 73.25 | 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 | {} | 2022-09-16 20:00:10 | |
| ¶ | pypath.inputs.stitch.stitch_links_interactions | 2022-09-16 20:01:24 | 2022-09-16 20:02:49 | 84.85 | 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 | {} | 2022-09-16 20:01:24 | |
| ¶ | pypath.inputs.string.string_effects | 2022-09-16 20:02:49 | 2022-09-16 20:02:56 | 7.56 | 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 | {} | 2022-09-16 20:02:49 | |
| ¶ | pypath.inputs.string.string_links_interactions | 2022-09-16 20:02:57 | 2022-09-16 20:03:27 | 29.27 | 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 | {} | 2022-09-16 20:02:57 | |
| ¶ | pypath.inputs.string.string_physical_interactions | 2022-09-16 20:03:27 | 2022-09-16 20:03:28 | 1.63 | 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 | {} | 2022-09-16 20:03:27 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2022-09-16 20:03:28 | 2022-09-16 20:03:31 | 2.39 | dict | {'A0AV02': (0.8363, 'Transporters', {'SLC', 'APC', 'SLC12'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC5', 'SLC', 'APC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) | 2,808 | {} | 2022-09-16 20:03:28 | |
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2022-09-16 20:03:31 | 2022-09-16 20:03:52 | 21.56 | 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 | {} | 2022-09-16 20:03:31 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2022-09-16 20:03:52 | 2022-09-16 20:03:53 | 0.69 | dict | {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid='21054788', putative=False), TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False)}, 'Q16613': {Talklr...(truncated) | 1,345 | {} | 2022-09-16 20:03:52 | |
| ¶ | pypath.inputs.talklr.talklr_interactions | 2022-09-16 20:03:53 | 2022-09-16 20:03:53 | 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 | {} | 2022-09-16 20:03:53 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2022-09-16 20:03:53 | 2022-09-16 20:03:53 | 0.02 | 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 | {} | 2022-09-16 20:03:53 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2022-09-16 20:03:53 | 2022-09-16 20:03:59 | 5.81 | dict | {'P60201': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(family='Synaptosomal Vesicle Fusion Pore (SVF-Pore)', tcid='1.F.1.1.1')}, 'O00299'...(truncated) | 2,119 | {'fixed': True} | 2022-09-16 20:03:53 | |
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2022-09-16 20:03:59 | 2022-09-16 20:03:59 | 0.03 | dict | {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) | 22,333 | {'size': 380} | 2022-09-16 20:03:59 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2022-09-16 20:03:59 | 2022-09-16 20:03:59 | 0.01 | dict | {'1.A.1': 'Voltage-gated Ion Channel (VIC)', '1.A.10': 'Glutamate-gated Ion Channel (GIC) of Neurotransmitter Receptors', '1.A.100': 'Rhabdoviridae Putative Viroporin, U5 (RV-U5)', '1.A.101': 'Peroxisomal Pore-forming Pex11 (Pex11)', '1.A.102': 'Influenza A viroporin PB1-F2 (PB1-F2)', '1.A.103': 'Si...(truncated) | 1,718 | {'fixed': True} | 2022-09-16 20:03:59 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2022-09-16 20:03:59 | 2022-09-16 20:04:01 | 2.24 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/tfcensus.py", line 72, in tfcensus_annotations
uniprots = mapping.map_names(ensg, 'ensembl', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 3404, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2099, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2101, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1777, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 2309, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 1476, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 227, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 257, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 415, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 593, in read_mapping_uniprot_list
uniprot_data = self._read_mapping_uniprot_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/utils/mapping.py", line 720, in _read_mapping_uniprot_list
c.fileobj.seek(0)
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-05-21 06:42:12 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2022-09-16 20:04:01 | 2022-09-16 20:04:06 | 4.45 | 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 | {} | 2022-09-16 20:04:01 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2022-09-16 20:04:06 | 2022-09-16 20:04:29 | 23.30 | set | {ThreedcomplexContact(pdb='5l52_1', uniprot_1='P25043', uniprot_2='P23724', chain_1='V', chain_2='L', n_residues=28.0, length_1=222, length_2=222, domain_s1=('',), domain_p1=('PF00227.21', 'PF12465.3'), domain_s2=('',), domain_p2=('PF00227.21',), ident=False, homo=False), ThreedcomplexContact(pdb='4...(truncated) | 259,922 | {'size': -362} | 2022-09-16 20:04:06 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2022-09-16 20:04:30 | 2022-09-16 20:07:26 | 176.33 | list | [<pypath.internals.intera.DomainDomain object at 0x7f6d55ad2910>, <pypath.internals.intera.DomainDomain object at 0x7f6d55ad28e0>, <pypath.internals.intera.DomainDomain object at 0x7f6d55ad2ac0>, <pypath.internals.intera.DomainDomain object at 0x7f6d55ad2b80>, <pypath.internals.intera.DomainDomain o...(truncated) | 524,825 | {'size': -814} | 2022-09-16 20:04:30 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2022-09-16 20:07:27 | 2022-09-16 20:07:35 | 7.58 | dict | {'5l52_1': {('P23724', 'P25043'): 27.5, ('P22141', 'P23638'): 11.5, ('P25043', 'P30657'): 12.0, ('P22141', 'P25451'): 10.0, ('P22141', 'P30656'): 16.5, ('P23639', 'P40302'): 1.0, ('P21242', 'P23638'): 1.0, ('P25043', 'P38624'): 9.0, ('P23638', 'P40303'): 29.5, ('P23639', 'P40303'): 1.5, ('P21243', '...(truncated) | 81,236 | {'size': -161} | 2022-09-16 20:07:27 | |
| ¶ | pypath.inputs.threedid.get_3did | 2022-09-16 20:07:35 | 2022-09-16 20:48:30 | 2,455.02 | tuple | ([<pypath.internals.intera.DomainDomain object at 0x7f6d8e4643d0>, <pypath.internals.intera.DomainDomain object at 0x7f6d6042e220>, <pypath.internals.intera.DomainDomain object at 0x7f6d6042edc0>, <pypath.internals.intera.DomainDomain object at 0x7f6d6042ea00>, <pypath.internals.intera.DomainDomain ...(truncated) | 2 | {} | 2022-09-16 20:07:35 | |
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2022-09-16 20:48:30 | 2022-09-16 20:49:02 | 32.05 | dict | {('Q13162', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'7lj1': ['Q06830', 'Q9BYN0'], '2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}, ('PF00578', 'PF02195'): {'pdbs': {'7lj1': ['Q06830', 'Q9BYN0'], '2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}}, ('P30048', 'Q9BYN0'): {...(truncated) | 3,532,938 | {'size': 257968} | 2022-09-16 20:48:30 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2022-09-16 20:50:20 | 2022-09-16 20:50:24 | 4.52 | dict | {'P05067': {TopdbAnnotation(membrane='Plasma membrane', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Cytoplasm', topology='Inside', score=89, tmregions=1), TopdbAnnotation(membrane='Plasma membrane', topology='Outside', score=89, tmregions=1), TopdbAnnotation(membrane='Plas...(truncated) | 1,248 | {} | 2022-09-16 20:50:20 | |
| ¶ | pypath.inputs.transmir.transmir_interactions | 2022-09-16 20:50:24 | 2022-09-16 20:50:25 | 0.62 | 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 | {} | 2022-09-16 20:50:24 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 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 | {} | 2022-09-16 20:50:25 | |
| ¶ | 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 | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 0.01 | list | [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '12601176;11983166;11290752', 'Calcium measurement;Patch clamp;Fusion protein-pull down assay;Fl...(truncated) | 359 | {} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.trip.trip_process | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'HEK293', 'Rat aortic vascular smooth muscle cell', 'Rat vascular smooth muscle cell', 'Porcine coronary artery'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.trip.trip_process_table |
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem._unichem_mapping |
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.info |
Not calling `pypath.inputs.unichem.info`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_info | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 0.02 | list | [UnichemSource(number='1', label='chembl', name='ChEMBL', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) | 41 | {'fixed': True} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 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 | {'fixed': True} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 0.04 | set | {'A0A1W2PNY6', 'Q6IF63', 'Q9H375', 'A0A024R5T1', 'A0A3G1GLZ6', 'A0A5C2GFC7', 'D6RAF6', 'A0A449C193', 'Q14774', 'B4DSV7', 'A0A068LL60', 'E1U0S6', 'E9PN80', 'Q99795', 'B7ZW27', 'P51617', 'M0R2Q7', 'A0A0J9YW51', 'Q5H963', 'B4DV50', 'A0A087WXZ5', 'A0A5C2GBC3', 'A0A0A7C5L1', 'A0A7I2V3F6', 'C6GLR0', 'G1EP...(truncated) | 204,961 | {'size': 776} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.uniprot._cleanup | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 0.00 | NoneType | None | 0 | {} | 2022-09-16 20:50:25 | |
| ¶ | 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 | 2022-09-16 20:50:25 | 2022-09-16 20:50:25 | 0.00 | set | {'Q6IF63', 'Q96SF7', 'Q14774', 'Q7L3S4', 'Q96CM4', 'Q99795', 'P51617', 'Q9H4W6', 'Q8NGK6', 'Q9BTN0', 'P27352', 'P54710', 'D6RF30', 'Q8WVM7', 'P02538', 'P0DUQ2', 'O43464', 'Q03426', 'P30533', 'Q8IYP9', 'Q6UWP2', 'Q8IYV9', 'P48052', 'Q32MH5', 'A0A1B0GVH4', 'Q9Y3B3', 'Q9Y6Z4', 'Q9Y3Y2', 'Q8NFP9', 'Q166...(truncated) | 20,398 | {'size': 22} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.uniprot.all_trembls | 2022-09-16 20:50:25 | 2022-09-16 20:50:38 | 12.94 | set | {'A0A1W2PNY6', 'Q9H375', 'A0A024R5T1', 'A0A3G1GLZ6', 'A0A5C2GFC7', 'D6RAF6', 'A0A449C193', 'B4DSV7', 'A0A068LL60', 'E1U0S6', 'E9PN80', 'B7ZW27', 'M0R2Q7', 'A0A0J9YW51', 'Q5H963', 'B4DV50', 'A0A087WXZ5', 'A0A5C2GBC3', 'A0A0A7C5L1', 'A0A7I2V3F6', 'C6GLR0', 'G1EP00', 'F5GZA7', 'B8XPJ7', 'F2Z3G0', 'A1Z5...(truncated) | 184,563 | {'size': 754} | 2022-09-16 20:50:25 | |
| ¶ | pypath.inputs.uniprot.all_uniprots | 2022-09-16 20:50:38 | 2022-09-16 20:50:38 | 0.00 | set | {'A0A1W2PNY6', 'Q6IF63', 'Q9H375', 'A0A024R5T1', 'A0A3G1GLZ6', 'A0A5C2GFC7', 'D6RAF6', 'A0A449C193', 'Q14774', 'B4DSV7', 'A0A068LL60', 'E1U0S6', 'E9PN80', 'Q99795', 'B7ZW27', 'P51617', 'M0R2Q7', 'A0A0J9YW51', 'Q5H963', 'B4DV50', 'A0A087WXZ5', 'A0A5C2GBC3', 'A0A0A7C5L1', 'A0A7I2V3F6', 'C6GLR0', 'G1EP...(truncated) | 204,961 | {'size': 776} | 2022-09-16 20:50:38 | |
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_db | 2022-09-16 20:50:38 | 2022-09-16 20:50:38 | 0.00 | set | {'A0A1W2PNY6', 'Q6IF63', 'Q9H375', 'A0A024R5T1', 'A0A3G1GLZ6', 'A0A5C2GFC7', 'D6RAF6', 'A0A449C193', 'Q14774', 'B4DSV7', 'A0A068LL60', 'E1U0S6', 'E9PN80', 'Q99795', 'B7ZW27', 'P51617', 'M0R2Q7', 'A0A0J9YW51', 'Q5H963', 'B4DV50', 'A0A087WXZ5', 'A0A5C2GBC3', 'A0A0A7C5L1', 'A0A7I2V3F6', 'C6GLR0', 'G1EP...(truncated) | 204,961 | {'size': 776} | 2022-09-16 20:50:38 | |
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2022-09-16 20:50:38 | 2022-09-16 20:50:39 | 0.73 | list | [['A0A023IN41', 'H0Y5F6'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZG6', 'Q96A32'], ['A0A024QZR6', 'Q9UII6'], ['A0A024R056', 'A0A140VJJ8'], ['A0A024R072', 'Q96S94'], ['A0A024R077', 'Q96S94'], ['A0A024R079', 'G3V1E2'], ['A0A024R...(truncated) | 71,955 | {'size': 53} | 2022-09-16 20:50:38 | |
| ¶ | pypath.inputs.uniprot.init_db | 2022-09-16 20:50:39 | 2022-09-16 20:50:39 | 0.05 | NoneType | None | 0 | {} | 2022-09-16 20:50:39 | |
| ¶ | 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 | 2022-09-16 20:50:39 | 2022-09-16 20:50:45 | 6.02 | dict | {'Q9H293': {UniprotFamily(family='IL-17', subfamily=None)}, 'Q6IE81': {UniprotFamily(family='JADE', subfamily=None)}, 'Q16558': {UniprotFamily(family='KCNMB (TC 8.A.14.1)', subfamily='KCNMB1')}, 'Q16322': {UniprotFamily(family='Potassium channel', subfamily='A (Shaker) (TC 1.A.1.2)')}, 'O15554': {Un...(truncated) | 14,383 | {'size': 28} | 2022-09-16 20:50:39 | |
| ¶ | 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 | 2022-09-16 20:50:45 | 2022-09-16 20:50:52 | 6.94 | dict | {'P0DP02': {UniprotKeyword(keyword='Immunoglobulin'), UniprotKeyword(keyword='Signal'), UniprotKeyword(keyword='Disulfide bond'), UniprotKeyword(keyword='Cell membrane'), UniprotKeyword(keyword='3D-structure'), UniprotKeyword(keyword='Reference proteome'), UniprotKeyword(keyword='Membrane'), Uniprot...(truncated) | 20,398 | {'size': 22} | 2022-09-16 20:50:45 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2022-09-16 20:50:52 | 2022-09-16 20:51:00 | 7.65 | dict | {'P0DP02': {UniprotLocation(location='Cell membrane', features=None), UniprotLocation(location='Secreted', features=None)}, 'Q9H293': {UniprotLocation(location='Secreted', features=None)}, 'Q6IE81': {UniprotLocation(location='Cytoplasm', features=None), UniprotLocation(location='Nucleus', features=N...(truncated) | 16,938 | {'size': 82} | 2022-09-16 20:50:52 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2022-09-16 20:51:00 | 2022-09-16 20:51:00 | 0.08 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 27,043 | {'size': 170} | 2022-09-16 20:51:00 | |
| ¶ | 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 | 2022-09-16 20:51:00 | 2022-09-16 20:51:02 | 1.46 | 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': {'Momi fir', 'Abies firma'}, 'O81086': {'Pinus grandis', 'Grand fir', 'Abie...(truncated) | 553,681 | {'size': 901} | 2022-09-16 20:51:00 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2022-09-16 20:51:02 | 2022-09-16 20:51:10 | 7.74 | dict | {'Q9H293': {UniprotTissue(tissue='Lung', level='low'), UniprotTissue(tissue='Prostate', level='low'), UniprotTissue(tissue='Testis', level='low'), UniprotTissue(tissue='Trachea', level='low'), UniprotTissue(tissue='Spinal cord', level='low'), UniprotTissue(tissue='Several tissues', level='low'), Uni...(truncated) | 9,989 | {'size': 51} | 2022-09-16 20:51:02 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2022-09-16 20:51:10 | 2022-09-16 20:51:36 | 26.21 | dict | {'Q16558': {UniprotTopology(topology='Cytoplasmic', start=1, end=18), UniprotTopology(topology='Cytoplasmic', start=179, end=191), UniprotTopology(topology='Extracellular', start=40, end=157), UniprotTopology(topology='Transmembrane', start=158, end=178), UniprotTopology(topology='Transmembrane', st...(truncated) | 5,223 | {'size': 6} | 2022-09-16 20:51:10 | |
| ¶ | 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 | 2022-09-16 20:51:36 | 2022-09-16 20:51:36 | 0.18 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/wang.py", line 144, in cui_interactions
raw = embo.embopress_supplementary(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embopress.py", line 99, in embopress_supplementary
fname = c.fname
AttributeError: 'Curl' object has no attribute 'fname'
|
{'broke': True} | 2022-05-21 07:30:34 | |||
| ¶ | pypath.inputs.wang.hsn_interactions | 2022-09-16 20:51:36 | 2022-09-16 20:51:36 | 0.12 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/wang.py", line 118, in hsn_interactions
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{} | 2022-05-17 07:28:52 | |||
| ¶ | pypath.inputs.wang.wang_annotations | 2022-09-16 20:51:36 | 2022-09-16 20:51:37 | 0.23 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/status-report.py", line 839, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/wang.py", line 267, in wang_annotations
data = func()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/wang.py", line 144, in cui_interactions
raw = embo.embopress_supplementary(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220916-173401/pypath_git/pypath/inputs/embopress.py", line 99, in embopress_supplementary
fname = c.fname
AttributeError: 'Curl' object has no attribute 'fname'
|
{'broke': True} | 2022-05-21 07:30:37 | |||
| ¶ | pypath.inputs.wang.wang_interactions | 2022-09-16 20:51:37 | 2022-09-16 20:51:37 | 0.41 | 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 | {} | 2022-09-16 20:51:37 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2022-09-16 20:51:37 | 2022-09-16 20:51:40 | 2.37 | list | [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) | 483 | {} | 2022-09-16 20:51:37 | |
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2022-09-16 20:51:40 | 2022-09-16 20:51:40 | 0.12 | list | [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) | 495 | {} | 2022-09-16 20:51:40 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2022-09-16 20:51:40 | 2022-09-16 20:51:40 | 0.20 | 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 | {} | 2022-09-16 20:51:40 |
The OmniPath Team • Saez Lab • 2022-09-16