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 2022-01-25 00:13:02 and 2022-01-25 03:27:49; pypath version: 0.14.0 (from git; eccfdb3 )
| Modules collected: | 150 |
|---|---|
| Modules failed to import: | 0 |
| Functions collected: | 469 |
| Functions run without error: | 188 |
| Functions returned empty value: | 6 |
| Functions skipped due to lack of arguments: | 118 |
| Functions run with error: | 163 |
| Function | Started | Finished | Elapsed (s) | Result type | Result repr | Result size | Error | Change since last time | Last succeeded | |
|---|---|---|---|---|---|---|---|---|---|---|
| ¶ | pypath.inputs.abs.abs_interactions | 2022-01-25 00:13:05 | 2022-01-25 00:13:06 | 0.33 | 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 | {} | 2022-01-25 00:13:05 | |
| ¶ | pypath.inputs.acsn.acsn_interactions | 2022-01-25 00:13:06 | 2022-01-25 00:13:06 | 0.64 | 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 | {} | 2022-01-25 00:13:06 | |
| ¶ | pypath.inputs.acsn.acsn_interactions_sif | 2022-01-25 00:13:06 | 2022-01-25 00:13:07 | 0.38 | 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 | {} | 2022-01-25 00:13:06 | |
| ¶ | pypath.inputs.adhesome.adhesome_annotations | 2022-01-25 00:13:07 | 2022-01-25 00:14:07 | 60.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/adhesome.py", line 87, in adhesome_annotations
for _uniprot in mapping.map_name(uniprot, 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:27:10 | |||
| ¶ | pypath.inputs.adhesome.adhesome_interactions | 2022-01-25 00:14:07 | 2022-01-25 00:14:07 | 0.32 | 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 | {} | 2022-01-25 00:14:07 | |
| ¶ | pypath.inputs.almen2009.almen2009_annotations | 2022-01-25 00:14:07 | 2022-01-25 00:15:09 | 61.74 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/almen2009.py", line 67, in almen2009_annotations
uniprots = mapping.map_name(row[0], 'ipi', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:28:38 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_annotations | 2022-01-25 00:15:09 | 2022-01-25 00:16:34 | 85.34 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 195, in baccin2019_annotations
ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 136, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 83, in raw_to_uniprots
itertools.product(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 84, in <genexpr>
*(id_translate(comp) for comp in components)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 55, in id_translate
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:28:40 | |||
| ¶ | pypath.inputs.baccin2019.baccin2019_interactions | 2022-01-25 00:16:34 | 2022-01-25 00:17:36 | 61.20 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 136, in baccin2019_interactions
ligand_components = raw_to_uniprots(rec[1])
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 83, in raw_to_uniprots
itertools.product(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 84, in <genexpr>
*(id_translate(comp) for comp in components)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/baccin2019.py", line 55, in id_translate
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:38:49 | |||
| ¶ | pypath.inputs.biogps.biogps_datasets | 2022-01-25 00:17:36 | 2022-01-25 00:17:36 | 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 | {} | 2022-01-25 00:17:36 | |
| ¶ | pypath.inputs.biogps.biogps_download |
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biogps.biogps_download_all | 2022-01-25 00:17:36 | 2022-01-25 00:18:11 | 35.20 | 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 | {} | 2022-01-25 00:17:36 | |
| ¶ | pypath.inputs.biogrid.biogrid_interactions | 2022-01-25 00:18:11 | 2022-01-25 00:18:21 | 9.16 | list | [BiogridInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridInteraction(partner_a='CDKN3', partner_b='CDK2', pmid='12745075'), BiogridInteraction(partner_a='PPARGC1B', partner_b='ESR1', pmid='11854298'), Biog...(truncated) | 6,532 | {} | 2022-01-25 00:18:11 | |
| ¶ | pypath.inputs.biomart.biomart_homology | 2022-01-25 00:18:21 | 2022-01-25 00:19:22 | 61.02 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/biomart.py", line 202, in biomart_homology
return list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/biomart.py", line 139, in biomart_query
for line in c.result:
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2022-01-24 00:39:34 | |||
| ¶ | pypath.inputs.biomart.biomart_microarray |
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.biomart.biomart_microarray_types | 2022-01-25 00:19:22 | 2022-01-25 00:19:22 | 0.16 | list | [{'format': 'EXPRESSION', 'type': 'OLIGO', 'vendor': 'PHALANX', 'description': None, 'array': 'OneArray', 'label': 'PHALANX OneArray'}, {'vendor': 'CODELINK', 'format': 'EXPRESSION', 'type': 'OLIGO', 'array': 'CODELINK', 'description': None, 'label': 'CODELINK CODELINK'}, {'vendor': 'ILLUMINA', 'for...(truncated) | 38 | {} | 2022-01-25 00:19:22 | |
| ¶ | pypath.inputs.biomart.biomart_query |
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ca1.ca1_interactions | 2022-01-25 00:19:22 | 2022-01-25 00:19:25 | 3.25 | list | [Ca1Interaction(source_label='GLYCINE', source_uniprot='NA', source_uniprot_mouse='NA', source_function='Ligand', source_location='Extracellular', target_label='NMDAR', target_uniprot='Q12879', target_uniprot_mouse='P35436', target_function='Receptor', target_location='Membrane', effect='+', interac...(truncated) | 1,788 | {} | 2022-01-25 00:19:22 | |
| ¶ | pypath.inputs.cancercellmap.ccmap_interactions | 2022-01-25 00:19:25 | 2022-01-25 00:19:26 | 0.79 | 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 | {} | 2022-01-25 00:19:25 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_annotations | 2022-01-25 00:19:26 | 2022-01-25 00:19:34 | 8.05 | defaultdict | defaultdict(<class 'set'>, {'46220502': {CancerDrugsAnnotation(label='Abemaciclib', indications='Advanced Breast Cancer; Metastatic Breast Cancer', last_updated='17/09/2020')}, '132971': {CancerDrugsAnnotation(label='Abiraterone', indications='Metastatic Castration Resistant Prostate Cancer', last_u...(truncated) | 197 | {'first': True} | 2022-01-25 00:19:26 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_download | 2022-01-25 00:19:34 | 2022-01-25 00:19:34 | 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) | 282 | {'first': True} | 2022-01-25 00:19:34 | |
| ¶ | pypath.inputs.cancerdrugs_db.cancerdrugs_db_interactions | 2022-01-25 00:19:34 | 2022-01-25 00:20:40 | 65.89 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cancerdrugs_db.py", line 112, in cancerdrugs_db_interactions
tar = mapping.map_name(tar, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'first': True} | 2022-01-25 00:19:34 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations | 2022-01-25 00:20:40 | 2022-01-25 00:21:40 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cancerdrugsdb.py", line 204, in cancerdrugsdb_annotations
data = cancerdrugsdb_interactions()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cancerdrugsdb.py", line 136, in cancerdrugsdb_interactions
target_uniprots = mapping.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:15 | |||
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_download | 2022-01-25 00:21:40 | 2022-01-25 00:21:40 | 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) | 282 | {} | 2022-01-25 00:21:40 | |
| ¶ | pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions | 2022-01-25 00:21:40 | 2022-01-25 00:22:40 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cancerdrugsdb.py", line 136, in cancerdrugsdb_interactions
target_uniprots = mapping.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:24 | |||
| ¶ | pypath.inputs.cancersea.cancersea_annotations | 2022-01-25 00:22:40 | 2022-01-25 00:23:40 | 60.27 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cancersea.py", line 67, in cancersea_annotations
uniprots = mapping.map_name(line[1], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:24 | |||
| ¶ | pypath.inputs.cell.cell_supplementary |
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellcall.cellcall_annotations | 2022-01-25 00:23:40 | 2022-01-25 00:24:46 | 66.14 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellcall.py", line 223, in cellcall_annotations
interactions = cellcall_interactions(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellcall.py", line 159, in cellcall_interactions
ligands = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:27 | |||
| ¶ | pypath.inputs.cellcall.cellcall_download | 2022-01-25 00:24:46 | 2022-01-25 00:24:46 | 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 | {} | 2022-01-25 00:24:46 | |
| ¶ | pypath.inputs.cellcall.cellcall_download_all | 2022-01-25 00:24:46 | 2022-01-25 00:24:47 | 0.91 | 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 | {} | 2022-01-25 00:24:46 | |
| ¶ | pypath.inputs.cellcall.cellcall_interactions | 2022-01-25 00:24:47 | 2022-01-25 00:25:47 | 60.07 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellcall.py", line 159, in cellcall_interactions
ligands = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:29 | |||
| ¶ | pypath.inputs.cellcellinteractions.cellcellinteractions_annotations | 2022-01-25 00:25:47 | 2022-01-25 00:26:48 | 60.68 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellcellinteractions.py", line 54, in cellcellinteractions_annotations
uniprots = mapping.map_name(row[0], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:31 | |||
| ¶ | pypath.inputs.cellchatdb._cellchatdb_organism | 2022-01-25 00:26:48 | 2022-01-25 00:26:48 | 0.00 | int | 9606 | None | {} | 2022-01-25 00:26:48 | |
| ¶ | 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 | 2022-01-25 00:26:48 | 2022-01-25 00:27:54 | 65.37 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 327, in cellchatdb_annotations
interactions = cellchatdb_interactions(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 231, in cellchatdb_interactions
_complexes = _cellchatdb_process_complexes(raw, organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 117, in _cellchatdb_process_complexes
uniprots = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 118, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:32 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_cofactors | 2022-01-25 00:27:54 | 2022-01-25 00:28:59 | 64.97 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 146, in cellchatdb_cofactors
return _cellchatdb_process_cofactors(raw, organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 163, in _cellchatdb_process_cofactors
uniprots = mapping.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:40 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_complexes | 2022-01-25 00:28:59 | 2022-01-25 00:30:04 | 64.95 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 100, in cellchatdb_complexes
return _cellchatdb_process_complexes(raw, organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 117, in _cellchatdb_process_complexes
uniprots = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 118, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:45 | |||
| ¶ | pypath.inputs.cellchatdb.cellchatdb_download | 2022-01-25 00:30:04 | 2022-01-25 00:30:09 | 5.32 | dict | {'interaction': interaction_name ... rownames 0 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 1 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 3 TGFB1_ACVR1B_TGFBR2 ... TGFB1_ACVR1B_TGFBR2 4 TGFB1_ACVR1C_TGFBR...(truncated) | 4 | {} | 2022-01-25 00:30:04 | |
| ¶ | pypath.inputs.cellchatdb.cellchatdb_interactions | 2022-01-25 00:30:09 | 2022-01-25 00:31:14 | 65.06 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 231, in cellchatdb_interactions
_complexes = _cellchatdb_process_complexes(raw, organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 117, in _cellchatdb_process_complexes
uniprots = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellchatdb.py", line 118, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:40:56 | |||
| ¶ | pypath.inputs.cellinker._cellinker_interactions_raw | 2022-01-25 00:31:14 | 2022-01-25 00:31:15 | 0.35 | 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 | {} | 2022-01-25 00:31:14 | |
| ¶ | pypath.inputs.cellinker._cellinker_uniprots |
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.cellinker.cellinker_annotations | 2022-01-25 00:31:15 | 2022-01-25 00:32:15 | 60.11 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 460, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 317, in cellinker_lr_interactions
complexes = dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 320, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 167, in components_to_complex
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 168, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 532, in _cellinker_uniprots
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:01 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complex_annotations | 2022-01-25 00:32:15 | 2022-01-25 00:33:15 | 60.03 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 517, in cellinker_complex_annotations
return cellinker_annotations(organism = organism, entity_type = 'complex')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 460, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 317, in cellinker_lr_interactions
complexes = dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 320, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 167, in components_to_complex
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 168, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 532, in _cellinker_uniprots
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:02 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes | 2022-01-25 00:33:15 | 2022-01-25 00:34:15 | 60.04 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 201, in cellinker_complexes
for cplex in components_to_complex(c.components, organism = organism):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 167, in components_to_complex
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 168, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 532, in _cellinker_uniprots
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:03 | |||
| ¶ | pypath.inputs.cellinker.cellinker_complexes_raw | 2022-01-25 00:34:15 | 2022-01-25 00:34:15 | 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 | {} | 2022-01-25 00:34:15 | |
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions | 2022-01-25 00:34:15 | 2022-01-25 00:35:15 | 60.03 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 317, in cellinker_lr_interactions
complexes = dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 320, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 167, in components_to_complex
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 168, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 532, in _cellinker_uniprots
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:03 | |||
| ¶ | pypath.inputs.cellinker.cellinker_lr_interactions_raw | 2022-01-25 00:35:15 | 2022-01-25 00:35:15 | 0.02 | 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 | {} | 2022-01-25 00:35:15 | |
| ¶ | pypath.inputs.cellinker.cellinker_protein_annotations | 2022-01-25 00:35:15 | 2022-01-25 00:36:15 | 60.03 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 499, in cellinker_protein_annotations
return cellinker_annotations(organism = organism, entity_type = 'protein')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 460, in cellinker_annotations
ia = cellinker_lr_interactions(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 317, in cellinker_lr_interactions
complexes = dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 320, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 167, in components_to_complex
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 168, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 532, in _cellinker_uniprots
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:03 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions | 2022-01-25 00:36:15 | 2022-01-25 00:37:15 | 60.16 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 388, in cellinker_smol_interactions
complexes = dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 391, in <genexpr>
components_to_complex(c.components, organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 167, in components_to_complex
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 168, in <genexpr>
_cellinker_uniprots(c.genesymbol, c.entrez, _organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellinker.py", line 532, in _cellinker_uniprots
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:04 | |||
| ¶ | pypath.inputs.cellinker.cellinker_smol_interactions_raw | 2022-01-25 00:37:15 | 2022-01-25 00:37:15 | 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 | {} | 2022-01-25 00:37:15 | |
| ¶ | 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 | 2022-01-25 00:37:15 | 2022-01-25 00:38:15 | 60.23 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 221, in cellphonedb_complex_annotations
return _cellphonedb_annotations(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 129, in _cellphonedb_annotations
names = name_method(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 210, in name_method
comp = get_stoichiometry(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 204, in get_stoichiometry
return tuple(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 205, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:04 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_complexes | 2022-01-25 00:38:15 | 2022-01-25 00:39:15 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 345, in cellphonedb_complexes
annot = cellphonedb_complex_annotations()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 221, in cellphonedb_complex_annotations
return _cellphonedb_annotations(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 129, in _cellphonedb_annotations
names = name_method(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 210, in name_method
comp = get_stoichiometry(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 204, in get_stoichiometry
return tuple(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 205, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:04 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_interactions | 2022-01-25 00:39:15 | 2022-01-25 00:40:15 | 60.23 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 281, in cellphonedb_interactions
ligands, receptors = cellphonedb_ligands_receptors()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 64, in cellphonedb_ligands_receptors
proteins = cellphonedb_protein_annotations()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 164, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 129, in _cellphonedb_annotations
names = name_method(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 160, in name_method
uniprot = mapping.map_names(uniprot, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:04 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_ligands_receptors | 2022-01-25 00:40:15 | 2022-01-25 00:41:15 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 64, in cellphonedb_ligands_receptors
proteins = cellphonedb_protein_annotations()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 164, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 129, in _cellphonedb_annotations
names = name_method(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 160, in name_method
uniprot = mapping.map_names(uniprot, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:05 | |||
| ¶ | pypath.inputs.cellphonedb.cellphonedb_protein_annotations | 2022-01-25 00:41:15 | 2022-01-25 00:42:15 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 164, in cellphonedb_protein_annotations
protein_annotations = _cellphonedb_annotations(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 129, in _cellphonedb_annotations
names = name_method(rec)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cellphonedb.py", line 160, in name_method
uniprot = mapping.map_names(uniprot, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:05 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_annotations | 2022-01-25 00:42:15 | 2022-01-25 00:43:30 | 74.68 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/celltalkdb.py", line 187, in celltalkdb_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:05 | |||
| ¶ | pypath.inputs.celltalkdb.celltalkdb_download | 2022-01-25 00:43:30 | 2022-01-25 00:43:30 | 0.00 | list | [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) | 3,398 | {} | 2022-01-25 00:43:30 | |
| ¶ | pypath.inputs.celltalkdb.celltalkdb_interactions | 2022-01-25 00:43:30 | 2022-01-25 00:43:30 | 0.01 | list | [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) | 3,398 | {} | 2022-01-25 00:43:30 | |
| ¶ | pypath.inputs.celltypist.celltypist_annotations | 2022-01-25 00:43:30 | 2022-01-25 00:44:30 | 60.23 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/celltypist.py", line 75, in celltypist_annotations
uniprots = mapping.map_names(genesymbols, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:14 | |||
| ¶ | pypath.inputs.compleat.compleat_complexes | 2022-01-25 00:44:30 | 2022-01-25 00:45:31 | 60.53 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/compleat.py", line 88, in compleat_complexes
uniprot = mapping.map_name0(entrez.strip(), 'entrez', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:41:14 | |||
| ¶ | pypath.inputs.compleat.compleat_raw | 2022-01-25 00:45:31 | 2022-01-25 00:45:31 | 0.06 | list | [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) | 9,704 | {} | 2022-01-25 00:45:31 | |
| ¶ | pypath.inputs.complexportal.complexportal_complexes | 2022-01-25 00:45:31 | 2022-01-25 00:46:14 | 43.14 | dict | {'COMPLEX:P84022_Q13485_Q15796': Complex SMAD2-SMAD3-SMAD4 complex: COMPLEX:P84022_Q13485_Q15796, 'COMPLEX:P16220_P18848': Complex bZIP transcription factor complex, ATF4-CREB1: COMPLEX:P16220_P18848, 'COMPLEX:P18846_P18848': Complex bZIP transcription factor complex, ATF1-ATF4: COMPLEX:P18846_P1884...(truncated) | 1,191 | {} | 2022-01-25 00:45:31 | |
| ¶ | pypath.inputs.comppi.comppi_interaction_locations | 2022-01-25 00:46:14 | 2022-01-25 00:47:15 | 61.08 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/comppi.py", line 132, in comppi_interaction_locations
mapping.map_name(l[0], 'uniprot', 'uniprot'),
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:42:04 | |||
| ¶ | pypath.inputs.comppi.comppi_locations | 2022-01-25 00:47:15 | 2022-01-25 00:48:15 | 60.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/comppi.py", line 148, in comppi_locations
for iloc in comppi_interaction_locations(organism = organism):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/comppi.py", line 132, in comppi_interaction_locations
mapping.map_name(l[0], 'uniprot', 'uniprot'),
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:42:59 | |||
| ¶ | pypath.inputs.connectomedb.connectomedb_annotations | 2022-01-25 00:48:15 | 2022-01-25 00:49:16 | 60.31 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/connectomedb.py", line 97, in connectomedb_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:43:55 | |||
| ¶ | pypath.inputs.connectomedb.connectomedb_interactions | 2022-01-25 00:49:16 | 2022-01-25 00:49:16 | 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 | {} | 2022-01-25 00:49:16 | |
| ¶ | pypath.inputs.corum.corum_complexes | 2022-01-25 00:49:16 | 2022-01-25 00:49:16 | 0.50 | 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 | {} | 2022-01-25 00:49:16 | |
| ¶ | pypath.inputs.cosmic.cancer_gene_census_annotations | 2022-01-25 00:49:16 | 2022-01-25 00:50:18 | 61.64 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cosmic.py", line 167, in cancer_gene_census_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:43:56 | |||
| ¶ | pypath.inputs.cpad.cpad_annotations | 2022-01-25 00:50:18 | 2022-01-25 00:51:30 | 71.69 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cpad.py", line 67, in cpad_annotations
uniprot = mapping.map_name0(regulator, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:43:59 | |||
| ¶ | pypath.inputs.cpad.cpad_pathway_cancer | 2022-01-25 00:51:30 | 2022-01-25 00:51:30 | 0.06 | tuple | ({'Glioma': {CpadPathwayCancer(pathway='STAT3 signaling pathway', cancer='Glioma', pathway_category='Jak-STAT signaling pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='induce apoptosis and cell-cycle arrest'), CpadPathwayCancer(pathway='NF-kappa B signaling pathway', cancer='Gliom...(truncated) | 2 | {} | 2022-01-25 00:51:30 | |
| ¶ | pypath.inputs.cpad.get_cpad | 2022-01-25 00:51:30 | 2022-01-25 00:51:30 | 0.05 | 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 | {} | 2022-01-25 00:51:30 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions | 2022-01-25 00:51:30 | 2022-01-25 00:51:34 | 4.67 | 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 | {} | 2022-01-25 00:51:30 | |
| ¶ | pypath.inputs.cpdb.cpdb_interactions_ltp | 2022-01-25 00:51:35 | 2022-01-25 00:51:38 | 2.93 | 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 | {} | 2022-01-25 00:51:35 | |
| ¶ | pypath.inputs.cspa.cspa_annotations | 2022-01-25 00:51:38 | 2022-01-25 00:52:39 | 61.22 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cspa.py", line 68, in cspa_annotations
for uniprot in mapping.map_name(row[1], 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:44:13 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_type_annotations | 2022-01-25 00:52:39 | 2022-01-25 00:53:42 | 62.80 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cspa.py", line 131, in cspa_cell_type_annotations
cell_type_data = cspa_cell_types(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cspa.py", line 104, in cspa_cell_types
for uniprot in mapping.map_name(row[0], 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:44:15 | |||
| ¶ | pypath.inputs.cspa.cspa_cell_types | 2022-01-25 00:53:42 | 2022-01-25 00:54:45 | 62.60 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/cspa.py", line 104, in cspa_cell_types
for uniprot in mapping.map_name(row[0], 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:44:18 | |||
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate | 2022-01-25 00:54:45 | 2022-01-25 00:54:47 | 2.74 | 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 | {} | 2022-01-25 00:54:45 | |
| ¶ | pypath.inputs.dbptm.dbptm_enzyme_substrate_old | 2022-01-25 00:54:48 | 2022-01-25 00:54:50 | 1.93 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/dbptm.py", line 101, in dbptm_enzyme_substrate_old
for k, data in iteritems(extra):
File "/usr/lib/python3/dist-packages/future/utils/__init__.py", line 311, in iteritems
func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
|
{} | 2022-01-07 23:35:25 | |||
| ¶ | pypath.inputs.dbptm.dbptm_interactions | 2022-01-25 00:54:50 | 2022-01-25 00:54:51 | 1.34 | 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 | {} | 2022-01-25 00:54:50 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions | 2022-01-25 00:54:51 | 2022-01-25 00:54:52 | 1.08 | list | [] | 0 | {} | 2022-01-25 00:54:51 | |
| ¶ | pypath.inputs.deathdomain.deathdomain_interactions_rescued | 2022-01-25 00:54:52 | 2022-01-25 00:54:52 | 0.16 | list | [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) | 184 | {} | 2022-01-25 00:54:52 | |
| ¶ | pypath.inputs.depod.depod_enzyme_substrate | 2022-01-25 00:54:52 | 2022-01-25 00:55:52 | 60.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/depod.py", line 116, in depod_enzyme_substrate
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:44:28 | |||
| ¶ | pypath.inputs.depod.depod_interactions | 2022-01-25 00:55:52 | 2022-01-25 00:55:52 | 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 | {} | 2022-01-25 00:55:52 | |
| ¶ | pypath.inputs.dgidb.dgidb_annotations | 2022-01-25 00:55:52 | 2022-01-25 00:56:54 | 62.05 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/dgidb.py", line 53, in dgidb_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:44:28 | |||
| ¶ | pypath.inputs.dgidb.get_dgidb_old | 2022-01-25 00:56:54 | 2022-01-25 00:58:57 | 122.87 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/dgidb.py", line 96, in get_dgidb_old
return mapping.map_names(genesymbols, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:44:31 | |||
| ¶ | pypath.inputs.dip.dip_interactions | 2022-01-25 00:58:57 | 2022-01-25 00:58:58 | 0.29 | 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 | {} | 2022-01-25 00:58:57 | |
| ¶ | pypath.inputs.dip.dip_login |
Not calling `pypath.inputs.dip.dip_login`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.disgenet.disgenet_annotations | 2022-01-25 00:58:58 | 2022-01-25 00:59:58 | 60.62 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/disgenet.py", line 70, in disgenet_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:45:35 | |||
| ¶ | pypath.inputs.domino.domino_ddi | 2022-01-25 00:59:58 | 2022-01-25 01:00:04 | 5.41 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/domino.py", line 243, in domino_ddi
domi = domino_enzsub()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/domino.py", line 417, in domino_enzsub
intera.Domain(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/internals/intera.py", line 655, in __init__
entity.Entity(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/core/entity.py", line 126, in __init__
self._bootstrap(identifier, id_type, entity_type, taxon)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/core/entity.py", line 156, in _bootstrap
if entity_type in self._smol_types:
TypeError: 'in <string>' requires string as left operand, not NoneType
|
{'broke': True} | 2022-01-24 00:45:40 | |||
| ¶ | pypath.inputs.domino.domino_enzsub | 2022-01-25 01:00:04 | 2022-01-25 01:00:04 | 0.43 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/domino.py", line 417, in domino_enzsub
intera.Domain(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/internals/intera.py", line 655, in __init__
entity.Entity(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/core/entity.py", line 126, in __init__
self._bootstrap(identifier, id_type, entity_type, taxon)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/core/entity.py", line 156, in _bootstrap
if entity_type in self._smol_types:
TypeError: 'in <string>' requires string as left operand, not NoneType
|
{'broke': True} | 2022-01-24 00:45:45 | |||
| ¶ | pypath.inputs.domino.domino_interactions | 2022-01-25 01:00:04 | 2022-01-25 01:00:05 | 0.42 | 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 | {} | 2022-01-25 01:00:04 | |
| ¶ | pypath.inputs.domino.get_domino | 2022-01-25 01:00:05 | 2022-01-25 01:00:05 | 0.38 | list | [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) | 14,539 | {} | 2022-01-25 01:00:05 | |
| ¶ | pypath.inputs.dorothea._process_resources |
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.dorothea.dorothea_full_raw | 2022-01-25 01:00:05 | 2022-01-25 01:00:13 | 8.26 | 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 | {} | 2022-01-25 01:00:05 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2022-01-25 01:00:13 | 2022-01-25 01:00:27 | 13.87 | 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 | {} | 2022-01-25 01:00:13 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2022-01-25 01:00:27 | 2022-01-25 01:00:28 | 0.37 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/dorothea.py", line 213, 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 | 2022-01-25 01:00:28 | 2022-01-25 01:00:28 | 0.12 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/dorothea.py", line 213, 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 | 2022-01-25 01:00:28 | 2022-01-25 01:00:29 | 1.71 | 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 | {} | 2022-01-25 01:00:28 | |
| ¶ | pypath.inputs.dorothea.get_dorothea_old | 2022-01-25 01:00:29 | 2022-01-25 01:00:30 | 0.37 | 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 | {} | 2022-01-25 01:00:29 | |
| ¶ | pypath.inputs.dorothea.dorothea_rda_raw | 2022-01-25 01:00:30 | 2022-01-25 01:00:31 | 1.20 | 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 | {} | 2022-01-25 01:00:30 | |
| ¶ | pypath.inputs.dorothea.dorothea_interactions | 2022-01-25 01:00:31 | 2022-01-25 01:00:45 | 13.74 | 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 | {} | 2022-01-25 01:00:31 | |
| ¶ | pypath.inputs.dorothea.dorothea_old_csv | 2022-01-25 01:00:45 | 2022-01-25 01:00:45 | 0.11 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/dorothea.py", line 213, 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 | 2022-01-25 01:00:45 | 2022-01-25 01:01:00 | 15.55 | 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 | {} | 2022-01-25 01:00:45 | |
| ¶ | pypath.inputs.elm.elm_domains | 2022-01-25 01:01:00 | 2022-01-25 01:01:01 | 0.90 | dict | {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')]}} | 2 | {} | 2022-01-25 01:01:00 | |
| ¶ | pypath.inputs.elm.elm_instances | 2022-01-25 01:01:01 | 2022-01-25 01:02:01 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/elm.py", line 118, in elm_instances
data = data.replace('"', '').split('\n')
AttributeError: 'NoneType' object has no attribute 'replace'
|
{'broke': True} | 2022-01-24 00:46:41 | |||
| ¶ | pypath.inputs.elm.elm_interactions | 2022-01-25 01:02:01 | 2022-01-25 01:03:01 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/elm.py", line 170, in elm_interactions
data = data.split('\n')
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:48:20 | |||
| ¶ | pypath.inputs.embrace._embrace_id_translation |
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.embrace.embrace_annotations | 2022-01-25 01:03:01 | 2022-01-25 01:04:04 | 62.43 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 162, in embrace_annotations
for rec in embrace_translated(organism = organism):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 92, in embrace_translated
ligands = _embrace_id_translation(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 62, in _embrace_id_translation
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:49:29 | |||
| ¶ | pypath.inputs.embrace.embrace_interactions | 2022-01-25 01:04:04 | 2022-01-25 01:05:04 | 60.10 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 128, in embrace_interactions
for rec in embrace_translated(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 92, in embrace_translated
ligands = _embrace_id_translation(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 62, in _embrace_id_translation
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:49:31 | |||
| ¶ | pypath.inputs.embrace.embrace_raw | 2022-01-25 01:05:04 | 2022-01-25 01:05:04 | 0.13 | 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 | {} | 2022-01-25 01:05:04 | |
| ¶ | pypath.inputs.embrace.embrace_translated | 2022-01-25 01:05:04 | 2022-01-25 01:06:04 | 60.11 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 92, in embrace_translated
ligands = _embrace_id_translation(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/embrace.py", line 62, in _embrace_id_translation
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 00:49:32 | |||
| ¶ | pypath.inputs.encode.encode_tf_mirna_interactions | 2022-01-25 01:06:04 | 2022-01-25 01:06:05 | 0.97 | 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 | {} | 2022-01-25 01:06:04 | |
| ¶ | pypath.inputs.ensembl.ensembl_organisms | 2022-01-25 01:06:05 | 2022-01-25 01:06:06 | 0.74 | 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) | 311 | {} | 2022-01-25 01:06:05 | |
| ¶ | pypath.inputs.exocarta._get_exocarta_vesiclepedia | 2022-01-25 01:06:06 | 2022-01-25 01:06:18 | 11.84 | 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 | {} | 2022-01-25 01:06:06 | |
| ¶ | pypath.inputs.exocarta.get_exocarta | 2022-01-25 01:06:18 | 2022-01-25 01:06:18 | 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 | {} | 2022-01-25 01:06:18 | |
| ¶ | pypath.inputs.exocarta.get_vesiclepedia | 2022-01-25 01:06:18 | 2022-01-25 01:07:21 | 63.50 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/exocarta.py", line 114, in _get_exocarta_vesiclepedia
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'broke': True} | 2022-01-24 00:49:44 | |||
| ¶ | 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 | 2022-01-25 01:07:21 | 2022-01-25 01:07:22 | 0.35 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 860, in get_go_quick
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{} | 2022-01-07 23:44:17 | |||
| ¶ | pypath.inputs.go.get_goslim | 2022-01-25 01:07:22 | 2022-01-25 01:07:22 | 0.89 | list | ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005622', 'GO:0005634', 'GO:0005635', 'GO:0...(truncated) | 143 | {} | 2022-01-25 01:07:22 | |
| ¶ | pypath.inputs.go.go_ancestors_quickgo | 2022-01-25 01:07:22 | 2022-01-25 01:20:09 | 766.48 | dict | {'C': {'GO:0042612': {('GO:0042611', 'is_a')}, 'GO:0042613': {('GO:0042611', 'is_a')}, 'GO:0032398': {('GO:0042611', 'is_a')}, 'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009426': {('GO:0110165', 'is_a'), ('GO:0030694', 'part_of')}, 'GO:0009429': {('GO:011016...(truncated) | 3 | {} | 2022-01-25 01:07:22 | |
| ¶ | pypath.inputs.go.go_ancestors_goose | 2022-01-25 01:20:09 | 2022-01-25 01:20:12 | 3.44 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 145, 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 | 2022-01-25 01:20:12 | 2022-01-25 01:20:16 | 3.65 | dict | {'C': {'GO:0042612': {('GO:0042611', 'is_a')}, 'GO:0042613': {('GO:0042611', 'is_a')}, 'GO:0032398': {('GO:0042611', 'is_a')}, 'GO:0034359': {('GO:0042627', 'is_a')}, 'GO:0034360': {('GO:0042627', 'is_a')}, 'GO:0009426': {('GO:0110165', 'is_a'), ('GO:0030694', 'part_of')}, 'GO:0009429': {('GO:011016...(truncated) | 3 | {} | 2022-01-25 01:20:12 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2022-01-25 01:20:16 | 2022-01-25 01:20:18 | 2.25 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6I0': {'GO:0019814', 'G...(truncated) | 3 | {} | 2022-01-25 01:20:16 | |
| ¶ | pypath.inputs.go.go_annotations_goa | 2022-01-25 01:20:19 | 2022-01-25 01:20:20 | 1.08 | dict | {'C': {'A0A024RBG1': {'GO:0005737', 'GO:0005634', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H8': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6H9': {'GO:0019814', 'GO:0005886', 'GO:0005615'}, 'A0A075B6I0': {'GO:0019814', 'G...(truncated) | 3 | {} | 2022-01-25 01:20:19 | |
| ¶ | pypath.inputs.go.go_annotations_goose | 2022-01-25 01:20:20 | 2022-01-25 01:20:22 | 2.70 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 795, 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 | 2022-01-25 01:20:22 | 2022-01-25 01:20:25 | 2.81 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 681, 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 | 2022-01-25 01:20:25 | 2022-01-25 01:20:33 | 8.20 | dict | {'Entry': ['Gene ontology IDs'], 'Q96NG5': ['GO:0000122', 'GO:0000977', 'GO:0000981', 'GO:0001227', 'GO:0005634', 'GO:0006357', 'GO:0046872'], 'Q6ZN19': ['GO:0000978', 'GO:0001228', 'GO:0005634', 'GO:0006357', 'GO:0046872'], 'Q9UI25': [''], 'Q86XN6': ['GO:0000978', 'GO:0000981', 'GO:0005634', 'GO:00...(truncated) | 20,376 | {} | 2022-01-25 01:20:25 | |
| ¶ | pypath.inputs.go.go_descendants_quickgo | 2022-01-25 01:20:33 | 2022-01-25 01:20:37 | 3.48 | dict | {'C': defaultdict(<class 'set'>, {'GO:0042611': {('GO:0042612', 'is_a'), ('GO:0042613', 'is_a'), ('GO:0032398', 'is_a')}, 'GO:0042627': {('GO:0034359', 'is_a'), ('GO:0034360', 'is_a')}, 'GO:0030694': {('GO:0009426', 'part_of'), ('GO:0009429', 'part_of')}, 'GO:0030689': {('GO:0030691', 'is_a'), ('GO:...(truncated) | 3 | {} | 2022-01-25 01:20:33 | |
| ¶ | pypath.inputs.go.go_descendants_goose | 2022-01-25 01:20:37 | 2022-01-25 01:20:40 | 2.63 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 222, in go_descendants_goose
anc = go_ancestors_goose(aspects = aspects)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 145, 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 | 2022-01-25 01:20:40 | 2022-01-25 01:20:43 | 3.50 | dict | {'C': defaultdict(<class 'set'>, {'GO:0042611': {('GO:0042612', 'is_a'), ('GO:0042613', 'is_a'), ('GO:0032398', 'is_a')}, 'GO:0042627': {('GO:0034359', 'is_a'), ('GO:0034360', 'is_a')}, 'GO:0030694': {('GO:0009426', 'part_of'), ('GO:0009429', 'part_of')}, 'GO:0030689': {('GO:0030691', 'is_a'), ('GO:...(truncated) | 3 | {} | 2022-01-25 01:20:40 | |
| ¶ | 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 | 2022-01-25 01:20:43 | 2022-01-25 01:20:46 | 2.85 | dict | {'C': {'GO:0042613': 'MHC class II protein complex', 'GO:0042611': 'MHC protein complex', 'GO:0042612': 'MHC class I protein complex', 'GO:0042627': 'chylomicron', 'GO:0042629': 'mast cell granule', 'GO:0042622': 'photoreceptor outer segment membrane', 'GO:0030692': 'Noc4p-Nop14p complex', 'GO:00306...(truncated) | 3 | {} | 2022-01-25 01:20:43 | |
| ¶ | pypath.inputs.go.go_terms_goose | 2022-01-25 01:20:46 | 2022-01-25 01:20:49 | 2.65 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 519, 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 | 2022-01-25 01:20:49 | 2022-01-25 01:20:51 | 2.82 | dict | {'C': {'GO:0042613': 'MHC class II protein complex', 'GO:0042611': 'MHC protein complex', 'GO:0042612': 'MHC class I protein complex', 'GO:0042627': 'chylomicron', 'GO:0042629': 'mast cell granule', 'GO:0042622': 'photoreceptor outer segment membrane', 'GO:0030692': 'Noc4p-Nop14p complex', 'GO:00306...(truncated) | 3 | {} | 2022-01-25 01:20:49 | |
| ¶ | pypath.inputs.go.go_terms_solr | 2022-01-25 01:20:51 | 2022-01-25 01:20:52 | 0.63 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/go.py", line 377, 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 | 2022-01-25 01:20:52 | 2022-01-25 01:20:53 | 0.48 | dict | {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) | 402 | {} | 2022-01-25 01:20:52 | |
| ¶ | pypath.inputs.graphviz.graphviz_attrs | 2022-01-25 01:20:53 | 2022-01-25 01:20:54 | 0.92 | tuple | ({'_background': {'type': 'string', 'default': '<none>', 'min': '', 'notes': ''}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'write only'}, 'bgcolor': {'type': 'colorcolorList', 'default': '<none>', 'min': '', 'notes': ''}, 'center': {'type': 'bool', 'default': 'false', 'min': '', 'no...(truncated) | 3 | {} | 2022-01-25 01:20:53 | |
| ¶ | pypath.inputs.guide2pharma.guide2pharma_complexes |
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_download | 2022-01-25 01:20:54 | 2022-01-25 01:21:58 | 64.28 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/guide2pharma.py", line 208, in guide2pharma_download
ligand_uniprots = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/guide2pharma.py", line 209, in <listcomp>
mapping.map_name0(ligand, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:04:27 | |||
| ¶ | pypath.inputs.guide2pharma.guide2pharma_interactions |
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.havugimana.get_havugimana | 2022-01-25 01:21:58 | 2022-01-25 01:22:00 | 1.80 | 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 | {} | 2022-01-25 01:21:58 | |
| ¶ | pypath.inputs.havugimana.havugimana_complexes | 2022-01-25 01:22:00 | 2022-01-25 01:22:00 | 0.04 | dict | {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) | 622 | {} | 2022-01-25 01:22:00 | |
| ¶ | pypath.inputs.hgnc.hgnc_genegroups | 2022-01-25 01:22:00 | 2022-01-25 01:23:07 | 67.10 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/hgnc.py", line 54, in hgnc_genegroups
uniprots = mapping.map_names(uniprots, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:04:34 | |||
| ¶ | pypath.inputs.hippie.hippie_interactions | 2022-01-25 01:23:07 | 2022-01-25 01:23:07 | 0.04 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/hippie.py", line 68, in hippie_interactions
for i, l in enumerate(c.result):
TypeError: 'NoneType' object is not iterable
|
{'broke': True} | 2022-01-24 01:04:43 | |||
| ¶ | pypath.inputs.homologene.get_homologene | 2022-01-25 01:23:07 | 2022-01-25 01:23:12 | 5.08 | 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 | {} | 2022-01-25 01:23:07 | |
| ¶ | 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 | 2022-01-25 01:23:12 | 2022-01-25 01:23:12 | 0.05 | 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 | {'size': 1} | 2022-01-25 01:23:12 | |
| ¶ | pypath.inputs.hpmr.hpmr_annotations | 2022-01-25 01:23:12 | 2022-01-25 01:23:12 | 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 | {} | 2022-01-25 01:23:12 | |
| ¶ | pypath.inputs.hpmr.hpmr_complexes | 2022-01-25 01:23:12 | 2022-01-25 01:23:12 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/hpmr.py", line 354, in hpmr_complexes
for cplex in hpmr_data['complexes']
KeyError: 'complexes'
|
{} | 2022-01-08 00:01:57 | |||
| ¶ | pypath.inputs.hpmr.hpmr_interactions | 2022-01-25 01:23:12 | 2022-01-25 01:23:12 | 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 | {'size': -15} | 2022-01-25 01:23:12 | |
| ¶ | pypath.inputs.hprd.get_hprd | 2022-01-25 01:23:12 | 2022-01-25 01:23:16 | 3.63 | list | [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) | 86,981 | {} | 2022-01-25 01:23:12 | |
| ¶ | pypath.inputs.hprd.hprd_enzyme_substrate | 2022-01-25 01:23:16 | 2022-01-25 01:23:17 | 1.58 | 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 | {} | 2022-01-25 01:23:16 | |
| ¶ | pypath.inputs.hprd.hprd_interactions | 2022-01-25 01:23:17 | 2022-01-25 01:23:19 | 1.56 | 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 | {} | 2022-01-25 01:23:17 | |
| ¶ | pypath.inputs.hprd.hprd_interactions_htp | 2022-01-25 01:23:19 | 2022-01-25 01:23:20 | 1.37 | 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 | {} | 2022-01-25 01:23:19 | |
| ¶ | pypath.inputs.htri.htri_interactions | 2022-01-25 01:23:20 | 2022-01-25 01:23:24 | 3.46 | 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 | {} | 2022-01-25 01:23:20 | |
| ¶ | pypath.inputs.humancellmap.humancellmap_annotations | 2022-01-25 01:23:24 | 2022-01-25 01:24:25 | 61.67 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/humancellmap.py", line 68, in humancellmap_annotations
for uniprot in mapping.map_name(l[9], 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:08:18 | |||
| ¶ | pypath.inputs.humap.humap2_complexes | 2022-01-25 01:24:25 | 2022-01-25 01:25:27 | 61.08 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/humap.py", line 77, in humap2_complexes
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/humap.py", line 78, in <genexpr>
mapping.map_name(uniprot, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:08:20 | |||
| ¶ | pypath.inputs.humap.humap_complexes | 2022-01-25 01:25:27 | 2022-01-25 01:26:27 | 60.79 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/humap.py", line 43, in humap_complexes
for uniprots in itertools.product(*(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/humap.py", line 44, in <genexpr>
mapping.map_name(entrez, 'entrez', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:08:23 | |||
| ¶ | pypath.inputs.huri._huri_interactions |
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.huri.hi_i_interactions | 2022-01-25 01:26:27 | 2022-01-25 01:27:29 | 61.30 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 321, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 287, in _map_ids
return mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:08:24 | |||
| ¶ | pypath.inputs.huri.hi_ii_interactions | 2022-01-25 01:27:29 | 2022-01-25 01:28:39 | 70.73 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 321, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 287, in _map_ids
return mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:08:28 | |||
| ¶ | pypath.inputs.huri.hi_iii_old | 2022-01-25 01:28:39 | 2022-01-25 01:28:39 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 94, 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 | 2022-01-25 01:28:39 | 2022-01-25 01:30:17 | 97.67 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 321, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 287, in _map_ids
return mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:08:47 | |||
| ¶ | pypath.inputs.huri.huri_interactions | 2022-01-25 01:30:17 | 2022-01-25 01:31:32 | 74.50 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 321, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 287, in _map_ids
return mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:09:38 | |||
| ¶ | pypath.inputs.huri.lit_bm_13_interactions | 2022-01-25 01:31:32 | 2022-01-25 01:31:32 | 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 | {} | 2022-01-25 01:31:32 | |
| ¶ | pypath.inputs.huri.lit_bm_17_interactions | 2022-01-25 01:31:32 | 2022-01-25 01:31:35 | 2.35 | 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 | {} | 2022-01-25 01:31:32 | |
| ¶ | pypath.inputs.huri.lit_bm_interactions | 2022-01-25 01:31:35 | 2022-01-25 01:32:36 | 60.74 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 257, in lit_bm_interactions
uniprots_a = mapping.map_name(row[0], 'ensembl', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1453, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 571, in read_mapping_uniprot_list
self.set_uniprot_space()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 626, in set_uniprot_space
self.uniprots = uniprot_input.all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:10:12 | |||
| ¶ | pypath.inputs.huri.rolland_hi_ii_14 | 2022-01-25 01:32:36 | 2022-01-25 01:32:39 | 3.07 | 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 | {} | 2022-01-25 01:32:36 | |
| ¶ | 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 | 2022-01-25 01:32:39 | 2022-01-25 01:33:40 | 61.04 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 321, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 287, in _map_ids
return mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:12:14 | |||
| ¶ | pypath.inputs.huri.yu2011_interactions | 2022-01-25 01:33:40 | 2022-01-25 01:34:42 | 62.32 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 321, in _huri_interactions
uniprots_a = _map_ids(id_a)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/huri.py", line 287, in _map_ids
return mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:12:15 | |||
| ¶ | pypath.inputs.i3d.get_i3d | 2022-01-25 01:34:42 | 2022-01-25 01:34:47 | 5.16 | 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 | {} | 2022-01-25 01:34:42 | |
| ¶ | 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 | 2022-01-25 01:34:47 | 2022-01-25 01:35:47 | 60.29 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 170, in icellnet_annotations
for ia in icellnet_interactions():
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 76, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 200, in _icellnet_get_components
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 200, in <listcomp>
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 204, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:12:25 | |||
| ¶ | pypath.inputs.icellnet.icellnet_complexes | 2022-01-25 01:35:47 | 2022-01-25 01:36:47 | 60.02 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 107, in icellnet_complexes
for ia in icellnet_interactions():
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 76, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 200, in _icellnet_get_components
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 200, in <listcomp>
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 204, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:12:26 | |||
| ¶ | pypath.inputs.icellnet.icellnet_interactions | 2022-01-25 01:36:47 | 2022-01-25 01:37:47 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 76, in icellnet_interactions
ligand_components = _icellnet_get_components(line, 'Ligand')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 200, in _icellnet_get_components
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 200, in <listcomp>
return [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/icellnet.py", line 204, in <genexpr>
mapping.map_name0(genesymbol, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:12:26 | |||
| ¶ | pypath.inputs.ielm.get_ielm |
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ielm.get_ielm_huge |
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.imweb._get_imweb | 2022-01-25 01:37:48 | 2022-01-25 01:37:49 | 1.62 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/imweb.py", line 76, in _get_imweb
hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])
File "/usr/lib/python3.9/json/__init__.py", line 339, in loads
raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not NoneType
|
{} | 2022-01-08 00:05:26 | |||
| ¶ | pypath.inputs.imweb.get_imweb | 2022-01-25 01:37:49 | 2022-01-25 01:37:49 | 0.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/imweb.py", line 115, in get_imweb
token = json.loads(fp.read())['token']
File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2022-01-08 00:05:27 | |||
| ¶ | pypath.inputs.imweb.get_imweb_req | 2022-01-25 01:37:49 | 2022-01-25 01:37:50 | 0.58 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/imweb.py", line 142, in get_imweb_req
token = json.loads(r0.text)['token']
File "/usr/lib/python3.9/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.9/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.9/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
{} | 2022-01-08 00:05:27 | |||
| ¶ | pypath.inputs.innatedb.innatedb_interactions | 2022-01-25 01:37:50 | 2022-01-25 01:37:52 | 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 | {} | 2022-01-25 01:37:50 | |
| ¶ | pypath.inputs.instruct.get_instruct | 2022-01-25 01:37:52 | 2022-01-25 01:37:54 | 1.93 | list | [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) | 11,470 | {} | 2022-01-25 01:37:52 | |
| ¶ | pypath.inputs.instruct.get_instruct_offsets | 2022-01-25 01:37:54 | 2022-01-25 01:37:54 | 0.49 | dict | {('10gs', 'P09211'): 0, ('11gs', 'P09211'): 0, ('12gs', 'P09211'): 0, ('13gs', 'P09211'): 0, ('14gs', 'P09211'): 0, ('16gs', 'P09211'): 0, ('17gs', 'P09211'): 0, ('18gs', 'P09211'): 0, ('19gs', 'P09211'): 0, ('1a00', 'P68871'): 0, ('1a00', 'P69905'): 0, ('1a01', 'P68871'): 0, ('1a01', 'P69905'): 0, ...(truncated) | 11,620 | {} | 2022-01-25 01:37:54 | |
| ¶ | pypath.inputs.intact._try_isoform |
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.intact.intact_interactions | 2022-01-25 01:37:54 | 2022-01-25 01:38:55 | 60.12 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/intact.py", line 113, in intact_interactions
data = c.result['intact.txt']
TypeError: 'NoneType' object is not subscriptable
|
{'broke': True} | 2022-01-24 01:12:33 | |||
| ¶ | pypath.inputs.integrins.get_integrins | 2022-01-25 01:38:55 | 2022-01-25 01:39:56 | 61.04 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/integrins.py", line 65, in get_integrins
return mapping.map_names(integrins, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:13:36 | |||
| ¶ | pypath.inputs.intogen.intogen_annotations | 2022-01-25 01:39:56 | 2022-01-25 01:40:56 | 60.40 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/intogen.py", line 74, in intogen_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:13:36 | |||
| ¶ | pypath.inputs.ipi._ipi_uniprot_pairs |
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.ipi.ipi_uniprot | 2022-01-25 01:40:56 | 2022-01-25 01:40:56 | 0.34 | 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 | {} | 2022-01-25 01:40:56 | |
| ¶ | pypath.inputs.iptmnet.iptmnet_interactions | 2022-01-25 01:40:56 | 2022-01-25 01:42:14 | 77.19 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/iptmnet.py", line 116, in iptmnet_interactions
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1763, in map_name
reflists.get_reflist(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/reflists.py", line 283, in get_reflist
return manager.which_list(id_type = id_type, ncbi_tax_id = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/reflists.py", line 99, in which_list
self.load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/reflists.py", line 122, in load
self.lists[key] = self._load(key)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/reflists.py", line 157, in _load
data = set(input_func(organism = ncbi_tax_id))
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:13:38 | |||
| ¶ | pypath.inputs.italk.italk_annotations | 2022-01-25 01:42:14 | 2022-01-25 01:43:14 | 60.64 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/italk.py", line 109, in italk_annotations
mapping.map_name(row[2], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:13:56 | |||
| ¶ | pypath.inputs.italk.italk_interactions | 2022-01-25 01:43:14 | 2022-01-25 01:44:14 | 60.03 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/italk.py", line 74, in italk_interactions
ligands = mapping.map_name(row[2], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:13:56 | |||
| ¶ | pypath.inputs.italk.italk_raw | 2022-01-25 01:44:14 | 2022-01-25 01:44:14 | 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 | {} | 2022-01-25 01:44:14 | |
| ¶ | pypath.inputs.kea.kea_enzyme_substrate | 2022-01-25 01:44:14 | 2022-01-25 01:45:16 | 62.18 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kea.py", line 111, in kea_enzyme_substrate
for rec in kea_interactions()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kea.py", line 78, in kea_interactions
e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:13:57 | |||
| ¶ | pypath.inputs.kea.kea_interactions | 2022-01-25 01:45:16 | 2022-01-25 01:46:16 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kea.py", line 78, in kea_interactions
e_uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:14:02 | |||
| ¶ | pypath.inputs.kegg.kegg_dbget |
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.kegg.kegg_interactions | 2022-01-25 01:46:16 | 2022-01-25 01:47:20 | 63.62 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 123, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 124, in <listcomp>
common.flat_list([
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 125, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:14:04 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus | 2022-01-25 01:47:20 | 2022-01-25 01:47:34 | 14.04 | set | {KeggMedicusRawInteraction(id_a='2770', id_b='113', name_a='GNAI1', name_b='ADCY7', effect='inhibition', itype='post_translational', pw_type='reference', type_a='gene', type_b='gene', network_id='N00403'), KeggMedicusRawInteraction(id_a='K19378', id_b='868', name_a='(H) H; Morbillivirus hemagglutin...(truncated) | 12,601 | {} | 2022-01-25 01:47:20 | |
| ¶ | pypath.inputs.kegg.kegg_medicus_complexes | 2022-01-25 01:47:34 | 2022-01-25 01:48:35 | 60.43 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 680, in kegg_medicus_complexes
cplexes = kegg_medicus_interactions(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 647, in kegg_medicus_interactions
process_partner(rec.id_a, rec.name_a, rec.type_a),
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 638, in process_partner
process_protein(ids, symbols)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 630, in process_protein
mapping.map_name(id_, 'entrez', 'uniprot') or
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:16:28 | |||
| ¶ | pypath.inputs.kegg.kegg_medicus_interactions | 2022-01-25 01:48:35 | 2022-01-25 01:49:35 | 60.37 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 647, in kegg_medicus_interactions
process_partner(rec.id_a, rec.name_a, rec.type_a),
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 638, in process_partner
process_protein(ids, symbols)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 630, in process_protein
mapping.map_name(id_, 'entrez', 'uniprot') or
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:16:30 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations | 2022-01-25 01:49:35 | 2022-01-25 01:50:35 | 60.11 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 192, in kegg_pathway_annotations
proteins, interactions = kegg_pathways()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 173, in kegg_pathways
data = kegg_interactions()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 123, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 124, in <listcomp>
common.flat_list([
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 125, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:16:31 | |||
| ¶ | pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons | 2022-01-25 01:50:35 | 2022-01-25 01:50:36 | 0.48 | dict | {'A8K7J7': {KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPath...(truncated) | 813 | {} | 2022-01-25 01:50:35 | |
| ¶ | pypath.inputs.kegg.kegg_pathways | 2022-01-25 01:50:36 | 2022-01-25 01:51:36 | 60.16 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 173, in kegg_pathways
data = kegg_interactions()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 123, in kegg_interactions
uentries = dict([(eid, common.uniq_list(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 124, in <listcomp>
common.flat_list([
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kegg.py", line 125, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:16:39 | |||
| ¶ | pypath.inputs.kinasedotcom.kinasedotcom_annotations | 2022-01-25 01:51:36 | 2022-01-25 01:52:41 | 65.70 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/kinasedotcom.py", line 67, in kinasedotcom_annotations
uniprots = mapping.map_name(rec[23].strip(), 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:16:46 | |||
| ¶ | pypath.inputs.kirouac2010.kirouac2010_interactions | 2022-01-25 01:52:41 | 2022-01-25 01:52:45 | 3.69 | list | [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) | 267 | {} | 2022-01-25 01:52:41 | |
| ¶ | pypath.inputs.laudanna.laudanna_directions | 2022-01-25 01:52:45 | 2022-01-25 01:52:46 | 0.42 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/laudanna.py", line 56, in laudanna_directions
LaudannaDirection(
TypeError: <lambda>() missing 1 required positional argument: 'target_genesymbol'
|
{} | 2022-01-08 00:09:37 | |||
| ¶ | pypath.inputs.laudanna.laudanna_effects | 2022-01-25 01:52:46 | 2022-01-25 01:52:46 | 0.38 | 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 | {} | 2022-01-25 01:52:46 | |
| ¶ | pypath.inputs.li2012.get_li2012 | 2022-01-25 01:52:46 | 2022-01-25 01:53:46 | 60.07 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 43, in get_li2012
xls = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-01-24 01:16:57 | |||
| ¶ | pypath.inputs.li2012.li2012_dmi | 2022-01-25 01:53:46 | 2022-01-25 01:54:54 | 67.59 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 133, in li2012_dmi
data = get_li2012()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 43, in get_li2012
xls = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-01-24 01:17:21 | |||
| ¶ | pypath.inputs.li2012.li2012_enzyme_substrate | 2022-01-25 01:54:54 | 2022-01-25 01:55:54 | 60.07 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 88, in li2012_enzyme_substrate
data = get_li2012()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 43, in get_li2012
xls = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-01-24 01:17:50 | |||
| ¶ | pypath.inputs.li2012.li2012_interactions | 2022-01-25 01:55:54 | 2022-01-25 01:56:54 | 60.04 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 57, in li2012_interactions
data = get_li2012()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/li2012.py", line 43, in get_li2012
xls = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{'broke': True} | 2022-01-24 01:17:50 | |||
| ¶ | pypath.inputs.lincs.lincs_compounds | 2022-01-25 01:56:54 | 2022-01-25 01:56:58 | 4.03 | 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 | {} | 2022-01-25 01:56:54 | |
| ¶ | pypath.inputs.lmpid.lmpid_dmi | 2022-01-25 01:56:58 | 2022-01-25 01:57:59 | 60.89 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/lmpid.py", line 96, in lmpid_dmi
data = load_lmpid(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/lmpid.py", line 48, in load_lmpid
uniprots = uniprot_input.get_db(organism = organism, swissprot = None)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:17:55 | |||
| ¶ | pypath.inputs.lmpid.lmpid_interactions | 2022-01-25 01:57:59 | 2022-01-25 01:58:59 | 60.50 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/lmpid.py", line 84, in lmpid_interactions
data = load_lmpid(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/lmpid.py", line 48, in load_lmpid
uniprots = uniprot_input.get_db(organism = organism, swissprot = None)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:17:56 | |||
| ¶ | pypath.inputs.lmpid.load_lmpid | 2022-01-25 01:58:59 | 2022-01-25 02:00:00 | 60.51 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/lmpid.py", line 48, in load_lmpid
uniprots = uniprot_input.get_db(organism = organism, swissprot = None)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:17:57 | |||
| ¶ | pypath.inputs.lncdisease.lncdisease_interactions | 2022-01-25 02:00:00 | 2022-01-25 02:00:00 | 0.20 | list | [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism='human', pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism='human', pmid='22244333')...(truncated) | 478 | {} | 2022-01-25 02:00:00 | |
| ¶ | pypath.inputs.lncrnadb.lncrnadb_interactions | 2022-01-25 02:00:00 | 2022-01-25 02:00:00 | 0.51 | 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 | {} | 2022-01-25 02:00:00 | |
| ¶ | pypath.inputs.locate.locate_localizations | 2022-01-25 02:00:00 | 2022-01-25 02:01:11 | 70.75 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/locate.py", line 115, in locate_localizations
this_uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:17:58 | |||
| ¶ | pypath.inputs.lrdb.lrdb_annotations | 2022-01-25 02:01:11 | 2022-01-25 02:02:11 | 60.35 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/lrdb.py", line 116, in lrdb_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:18:39 | |||
| ¶ | pypath.inputs.lrdb.lrdb_interactions | 2022-01-25 02:02:11 | 2022-01-25 02:02:11 | 0.04 | list | [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) | 3,251 | {} | 2022-01-25 02:02:11 | |
| ¶ | pypath.inputs.macrophage._trim_gname |
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.macrophage.macrophage_interactions | 2022-01-25 02:02:11 | 2022-01-25 02:02:12 | 0.28 | list | [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) | 4,516 | {} | 2022-01-25 02:02:11 | |
| ¶ | pypath.inputs.matrisome.__matrisome_annotations_2 | 2022-01-25 02:02:12 | 2022-01-25 02:02:28 | 15.94 | set | {'SERPINF2', 'PLXDC2', 'P4ha1', 'Col5a3', 'COL8A2', 'TGFBI', 'Adamts9', 'Cilp2', 'Try10', 'PLG', 'SERPINB12', 'Col12a1', 'Vwa1', 'Sftpc', 'IL17D', 'Col8a2', 'Col14a1', 'HSPG2', 'F13b', 'Ambp', 'Angptl1', 'ADAMTS13', 'Angptl2', 'Plod3', 'NPNT', 'VCAN', 'Anxa11', 'S100A4', 'F13a1', 'TGM1', 'Loxl2', 'L...(truncated) | 744 | {} | 2022-01-25 02:02:12 | |
| ¶ | pypath.inputs.matrisome.matrisome_annotations | 2022-01-25 02:02:28 | 2022-01-25 02:03:28 | 60.68 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrisome.py", line 66, in matrisome_annotations
uniprots = mapping.map_names(uniprots, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:18:57 | |||
| ¶ | pypath.inputs.matrixdb._matrixdb_protein_list |
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.matrixdb.matrixdb_annotations | 2022-01-25 02:03:28 | 2022-01-25 02:04:29 | 60.34 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 164, in matrixdb_annotations
for uniprot in method(organism = organism):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 131, in matrixdb_membrane_proteins
return _matrixdb_protein_list('membrane', organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 113, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:18:57 | |||
| ¶ | pypath.inputs.matrixdb.matrixdb_ecm_proteins | 2022-01-25 02:04:29 | 2022-01-25 02:05:29 | 60.12 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 148, in matrixdb_ecm_proteins
return _matrixdb_protein_list('ecm', organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 113, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:19:00 | |||
| ¶ | pypath.inputs.matrixdb.matrixdb_interactions | 2022-01-25 02:05:29 | 2022-01-25 02:05:29 | 0.16 | list | [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) | 425 | {} | 2022-01-25 02:05:29 | |
| ¶ | pypath.inputs.matrixdb.matrixdb_membrane_proteins | 2022-01-25 02:05:29 | 2022-01-25 02:06:29 | 60.05 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 131, in matrixdb_membrane_proteins
return _matrixdb_protein_list('membrane', organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 113, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:19:00 | |||
| ¶ | pypath.inputs.matrixdb.matrixdb_secreted_proteins | 2022-01-25 02:06:29 | 2022-01-25 02:07:29 | 60.20 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 139, in matrixdb_secreted_proteins
return _matrixdb_protein_list('secreted', organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/matrixdb.py", line 113, in _matrixdb_protein_list
proteins = mapping.map_names(proteins, 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:19:02 | |||
| ¶ | pypath.inputs.mcam.mcam_cell_adhesion_molecules | 2022-01-25 02:07:29 | 2022-01-25 02:08:30 | 61.07 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/mcam.py", line 37, in mcam_cell_adhesion_molecules
return {
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/mcam.py", line 41, in <setcomp>
for uniprot in mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:19:02 | |||
| ¶ | pypath.inputs.membranome.membranome_annotations | 2022-01-25 02:08:30 | 2022-01-25 02:09:52 | 81.38 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/membranome.py", line 69, in membranome_annotations
uniprots = mapping.map_name(p['uniprotcode'], 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:19:03 | |||
| ¶ | pypath.inputs.mimp.get_kinase_class | 2022-01-25 02:09:52 | 2022-01-25 02:09:53 | 1.19 | 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 | {} | 2022-01-25 02:09:52 | |
| ¶ | pypath.inputs.mimp.mimp_enzyme_substrate | 2022-01-25 02:09:53 | 2022-01-25 02:09:56 | 2.96 | 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 | {} | 2022-01-25 02:09:53 | |
| ¶ | pypath.inputs.mimp.mimp_interactions | 2022-01-25 02:09:56 | 2022-01-25 02:09:56 | 0.36 | 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 | {} | 2022-01-25 02:09:56 | |
| ¶ | pypath.inputs.mir2disease.mir2disease_interactions | 2022-01-25 02:09:56 | 2022-01-25 02:09:57 | 0.23 | 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 | {} | 2022-01-25 02:09:56 | |
| ¶ | pypath.inputs.mirbase.get_mirbase_aliases | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.08 | tuple | ({'MIMAT0000062': {'hsa-let-7a-5p', 'hsa-let-7a'}, 'MIMAT0000063': {'hsa-let-7b', 'hsa-let-7b-5p'}, 'MIMAT0000064': {'hsa-let-7c', 'hsa-let-7c-5p'}, 'MIMAT0000065': {'hsa-let-7d', 'hsa-let-7d-5p'}, 'MIMAT0000066': {'hsa-let-7e', 'hsa-let-7e-5p'}, 'MIMAT0000067': {'hsa-let-7f-5p', 'hsa-let-7f'}, 'MIM...(truncated) | 2 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirbase.mirbase_ids | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.09 | list | [('MIMAT0000062', 'MI0000062'), ('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000068', 'MI...(truncated) | 3,027 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.06 | list | [('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000064', 'hsa-let-7c'), ('MIMAT0000064', 'hsa-let-7c-5p'), ('MIMAT0000065', 'hsa-let-7d'), ('MIMAT0000065', 'hsa-let-7d-5p'), ('MIMAT0000066', 'hsa-let-7e'),...(truncated) | 3,487 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirbase.mirbase_mature_all | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.09 | list | ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) | 3,027 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.06 | list | [('MI0000060', 'hsa-let-7a-1'), ('MI0000060', 'hsa-let-7a-1L'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7c'), ('MI0000064', 'hsa-let...(truncated) | 2,173 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_all | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.09 | list | ['MI0000062', 'MI0000060', 'MI0000061', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000068', 'MI0000067', 'MI0000069', 'MI0000115', 'MI0000070', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000075', 'MI0000074', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) | 3,027 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirbase.mirbase_precursor_to_mature | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.18 | list | [('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0000062'), ('hsa-let-7a-2L', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMA...(truncated) | 3,361 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirdeathdb.mirdeathdb_interactions | 2022-01-25 02:09:57 | 2022-01-25 02:09:57 | 0.20 | list | [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) | 462 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirecords.mirecords_interactions | 2022-01-25 02:09:57 | 2022-01-25 02:10:02 | 4.66 | list | [MirecordsInteraction(mirna_name='hsa-miR-23a', target_refseq='NM_198155', target_genesymbol='C21orf33', mirna_organism='Homo sapiens', target_organism='Homo sapiens', pmid='12808467'), MirecordsInteraction(mirna_name='mmu-miR-434-3p', target_refseq='NM_184109', target_genesymbol='Rtl1', mirna_organ...(truncated) | 3,106 | {} | 2022-01-25 02:09:57 | |
| ¶ | pypath.inputs.mirtarbase._mirtarbase_interactions |
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.mirtarbase.mirtarbase_interactions | 2022-01-25 02:10:02 | 2022-01-25 02:10:17 | 15.31 | list | [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism='Mus musculus', target_genesymbol='Cd320', target_entrez='54219', target_organism='Mus musculus', target_site='AGAGACTGGGGTCCTCAGACACTCCC', method='Luciferase reporter assay//qRT-PCR//Western blot', catego...(truncated) | 21,560 | {} | 2022-01-25 02:10:02 | |
| ¶ | 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 | 2022-01-25 02:10:17 | 2022-01-25 02:10:18 | 0.31 | 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 | {} | 2022-01-25 02:10:17 | |
| ¶ | pypath.inputs.msigdb.msigdb_annotations | 2022-01-25 02:10:18 | 2022-01-25 02:11:58 | 99.98 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/msigdb.py", line 312, in msigdb_annotations
for uniprot in mapping.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:19:58 | |||
| ¶ | pypath.inputs.msigdb.msigdb_download | 2022-01-25 02:11:58 | 2022-01-25 02:12:19 | 21.36 | dict | {'chr1p12': {'NBPF7', 'RBMX2P3', 'WARS2-AS1', 'NOTCH2P1', 'ZNF697', 'AL139420.1', 'LINC01780', 'NOTCH2', 'HMGCS2', 'TENT5C', 'RNA5SP56', 'GDAP2', 'GAPDHP27', 'RPL6P2', 'RPS3AP12', 'GAPDHP23', 'PSMC1P12', 'REG4', 'PFN1P9', 'MAN1A2', 'WDR3', 'HSD3BP3', 'VTCN1', 'HSD3B2', 'GAPDHP33', 'VDAC2P3', 'WARS2-...(truncated) | 32,284 | {} | 2022-01-25 02:11:58 | |
| ¶ | pypath.inputs.msigdb.msigdb_download_collections | 2022-01-25 02:12:20 | 2022-01-25 02:12:20 | 0.46 | dict | {('hallmark', 'h.all'): {'HALLMARK_TNFA_SIGNALING_VIA_NFKB': {'TNC', 'HBEGF', 'DUSP5', 'NR4A2', 'LITAF', 'G0S2', 'CCNL1', 'BTG2', 'GADD45B', 'IL23A', 'TANK', 'IFNGR2', 'SERPINB8', 'KLF4', 'RELA', 'PPP1R15A', 'ATP2B1', 'ABCA1', 'SOCS3', 'FOSL1', 'SPHK1', 'EDN1', 'MARCKS', 'NFE2L2', 'SPSB1', 'TNIP1', ...(truncated) | 13 | {} | 2022-01-25 02:12:20 | |
| ¶ | pypath.inputs.ncrdeathdb.ncrdeathdb_interactions | 2022-01-25 02:12:20 | 2022-01-25 02:12:21 | 0.38 | 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 | {} | 2022-01-25 02:12:20 | |
| ¶ | pypath.inputs.negatome.negatome_interactions | 2022-01-25 02:12:21 | 2022-01-25 02:12:21 | 0.08 | 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 | {} | 2022-01-25 02:12:21 | |
| ¶ | pypath.inputs.netbiol._netbiol_interactions |
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.netbiol.arn_interactions | 2022-01-25 02:12:21 | 2022-01-25 02:12:21 | 0.14 | list | [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) | 95 | {} | 2022-01-25 02:12:21 | |
| ¶ | pypath.inputs.netbiol.nrf2ome_interactions | 2022-01-25 02:12:21 | 2022-01-25 02:12:21 | 0.14 | list | [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) | 109 | {} | 2022-01-25 02:12:21 | |
| ¶ | pypath.inputs.netpath.netpath_interactions | 2022-01-25 02:12:21 | 2022-01-25 02:12:23 | 1.72 | 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 | {} | 2022-01-25 02:12:21 | |
| ¶ | pypath.inputs.netpath.netpath_names | 2022-01-25 02:12:23 | 2022-01-25 02:12:23 | 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 | {} | 2022-01-25 02:12:23 | |
| ¶ | pypath.inputs.netpath.netpath_pathway_annotations | 2022-01-25 02:12:23 | 2022-01-25 02:13:24 | 60.99 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/netpath.py", line 214, in netpath_pathway_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:22:14 | |||
| ¶ | pypath.inputs.ontology.listof_ontologies | 2022-01-25 02:13:24 | 2022-01-25 02:13:25 | 0.69 | dict | {'ornaseq': 'Ontology for RNA sequencing (ORNASEQ)', 'orth': 'Orthology Ontology', 'pdro': 'The Prescription of Drugs Ontology', 'peco': 'Plant Experimental Conditions Ontology', 'phi': 'PHI-base Ontology', 'planp': 'Planarian Phenotype Ontology (PLANP)', 'po': 'Plant Ontology', 'ppo': 'Plant Phenol...(truncated) | 273 | {} | 2022-01-25 02:13:24 | |
| ¶ | pypath.inputs.ontology.ontology |
Not calling `pypath.inputs.ontology.ontology`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.opm.opm_annotations | 2022-01-25 02:13:25 | 2022-01-25 02:14:34 | 69.71 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/opm.py", line 97, in opm_annotations
uniprot = mapping.map_name0(this_name, 'protein-name', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:22:34 | |||
| ¶ | pypath.inputs.oreganno.oreganno_interactions | 2022-01-25 02:14:34 | 2022-01-25 02:15:34 | 60.05 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/oreganno.py", line 76, in oreganno_interactions
for l in oreganno_raw():
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/oreganno.py", line 43, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{'broke': True} | 2022-01-24 01:22:44 | |||
| ¶ | pypath.inputs.oreganno.oreganno_raw | 2022-01-25 02:15:34 | 2022-01-25 02:16:34 | 60.06 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/oreganno.py", line 43, in oreganno_raw
_ = next(data)
TypeError: 'NoneType' object is not an iterator
|
{'broke': True} | 2022-01-24 01:24:37 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_annotations | 2022-01-25 02:16:34 | 2022-01-25 02:17:35 | 60.38 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/panglaodb.py", line 84, in panglaodb_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:24:50 | |||
| ¶ | pypath.inputs.panglaodb.panglaodb_raw | 2022-01-25 02:17:35 | 2022-01-25 02:17:35 | 0.05 | 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 | {} | 2022-01-25 02:17:35 | |
| ¶ | 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 | 2022-01-25 02:17:35 | 2022-01-25 02:17:48 | 13.27 | list | [PathwayCommonsInteraction(id_a='A1BG', interaction_type='interacts-with', id_b='CRISP3', resource='HPRD'), PathwayCommonsInteraction(id_a='A1CF', interaction_type='interacts-with', id_b='ABCA9', resource='HPRD'), PathwayCommonsInteraction(id_a='A1CF', interaction_type='interacts-with', id_b='APOBEC...(truncated) | 1,261,865 | {} | 2022-01-25 02:17:35 | |
| ¶ | 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 | 2022-01-25 02:17:49 | 2022-01-25 02:17:49 | 0.28 | 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 | {} | 2022-01-25 02:17:49 | |
| ¶ | pypath.inputs.pdb.pdb_chains | 2022-01-25 02:17:49 | 2022-01-25 02:17:55 | 5.51 | 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 | {} | 2022-01-25 02:17:49 | |
| ¶ | pypath.inputs.pdb.pdb_complexes | 2022-01-25 02:17:57 | 2022-01-25 02:18:04 | 6.68 | 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) | 39,114 | {} | 2022-01-25 02:17:57 | |
| ¶ | pypath.inputs.pdb.pdb_uniprot | 2022-01-25 02:18:04 | 2022-01-25 02:18:07 | 3.25 | tuple | ({'P02185': {('2eb8', 'X-ray', 1.65), ('5ut8', 'X-ray', 1.78), ('107m', 'X-ray', 2.09), ('4fwx', 'X-ray', 1.9), ('6f17', 'X-ray', 1.45), ('4fwz', 'X-ray', 1.9), ('1yoh', 'X-ray', 1.65), ('6e04', 'X-ray', 2.0), ('7cez', 'X-ray', 1.57), ('2zt3', 'X-ray', 1.21), ('5utc', 'X-ray', 1.8), ('5b84', 'X-ray'...(truncated) | 2 | {} | 2022-01-25 02:18:04 | |
| ¶ | pypath.inputs.pdzbase.pdzbase_interactions | 2022-01-25 02:18:07 | 2022-01-25 02:18:08 | 0.68 | 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 | {} | 2022-01-25 02:18:07 | |
| ¶ | pypath.inputs.pepcyber.pepcyber_details |
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pepcyber.pepcyber_interactions | 2022-01-25 02:18:08 | 2022-01-25 02:31:00 | 772.21 | 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 | {} | 2022-01-25 02:18:08 | |
| ¶ | pypath.inputs.pfam._pfam_uniprot |
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.pfam.pfam_names | 2022-01-25 02:31:00 | 2022-01-25 02:31:01 | 0.87 | 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 | {} | 2022-01-25 02:31:00 | |
| ¶ | pypath.inputs.pfam.pfam_pdb | 2022-01-25 02:31:01 | 2022-01-25 02:31:04 | 2.74 | tuple | ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '102l': {'PF00959': PfamDomain(chain='A', start=24, end=149)}, '102m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '103l': {'PF00959': PfamDomain(chain='A', start=24, end=151)}, '103m': {'PF00042': PfamDomain(chain='A', star...(truncated) | 2 | {} | 2022-01-25 02:31:01 | |
| ¶ | pypath.inputs.pfam.pfam_regions | 2022-01-25 02:31:04 | 2022-01-25 02:35:30 | 265.84 | tuple | ({}, {}) | 2 | {} | 2022-01-25 02:31:04 | |
| ¶ | pypath.inputs.pfam.pfam_uniprot | 2022-01-25 02:35:30 | 2022-01-25 02:40:15 | 284.48 | tuple | ({'Q7Z3T8': {'PF01363', 'PF11979'}, 'Q8WVZ1': {'PF01529'}, 'A5PKW4': {'PF15410', 'PF01369'}, 'Q9Y291': {'PF08293'}, 'Q8NC74': {'PF10482'}, 'P05423': {'PF05132'}, 'O00391': {'PF18371', 'PF00085', 'PF18108', 'PF04777'}, 'Q9UIV8': {'PF00079'}, 'Q8NC24': {'PF12606'}, 'P00491': {'PF01048'}, 'Q7L099': {'P...(truncated) | 2 | {} | 2022-01-25 02:35:30 | |
| ¶ | pypath.inputs.phobius.phobius_annotations | 2022-01-25 02:40:15 | 2022-01-25 02:40:15 | 0.36 | 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 | {} | 2022-01-25 02:40:15 | |
| ¶ | pypath.inputs.phosphatome.phosphatome_annotations | 2022-01-25 02:40:15 | 2022-01-25 02:41:22 | 67.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphatome.py", line 67, in phosphatome_annotations
uniprots = mapping.map_name(rec[0], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:49:38 | |||
| ¶ | pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate | 2022-01-25 02:41:22 | 2022-01-25 02:41:24 | 1.69 | 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 | {} | 2022-01-25 02:41:22 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_interactions | 2022-01-25 02:41:24 | 2022-01-25 02:41:25 | 0.63 | 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 | {} | 2022-01-25 02:41:24 | |
| ¶ | pypath.inputs.phosphoelm.phosphoelm_kinases | 2022-01-25 02:41:25 | 2022-01-25 02:41:25 | 0.11 | dict | {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) | 247 | {} | 2022-01-25 02:41:25 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate | 2022-01-25 02:41:25 | 2022-01-25 02:41:26 | 0.94 | 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 | {} | 2022-01-25 02:41:25 | |
| ¶ | pypath.inputs.phosphonetworks.phosphonetworks_interactions | 2022-01-25 02:41:26 | 2022-01-25 02:41:26 | 0.02 | list | [['PRKACA', 'RUVBL2'], ['DYRK2', 'CAMKK1'], ['MAPK1', 'SMAD1'], ['MAPK15', 'ETS1'], ['BTK', 'NFKBIA'], ['CSNK2A1', 'STC2'], ['CDK4', 'UBTF'], ['TNNI3K', 'PRDM10'], ['EPHA3', 'FUSIP1'], ['FASTK', 'CBL'], ['LCK', 'CTTN'], ['CSNK1A1', 'SLC4A1'], ['PRKACA', 'CAMKK1'], ['STK3', 'EIF4ENIF1'], ['SRPK1', 'M...(truncated) | 1,821 | {} | 2022-01-25 02:41:26 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_directions | 2022-01-25 02:41:26 | 2022-01-25 02:41:26 | 0.27 | list | [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) | 9,269 | {} | 2022-01-25 02:41:26 | |
| ¶ | pypath.inputs.phosphopoint.phosphopoint_interactions | 2022-01-25 02:41:26 | 2022-01-25 02:41:26 | 0.06 | 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 | {} | 2022-01-25 02:41:26 | |
| ¶ | pypath.inputs.phosphosite._phosphosite_filter_organism |
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.phosphosite.phosphosite_directions | 2022-01-25 02:41:26 | 2022-01-25 02:41:26 | 0.01 | 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 | {} | 2022-01-25 02:41:26 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_enzyme_substrate | 2022-01-25 02:41:26 | 2022-01-25 02:41:26 | 0.39 | 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) | 13,127 | {} | 2022-01-25 02:41:26 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions | 2022-01-25 02:41:26 | 2022-01-25 02:41:26 | 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 | {} | 2022-01-25 02:41:26 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_all | 2022-01-25 02:41:26 | 2022-01-25 02:42:26 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1175, in phosphosite_interactions_all
return phosphosite_interactions_curated() + phosphosite_interactions_noref()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1140, in phosphosite_interactions_curated
return _phosphosite_filter_organism(result, ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1117, in _phosphosite_filter_organism
all_uniprots = uniprot_input.all_uniprots(organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:49:51 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_curated | 2022-01-25 02:42:26 | 2022-01-25 02:43:26 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1140, in phosphosite_interactions_curated
return _phosphosite_filter_organism(result, ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1117, in _phosphosite_filter_organism
all_uniprots = uniprot_input.all_uniprots(organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:49:51 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_new | 2022-01-25 02:43:26 | 2022-01-25 02:43:26 | 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 | {} | 2022-01-25 02:43:26 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_interactions_noref | 2022-01-25 02:43:26 | 2022-01-25 02:44:26 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1157, in phosphosite_interactions_noref
return _phosphosite_filter_organism(result, ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 1117, in _phosphosite_filter_organism
all_uniprots = uniprot_input.all_uniprots(organism = ncbi_tax_id)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:49:51 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_ptm_orthology | 2022-01-25 02:44:26 | 2022-01-25 02:44:32 | 5.29 | 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')}}, ('P31946', 1, 'S', 6, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'S', 6, 10090...(truncated) | 198,541 | {} | 2022-01-25 02:44:26 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_ptms | 2022-01-25 02:44:32 | 2022-01-25 02:44:32 | 0.00 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 335, in phosphosite_ptms
res = intera.Residue(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/internals/intera.py", line 90, in __init__
entity.Entity(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/core/entity.py", line 126, in __init__
self._bootstrap(identifier, id_type, entity_type, taxon)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/core/entity.py", line 156, in _bootstrap
if entity_type in self._smol_types:
TypeError: 'in <string>' requires string as left operand, not NoneType
|
{'broke': True} | 2022-01-24 01:49:57 | |||
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites | 2022-01-25 02:44:32 | 2022-01-25 02:44:33 | 0.55 | dict | {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'protein degradation', 'phosphorylation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) | 5,298 | {} | 2022-01-25 02:44:32 | |
| ¶ | pypath.inputs.phosphosite.phosphosite_regsites_one_organism | 2022-01-25 02:44:33 | 2022-01-25 02:46:25 | 112.02 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 515, in phosphosite_regsites_one_organism
dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/phosphosite.py", line 520, in <lambda>
homologene.homologene_uniprot_dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/homologene.py", line 181, in homologene_uniprot_dict
mapping.map_name(e, 'entrez', 'uniprot', target)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:50:26 | |||
| ¶ | 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 | 2022-01-25 02:46:25 | 2022-01-25 02:47:25 | 60.04 | Obo | <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> | None | {} | 2022-01-25 02:46:25 | |
| ¶ | pypath.inputs.pro.pro_mapping | 2022-01-25 02:47:25 | 2022-01-25 02:47:25 | 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) | 316,288 | {} | 2022-01-25 02:47:25 | |
| ¶ | pypath.inputs.progeny.progeny_annotations | 2022-01-25 02:47:26 | 2022-01-25 02:48:29 | 63.11 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/progeny.py", line 108, in progeny_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:52:28 | |||
| ¶ | pypath.inputs.progeny.progeny_raw | 2022-01-25 02:48:29 | 2022-01-25 02:48:31 | 2.01 | DataFrame | gene pathway weight p.value 0 RFC2 EGFR 1.470647 0.001655 1 ESRRA EGFR 0.178590 0.211838 2 HNRNPK EGFR 0.306699 0.084560 3 CBX6 EGFR -0.675507 0.017641 4 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) | 274,143 | {} | 2022-01-25 02:48:29 | |
| ¶ | pypath.inputs.proteinatlas.get_proteinatlas | 2022-01-25 02:48:31 | 2022-01-25 02:49:31 | 60.46 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/proteinatlas.py", line 59, in get_proteinatlas
uniprots = mapping.map_name(l[1], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:52:44 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_annotations | 2022-01-25 02:49:31 | 2022-01-25 02:50:31 | 60.02 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/proteinatlas.py", line 124, in proteinatlas_annotations
data = get_proteinatlas(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/proteinatlas.py", line 59, in get_proteinatlas
uniprots = mapping.map_name(l[1], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:53:45 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_secretome_annotations | 2022-01-25 02:50:31 | 2022-01-25 02:51:33 | 61.47 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/proteinatlas.py", line 259, in proteinatlas_secretome_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:55:38 | |||
| ¶ | pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations | 2022-01-25 02:51:33 | 2022-01-25 02:52:33 | 60.25 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/proteinatlas.py", line 223, in proteinatlas_subcellular_annotations
uniprots = mapping.map_name(rec['Gene name'], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:55:40 | |||
| ¶ | pypath.inputs.protmapper.get_protmapper | 2022-01-25 02:52:33 | 2022-01-25 02:52:44 | 10.64 | 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 | {} | 2022-01-25 02:52:33 | |
| ¶ | pypath.inputs.protmapper.protmapper_enzyme_substrate | 2022-01-25 02:52:44 | 2022-01-25 02:52:45 | 0.72 | list | [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'22304920', '24727247', '25728676', '24357804', '25545367'}, 'substrate': 'P15336', 'databases': {'PhosphoSite', 'SIGNOR', 'Sparser', 'REACH'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'23708658', '24727247'}, ...(truncated) | 22,139 | {} | 2022-01-25 02:52:44 | |
| ¶ | 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 | 2022-01-25 02:52:45 | 2022-01-25 02:52:45 | 0.68 | list | [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) | 1,894 | {} | 2022-01-25 02:52:45 | |
| ¶ | pypath.inputs.ramilowski2015.ramilowski_locations | 2022-01-25 02:52:45 | 2022-01-25 02:53:48 | 62.70 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/ramilowski2015.py", line 157, in ramilowski_locations
uniprots = mapping.map_name(l[3], 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:55:54 | |||
| ¶ | pypath.inputs.rdata._patch_rdata | 2022-01-25 02:53:48 | 2022-01-25 02:53:48 | 0.00 | NoneType | None | None | {} | 2022-01-25 02:53:48 | |
| ¶ | 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 | 2022-01-25 02:53:48 | 2022-01-25 02:53:50 | 2.40 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 957, in _reactome_reactions
soup = reactome_bs()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 135, in reactome_bs
sbml = reactome_sbml()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2022-01-08 00:48:01 | |||
| ¶ | pypath.inputs.reaction._reactome_reactions_et | 2022-01-25 02:53:50 | 2022-01-25 02:53:53 | 2.40 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 1014, in _reactome_reactions_et
sbml = reactome_sbml()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2022-01-08 00:48:04 | |||
| ¶ | pypath.inputs.reaction._reactome_res |
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction._reactome_species |
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.acsn_biopax | 2022-01-25 02:53:53 | 2022-01-25 02:53:54 | 1.07 | 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 | {} | 2022-01-25 02:53:53 | |
| ¶ | pypath.inputs.reaction.acsn_interactions_2 |
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.get_acsn_effects | 2022-01-25 02:53:54 | 2022-01-25 02:53:54 | 0.12 | 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 | {} | 2022-01-25 02:53:54 | |
| ¶ | 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 | 2022-01-25 02:53:54 | 2022-01-25 02:55:02 | 67.75 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 1156, in get_reactions
rea.load_all()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/pyreact.py", line 1300, in load_all
self.load_netpath()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/pyreact.py", line 1266, in load_netpath
self.add_dataset(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/pyreact.py", line 1313, in add_dataset
self.merge()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/pyreact.py", line 1340, in merge
self.merge_proteins()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/pyreact.py", line 1532, in merge_proteins
target_id, id_attrs = map_protein_ids(ids)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/pyreact.py", line 1505, in map_protein_ids
self.mapper.map_name(id_a['id'], std_id_type,
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{} | 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 | 2022-01-25 02:55:02 | 2022-01-25 02:55:09 | 6.91 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 121, in panther_biopax
c = curl.Curl(url, silent = False, large = True).values()
AttributeError: 'Curl' object has no attribute 'values'
|
{} | 2022-01-08 00:50:32 | |||
| ¶ | pypath.inputs.reaction.panther_interactions |
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.pid_biopax | 2022-01-25 02:55:09 | 2022-01-25 02:55:11 | 2.32 | NoneType | None | None | {} | 2022-01-25 02:55:09 | |
| ¶ | 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 | 2022-01-25 02:55:11 | 2022-01-25 02:56:11 | 60.09 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 92, in reactome_biopax
fileobj = c.result[fname]
TypeError: 'NoneType' object is not subscriptable
|
{'broke': True} | 2022-01-24 01:58:30 | |||
| ¶ | pypath.inputs.reaction.reactome_bs | 2022-01-25 02:56:11 | 2022-01-25 02:56:14 | 2.46 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 135, in reactome_bs
sbml = reactome_sbml()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2022-01-08 00:51:01 | |||
| ¶ | pypath.inputs.reaction.reactome_interactions |
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.reaction.reactome_sbml | 2022-01-25 02:56:14 | 2022-01-25 02:56:16 | 2.39 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/reaction.py", line 63, in reactome_sbml
sbml = c.fileobj
AttributeError: 'Curl' object has no attribute 'fileobj'
|
{} | 2022-01-08 00:51:04 | |||
| ¶ | pypath.inputs.scconnect.scconnect_annotations | 2022-01-25 02:56:16 | 2022-01-25 02:57:16 | 60.32 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 112, in scconnect_annotations
uniprots = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 113, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:59:09 | |||
| ¶ | pypath.inputs.scconnect.scconnect_complexes | 2022-01-25 02:57:16 | 2022-01-25 02:58:16 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 151, in scconnect_complexes
annot = scconnect_annotations(organism = organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 112, in scconnect_annotations
uniprots = [
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 113, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:59:10 | |||
| ¶ | pypath.inputs.scconnect.scconnect_interactions | 2022-01-25 02:58:16 | 2022-01-25 02:59:17 | 60.95 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 259, in scconnect_interactions
for ligand_target in itertools.product(ligands, targets):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 198, in process_partner
[
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/scconnect.py", line 199, in <listcomp>
mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 01:59:10 | |||
| ¶ | pypath.inputs.science.science_download |
Not calling `pypath.inputs.science.science_download`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signalink.signalink_annotations | 2022-01-25 02:59:17 | 2022-01-25 03:00:19 | 61.36 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signalink.py", line 202, in signalink_annotations
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:10:28 | |||
| ¶ | pypath.inputs.signalink.signalink_function_annotations | 2022-01-25 03:00:19 | 2022-01-25 03:01:19 | 60.46 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signalink.py", line 227, in signalink_function_annotations
return signalink_annotations(organism = organism)['function']
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signalink.py", line 202, in signalink_annotations
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:10:30 | |||
| ¶ | pypath.inputs.signalink.signalink_interactions | 2022-01-25 03:01:19 | 2022-01-25 03:01:20 | 0.46 | 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 | {} | 2022-01-25 03:01:19 | |
| ¶ | pypath.inputs.signalink.signalink_pathway_annotations | 2022-01-25 03:01:20 | 2022-01-25 03:02:20 | 60.46 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signalink.py", line 222, in signalink_pathway_annotations
return signalink_annotations(organism = organism)['pathway']
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signalink.py", line 202, in signalink_annotations
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:10:31 | |||
| ¶ | pypath.inputs.signor.signor_complexes | 2022-01-25 03:02:20 | 2022-01-25 03:02:21 | 0.55 | 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) | 3,195 | {} | 2022-01-25 03:02:20 | |
| ¶ | pypath.inputs.signor.signor_enzyme_substrate | 2022-01-25 03:02:21 | 2022-01-25 03:02:23 | 2.29 | list | [{'typ': 'phosphorylation', 'resnum': 114, 'instance': 'NRFTRRASVCAEAYN', 'substrate': 'P31323', 'start': 107, 'end': 121, 'kinase': 'P31323', 'resaa': 'S', 'motif': 'NRFTRRASVCAEAYN', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'15822905'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) | 9,972 | {'size': 1} | 2022-01-25 03:02:21 | |
| ¶ | pypath.inputs.signor.signor_interactions | 2022-01-25 03:02:23 | 2022-01-25 03:02:23 | 0.48 | list | [SignorInteraction(source='P31321', target='P22694', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='down-regulates activity', mechanism='binding', ncbi_tax_id='9606', pubmeds='26687711', direct=True, ptm_type='binding', ptm_residue='', ptm_motif=''), ...(truncated) | 35,831 | {'size': 43} | 2022-01-25 03:02:23 | |
| ¶ | pypath.inputs.signor.signor_pathway_annotations | 2022-01-25 03:02:23 | 2022-01-25 03:03:26 | 62.76 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signor.py", line 334, in signor_pathway_annotations
proteins, interactions = signor_pathways()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/signor.py", line 311, in signor_pathways
mapping.map_name(row[4], 'uniprot', 'uniprot'),
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:10:35 | |||
| ¶ | pypath.inputs.signor.signor_pathways |
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.signor.signor_protein_families | 2022-01-25 03:03:26 | 2022-01-25 03:03:26 | 0.00 | dict | {'SIGNOR-PF1': ['P28482', 'P27361'], 'SIGNOR-PF2': ['Q9HBW0', 'Q9UBY5', 'Q92633'], 'SIGNOR-PF3': ['O14610', 'O60262', 'Q9P2W3', 'P63215', 'P63211', 'P50150', 'P59768', 'P63218', 'P61952', 'Q9UK08', 'Q9UBI6', 'P50151'], 'SIGNOR-PF4': ['P28482', 'P27361'], 'SIGNOR-PF5': ['P01137', 'P10600', 'P61812'],...(truncated) | 87 | {'size': 1} | 2022-01-25 03:03:26 | |
| ¶ | pypath.inputs.spike.spike_interactions | 2022-01-25 03:03:26 | 2022-01-25 03:03:37 | 10.69 | list | [['836', 'CASP3', '8669', 'EIF3J', '1', '10672017', '1', '2', '', 'Published research', '', 'Proteolytic Processing'], ['836', 'CASP3', '3691', 'ITGB4', '1', '17178732', '1', '2', '', 'Published research', '', 'Proteolytic Processing'], ['407042', 'MIR34C', '4609', 'MYC', '1', '20212154', '1', '2', ...(truncated) | 3,842 | {} | 2022-01-25 03:03:26 | |
| ¶ | pypath.inputs.stitch.stitch_interactions | 2022-01-25 03:03:37 | 2022-01-25 03:05:09 | 91.72 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/stitch.py", line 52, in stitch_interactions
for l in c.result:
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/share/curl.py", line 776, in iterfile
for line in fileobj:
File "/usr/lib/python3.9/gzip.py", line 313, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.9/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.9/gzip.py", line 495, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid distance code
|
{'broke': True} | 2022-01-24 02:11:11 | |||
| ¶ | pypath.inputs.string.string_effects | 2022-01-25 03:05:09 | 2022-01-25 03:05:16 | 7.73 | list | [StringInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringInteraction(source='ENSP00000000233', target...(truncated) | 2,250,122 | {} | 2022-01-25 03:05:09 | |
| ¶ | pypath.inputs.surfaceome.surfaceome_annotations | 2022-01-25 03:05:18 | 2022-01-25 03:06:21 | 63.55 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/surfaceome.py", line 43, in surfaceome_annotations
return dict(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/surfaceome.py", line 55, in <genexpr>
for uniprot in mapping.map_name(r[1], 'uniprot', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:12:40 | |||
| ¶ | pypath.inputs.switches_elm.get_switches_elm | 2022-01-25 03:06:21 | 2022-01-25 03:06:36 | 14.46 | 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 | {} | 2022-01-25 03:06:21 | |
| ¶ | pypath.inputs.talklr.talklr_annotations | 2022-01-25 03:06:36 | 2022-01-25 03:07:36 | 60.59 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/talklr.py", line 109, in talklr_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:12:49 | |||
| ¶ | pypath.inputs.talklr.talklr_interactions | 2022-01-25 03:07:36 | 2022-01-25 03:07:36 | 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 | {} | 2022-01-25 03:07:36 | |
| ¶ | pypath.inputs.talklr.talklr_raw | 2022-01-25 03:07:36 | 2022-01-25 03:07:36 | 0.03 | DataFrame | Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) | 2,422 | {} | 2022-01-25 03:07:36 | |
| ¶ | pypath.inputs.tcdb.tcdb_annotations | 2022-01-25 03:07:36 | 2022-01-25 03:08:41 | 64.66 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/tcdb.py", line 103, in tcdb_annotations
uniprots = mapping.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:12:51 | |||
| ¶ | pypath.inputs.tcdb.tcdb_classes | 2022-01-25 03:08:41 | 2022-01-25 03:08:41 | 0.06 | dict | {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) | 21,784 | {} | 2022-01-25 03:08:41 | |
| ¶ | pypath.inputs.tcdb.tcdb_families | 2022-01-25 03:08:41 | 2022-01-25 03:08:41 | 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) | 1,653 | {} | 2022-01-25 03:08:41 | |
| ¶ | pypath.inputs.tfcensus.tfcensus_annotations | 2022-01-25 03:08:41 | 2022-01-25 03:09:41 | 60.06 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/tfcensus.py", line 71, in tfcensus_annotations
uniprots = mapping.map_names(ensg, 'ensembl', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3261, in map_names
return mapper.map_names(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2054, in map_names
return set.union(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2056, in <genexpr>
self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1453, in which_table
reader = MapReader(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 571, in read_mapping_uniprot_list
self.set_uniprot_space()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 626, in set_uniprot_space
self.uniprots = uniprot_input.all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:12:57 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_chains | 2022-01-25 03:09:41 | 2022-01-25 03:09:49 | 7.29 | 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 | {} | 2022-01-25 03:09:41 | |
| ¶ | pypath.inputs.threedcomplex.threedcomplex_contacts | 2022-01-25 03:09:49 | 2022-01-25 03:10:54 | 65.65 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/threedcomplex.py", line 214, in threedcomplex_contacts
for l in contact.split('\n'):
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:13:05 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_ddi | 2022-01-25 03:10:54 | 2022-01-25 03:12:00 | 65.70 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/threedcomplex.py", line 61, in threedcomplex_ddi
contacts = contacts or threedcomplex_contacts()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/threedcomplex.py", line 214, in threedcomplex_contacts
for l in contact.split('\n'):
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:13:42 | |||
| ¶ | pypath.inputs.threedcomplex.threedcomplex_nresidues | 2022-01-25 03:12:00 | 2022-01-25 03:13:06 | 65.84 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/threedcomplex.py", line 277, in threedcomplex_nresidues
for contact in threedcomplex_contacts():
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/threedcomplex.py", line 214, in threedcomplex_contacts
for l in contact.split('\n'):
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:16:55 | |||
| ¶ | pypath.inputs.threedid.get_3did | 2022-01-25 03:13:06 | 2022-01-25 03:14:15 | 68.70 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/threedid.py", line 260, in get_3did
all_unip = set(uniprot_input.all_uniprots(organism = organism))
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:17:04 | |||
| ¶ | pypath.inputs.threedid.get_3did_ddi | 2022-01-25 03:14:15 | 2022-01-25 03:14:48 | 33.39 | dict | {('Q06830', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}, ('PF00578', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}}, ('Q13162', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0...(truncated) | 3,272,215 | {} | 2022-01-25 03:14:15 | |
| ¶ | pypath.inputs.topdb.topdb_annotations | 2022-01-25 03:15:48 | 2022-01-25 03:16:50 | 62.21 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/topdb.py", line 79, in topdb_annotations
uniprots = set(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/topdb.py", line 80, in <genexpr>
mapping.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:48:44 | |||
| ¶ | pypath.inputs.transmir.transmir_interactions | 2022-01-25 03:16:50 | 2022-01-25 03:16:51 | 0.81 | 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 | {} | 2022-01-25 03:16:50 | |
| ¶ | pypath.inputs.trip.take_a_trip | 2022-01-25 03:16:51 | 2022-01-25 03:18:30 | 98.20 | 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 | {} | 2022-01-25 03:16:51 | |
| ¶ | 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 | 2022-01-25 03:18:30 | 2022-01-25 03:18:30 | 0.01 | list | [['P48995', 'Q12791', '25139746;19168436', 'Co-immunofluorescence staining;Co-immunoprecipitation', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '12601176;11290752;11983166', 'Calcium measurement;Fusion protein-pull down assay;Patch clamp;Fl...(truncated) | 359 | {} | 2022-01-25 03:18:30 | |
| ¶ | pypath.inputs.trip.trip_process | 2022-01-25 03:18:30 | 2022-01-25 03:18:30 | 0.01 | dict | {('P48995', 'Q12791'): {'refs': {'25139746', '19168436'}, 'methods': {'Co-immunofluorescence staining', 'Co-immunoprecipitation'}, 'tissues': {'Porcine coronary artery', 'Rat vascular smooth muscle cell', 'HEK293', 'Rat aortic vascular smooth muscle cell'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) | 359 | {} | 2022-01-25 03:18:30 | |
| ¶ | 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 | 2022-01-25 03:18:30 | 2022-01-25 03:18:30 | 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 | {} | 2022-01-25 03:18:30 | |
| ¶ | pypath.inputs.unichem.unichem_mapping |
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.unichem.unichem_sources | 2022-01-25 03:18:30 | 2022-01-25 03:18:30 | 0.02 | dict | {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '11': 'ibm', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma'...(truncated) | 41 | {} | 2022-01-25 03:18:30 | |
| ¶ | pypath.inputs.uniprot._all_uniprots | 2022-01-25 03:18:30 | 2022-01-25 03:19:30 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:50:28 | |||
| ¶ | pypath.inputs.uniprot._cleanup | 2022-01-25 03:19:30 | 2022-01-25 03:19:30 | 0.01 | NoneType | None | None | {} | 2022-01-25 03:19:30 | |
| ¶ | 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 | 2022-01-25 03:19:30 | 2022-01-25 03:19:30 | 0.01 | set | {'O00592', 'P48995', 'P24723', 'Q96GW7', 'Q9HD90', 'Q96NE9', 'P59666', 'Q8TCC3', 'Q9Y291', 'Q8NC74', 'Q6ZRX8', 'P01877', 'P16422', 'Q9Y5J6', 'Q6ZT89', 'O75293', 'Q71RH2', 'Q9BRC7', 'B2RXH2', 'Q9Y547', 'Q9BYG5', 'Q9UK00', 'Q9GZN2', 'A0A075B6S6', 'Q16633', 'P68402', 'P55209', 'Q6P5Z2', 'Q9UHW9', 'P050...(truncated) | 20,375 | {} | 2022-01-25 03:19:30 | |
| ¶ | pypath.inputs.uniprot.all_trembls | 2022-01-25 03:19:30 | 2022-01-25 03:19:48 | 18.50 | set | {'Q6IV50', 'A0A7T0PYS1', 'A0A096LPJ4', 'A0A024R057', 'Q53XM5', 'Q53T75', 'H9M5B5', 'I3L298', 'K7ELG4', 'K4GXX7', 'B4DVA7', 'B9EK54', 'J3KPI3', 'A0A2U7MWD5', 'V5JA74', 'A0A0E3T519', 'E5RHM4', 'Q8N7X6', 'J3KSC7', 'A0A890W0J7', 'M0QX83', 'Q24M88', 'A0A514YDT9', 'G9HWC0', 'A0A2I6J4C3', 'J7K726', 'A0A024...(truncated) | 183,336 | {} | 2022-01-25 03:19:30 | |
| ¶ | pypath.inputs.uniprot.all_uniprots | 2022-01-25 03:19:48 | 2022-01-25 03:20:48 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:50:48 | |||
| ¶ | pypath.inputs.uniprot.deleted_uniprot_genesymbol |
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.uniprot.get_db | 2022-01-25 03:20:48 | 2022-01-25 03:21:48 | 60.02 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:50:48 | |||
| ¶ | pypath.inputs.uniprot.get_uniprot_sec | 2022-01-25 03:21:48 | 2022-01-25 03:22:48 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 783, in test_input
for i, rec in enumerate(value_gen):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:50:48 | |||
| ¶ | pypath.inputs.uniprot.init_db | 2022-01-25 03:22:48 | 2022-01-25 03:23:48 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 02:50:48 | |||
| ¶ | 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 | 2022-01-25 03:23:48 | 2022-01-25 03:23:55 | 6.46 | dict | {'Q96NG5': {UniprotFamily(family='Krueppel C2H2-type zinc-finger protein', subfamily=None)}, 'Q6ZN19': {UniprotFamily(family='Krueppel C2H2-type zinc-finger protein', subfamily=None)}, 'Q86XN6': {UniprotFamily(family='Krueppel C2H2-type zinc-finger protein', subfamily=None)}, 'A8MUZ8': {UniprotFamil...(truncated) | 14,348 | {} | 2022-01-25 03:23:48 | |
| ¶ | 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 | 2022-01-25 03:23:55 | 2022-01-25 03:24:01 | 6.42 | dict | {'Q96NG5': {UniprotKeyword(keyword='Alternative splicing'), UniprotKeyword(keyword='Zinc'), UniprotKeyword(keyword='Repeat'), UniprotKeyword(keyword='Metal-binding'), UniprotKeyword(keyword='Nucleus'), UniprotKeyword(keyword='Zinc-finger'), UniprotKeyword(keyword='Reference proteome'), UniprotKeywor...(truncated) | 20,375 | {} | 2022-01-25 03:23:55 | |
| ¶ | pypath.inputs.uniprot.uniprot_locations | 2022-01-25 03:24:01 | 2022-01-25 03:24:09 | 7.91 | dict | {'Q96NG5': {UniprotLocation(location='Nucleus', features=None)}, 'Q6ZN19': {UniprotLocation(location='Nucleus', features=None)}, 'Q86XN6': {UniprotLocation(location='Nucleus', features=None)}, 'A8MUZ8': {UniprotLocation(location='Nucleus', features=None)}, 'Q08ER8': {UniprotLocation(location='Nucleu...(truncated) | 16,812 | {} | 2022-01-25 03:24:01 | |
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids | 2022-01-25 03:24:09 | 2022-01-25 03:25:09 | 60.01 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 1211, in uniprot_ncbi_taxids
_ = next(c.result)
TypeError: 'NoneType' object is not an iterator
|
{'broke': True} | 2022-01-24 02:51:27 | |||
| ¶ | pypath.inputs.uniprot.uniprot_ncbi_taxids_2 | 2022-01-25 03:25:09 | 2022-01-25 03:25:09 | 0.09 | dict | {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) | 26,745 | {} | 2022-01-25 03:25:09 | |
| ¶ | 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 | 2022-01-25 03:25:09 | 2022-01-25 03:25:11 | 2.10 | dict | {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'H8ZM71': {'Abies balsamea', 'Pinus balsamea', 'Balsam fir'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Grand fir', 'Pinus grandis', 'Abie...(truncated) | 551,796 | {} | 2022-01-25 03:25:09 | |
| ¶ | pypath.inputs.uniprot.uniprot_tissues | 2022-01-25 03:25:12 | 2022-01-25 03:25:20 | 8.40 | dict | {'Q9GZX5': {UniprotTissue(tissue='Wide', level='undefined')}, 'Q9GZP7': {UniprotTissue(tissue='Lung', level='low'), UniprotTissue(tissue='Kidney', level='low'), UniprotTissue(tissue='Olfactory mucosa', level='undefined'), UniprotTissue(tissue='Brain', level='low')}, 'Q9NY84': {UniprotTissue(tissue='...(truncated) | 9,904 | {} | 2022-01-25 03:25:12 | |
| ¶ | pypath.inputs.uniprot.uniprot_topology | 2022-01-25 03:25:20 | 2022-01-25 03:25:46 | 25.06 | dict | {'Q9GZP7': {UniprotTopology(topology='Extracellular', start=1, end=56), UniprotTopology(topology='Cytoplasmic', start=248, end=274), UniprotTopology(topology='Transmembrane', start=57, end=77), UniprotTopology(topology='Transmembrane', start=275, end=295), UniprotTopology(topology='Cytoplasmic', sta...(truncated) | 5,210 | {} | 2022-01-25 03:25:20 | |
| ¶ | pypath.inputs.uniprot.valid_uniprot |
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wang.get_hsn | 2022-01-25 03:25:46 | 2022-01-25 03:25:46 | 0.38 | list | [['1909', 'EDNRA', '4683', 'NBN', 'Pos'], ['7040', 'TGFB1', '7040', 'TGFB1', 'Neg'], ['9669', 'EIF5B', '6135', 'RPL11', 'Pos'], ['367', 'AR', '7337', 'UBE3A', 'Phy'], ['5291', 'PIK3CB', '57580', 'PREX1', 'Pos'], ['5568', 'PRKACG', '1499', 'CTNNB1', 'Pos'], ['156', 'ADRBK1', '155', 'ADRB3', 'Pos'], [...(truncated) | 62,937 | {} | 2022-01-25 03:25:46 | |
| ¶ | pypath.inputs.wang.wang_interactions | 2022-01-25 03:25:46 | 2022-01-25 03:25:46 | 0.36 | list | [['EDNRA', 'NBN', '+'], ['TGFB1', 'TGFB1', '-'], ['EIF5B', 'RPL11', '+'], ['AR', 'UBE3A', '0'], ['PIK3CB', 'PREX1', '+'], ['PRKACG', 'CTNNB1', '+'], ['ADRBK1', 'ADRB3', '+'], ['ITGA2B', 'ACTN4', '0'], ['MCM7', 'UBE3A', '-'], ['CD4', 'ITK', '+'], ['STAT3', 'MYC', '+'], ['ZBTB17', 'NDRG2', '-'], ['CSN...(truncated) | 62,937 | {} | 2022-01-25 03:25:46 | |
| ¶ | pypath.inputs.wojtowicz2020._id_translate |
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments. |
{} | never | ||||||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_interactions | 2022-01-25 03:25:46 | 2022-01-25 03:26:48 | 62.08 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/wojtowicz2020.py", line 85, in wojtowicz2020_interactions
preys = _id_translate(rec.prey_gene_name)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/wojtowicz2020.py", line 71, in _id_translate
return mapping.map_name(name, 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3171, in map_name
return mapper.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 03:16:44 | |||
| ¶ | pypath.inputs.wojtowicz2020.wojtowicz2020_raw | 2022-01-25 03:26:48 | 2022-01-25 03:26:49 | 0.10 | 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 | {} | 2022-01-25 03:26:48 | |
| ¶ | pypath.inputs.zhong2015.zhong2015_annotations | 2022-01-25 03:26:49 | 2022-01-25 03:27:49 | 60.16 |
Traceback (most recent call last):
File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 763, in test_input
value = fun(*_args, **_kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/zhong2015.py", line 61, in zhong2015_annotations
uniprot = mapping.map_name0(rec[0], 'genesymbol', 'uniprot')
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 3202, in map_name0
return mapper.map_name0(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1573, in map_name0
names = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1947, in map_name
mapped_names = self.uniprot_cleanup(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1976, in uniprot_cleanup
uniprots = self.primary_uniprot(uniprots)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2446, in primary_uniprot
primary = self.map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1750, in map_name
mapped_names = self._map_name(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2264, in _map_name
tbl = self.which_table(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 1352, in which_table
self.load_mapping(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 2820, in load_mapping
reader = MapReader(param = resource, **kwargs)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 224, in __init__
self.load()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 254, in load
self.read()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 412, in read
getattr(self, method)()
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/utils/mapping.py", line 523, in read_mapping_file
for i, line in enumerate(infile):
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 457, in get_uniprot_sec
proteome = all_uniprots(organism=organism)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 80, in all_uniprots
return get_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 120, in get_db
init_db(organism = organism, swissprot = swissprot)
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 106, in init_db
globals()['db'][key] = _all_uniprots(
File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220125-001302/pypath/inputs/uniprot.py", line 74, in _all_uniprots
l.strip() for l in data.split('\n')[1:] if l.strip()
AttributeError: 'NoneType' object has no attribute 'split'
|
{'broke': True} | 2022-01-24 03:16:47 |
The OmniPath Team • Saez Lab • 2022-01-25