You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The GOLD to MongoDB process can't"just be restarted" after an error like this without removing the offending identifier from the input file
2025-01-10 07:49:57,990 - WARNING - Duplicate key error for Gs0110165
2025-01-10 07:49:57,990 - INFO - Processing study Gs0110166...
2025-01-10 07:49:57,990 - INFO - Fetching study: Gs0110166
Traceback (most recent call last):
File "/home/mark/gitrepos/sample-annotator/sample_annotator/gold_to_mongo.py", line 160, in
main()
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 1161, in call
return self.main(*args, **kwargs)
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/home/mark/gitrepos/sample-annotator/sample_annotator/gold_to_mongo.py", line 128, in main
study = gc.fetch_study(study_id, **args)
File "/home/mark/gitrepos/sample-annotator/sample_annotator/clients/gold_client.py", line 162, in fetch_study
study = results[0]
IndexError: list index out of range
make: *** [make-gold-cache.Makefile:39: load-gold-biosamples-into-mongo] Error 1
The text was updated successfully, but these errors were encountered:
turbomam
changed the title
Another error, but this one can't just be restarted
Handle IndexError: list index out of range from study = results[0] from gold_client.py line 162, in fetch_study
Jan 14, 2025
The GOLD to MongoDB process can't"just be restarted" after an error like this without removing the offending identifier from the input file
2025-01-10 07:49:57,990 - WARNING - Duplicate key error for Gs0110165
2025-01-10 07:49:57,990 - INFO - Processing study Gs0110166...
2025-01-10 07:49:57,990 - INFO - Fetching study: Gs0110166
Traceback (most recent call last):
File "/home/mark/gitrepos/sample-annotator/sample_annotator/gold_to_mongo.py", line 160, in
main()
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 1161, in call
return self.main(*args, **kwargs)
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mark/.cache/pypoetry/virtualenvs/sample-annotator-O-SG-H46-py3.10/lib/python3.10/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/home/mark/gitrepos/sample-annotator/sample_annotator/gold_to_mongo.py", line 128, in main
study = gc.fetch_study(study_id, **args)
File "/home/mark/gitrepos/sample-annotator/sample_annotator/clients/gold_client.py", line 162, in fetch_study
study = results[0]
IndexError: list index out of range
make: *** [make-gold-cache.Makefile:39: load-gold-biosamples-into-mongo] Error 1
Originally posted by @turbomam in #125 (comment)
The text was updated successfully, but these errors were encountered: