AlexsLemonade / AlexsLemonade/refinebio
Figure out why the MetaSRA keyword importer failed on prod
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
Importing all of the MetaSRA data
### Problem or idea
```
ubuntu@ip-10-0-38-47:~$ docker logs brave_taussig
Traceback (most recent call last):
File "manage.py", line 22, in
execute_from_command_line(sys.argv)
File "/usr/local/lib/python3.6/dist-packages/django/core/management/__init__.py", line 419, in execute_from_command_line
utility.execute()
File "/usr/local/lib/python3.6/dist-packages/django/core/management/__init__.py", line 413, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/usr/local/lib/python3.6/dist-packages/django/core/management/base.py", line 354, in run_from_argv
self.execute(*args, **cmd_options)
File "/usr/local/lib/python3.6/dist-packages/django/core/management/base.py", line 398, in execute
output = self.handle(*args, **options)
File "/home/user/data_refinery_foreman/foreman/management/commands/import_external_sample_keywords.py", line 120, in handle
import_keywords(keywords, source)
File "/home/user/data_refinery_foreman/foreman/management/commands/import_external_sample_keywords.py", line 59, in import_keywords
sample=sample, source=source, name=OntologyTerm.get_or_create_from_api(keyword),
File "/usr/local/lib/python3.6/dist-packages/data_refinery_common/models/ontology_term.py", line 195, in get_or_create_from_api
return cls._create_from_api(ontology_term)
File "/usr/local/lib/python3.6/dist-packages/data_refinery_common/models/ontology_term.py", line 185, in _create_from_api
term.human_readable_name = get_human_readable_name_from_api(ontology_term)
File "/usr/local/lib/python3.6/dist-packages/data_refinery_common/models/ontology_term.py", line 56, in get_human_readable_name_from_api
return get_human_readable_name_from_cellosaurus(ontology_term)
File "/usr/local/lib/python3.6/dist-packages/data_refinery_common/models/ontology_term.py", line 33, in get_human_readable_name_from_cellosaurus
raise ValueError("Could not find a human-readable name for '{}'".format(ontology_term))
ValueError: Could not find a human-readable name for 'CVCL:A596'
```
### Solution or next step
Is `CVCL:A596` even a valid ontology term? I should have already imported the entire cellosaurus ontology
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with foreman/management/commands/import_external_sample_keywords.py and data_refinery_common/models/ontology_term.py, following the traceback through get_human_readable_name_from_cellosaurus for CVCL:A596. Check whether that term exists in the imported Cellosaurus ontology and determine why the production import cannot resolve its human-readable name. Done means the term's validity and the import failure's cause are documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- django, docker, python
- Domain
- backend, data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100