AlexsLemonade / AlexsLemonade/refinebio

Figure out why the MetaSRA keyword importer failed on prod

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Dominant language
Python
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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

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