subsample null
Closed this issue · 2 comments
nsheff commented
Geofetch is populating every PEP config file with:
subsample_table: null
But this is a problem, because then eido won't let you validate:
Traceback (most recent call last):
File "/home/ns5bc/.local/bin/eido", line 8, in <module>
sys.exit(main())
File "/home/ns5bc/.local/lib/python3.8/site-packages/eido/cli.py", line 62, in main
validate_project(p, args.schema, args.exclude_case)
File "/home/ns5bc/.local/lib/python3.8/site-packages/eido/eido.py", line 114, in validate_project
_validate_object(project_dict, _preprocess_schema(schema_dict), exclude_case)
File "/home/ns5bc/.local/lib/python3.8/site-packages/eido/eido.py", line 95, in _validate_object
jsonschema.validate(object, schema)
File "/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/jsonschema/validators.py", line 934, in validate
raise error
jsonschema.exceptions.ValidationError: None is not of type 'string'
Failed validating 'type' in schema['properties']['_config']['properties']['subsample_table']:
{'description': 'Path to the subsample annotation table with one row '
'per subsample and sample_name attribute matching an '
'entry in the sample table',
'type': 'string'}
On instance['_config']['subsample_table']:
None
So, I can't run looper
on anything downloaded from geofetch, and the error message is hard to understand. This is a problem with the combination of geofetch and eido.
- Should geofetch put
subsample_table: null
? - Should eido require submsample_table to not be null?
khoroshevskyi commented
I think, it's problem in geofetch, not eido, I will fix it
khoroshevskyi commented
This issue is solved and will be available in release v0.11.0