nanoDESI is now part of IMS

nanoDESI is now part of IMS. That means the assay team will locally validate a submission with assay_type nanoDESI and will be validated against the metadatada/dir structure schema files ims.yaml.

I removed the file nano.yaml and updated ims.yaml. However the code is complaining

Running: src/generate_docs.py nano docs-test/nano
Traceback (most recent call last):
  File "src/generate_docs.py", line 88, in <module>
    sys.exit(main())  # pragma: no cover
  File "src/generate_docs.py", line 39, in main
    directory_schema = get_directory_schema(args.type)
  File "/private/tmp/ingest-validation-tools/src/ingest_validation_tools/schema_loader.py", line 213, in get_directory_schema
    schema = load_yaml(_directory_schemas_path / f'{directory_type}.yaml')
  File "/private/tmp/ingest-validation-tools/src/ingest_validation_tools/yaml_include_loader.py", line 19, in load_yaml
    expanded_text = _load_includes(path)
  File "/private/tmp/ingest-validation-tools/src/ingest_validation_tools/yaml_include_loader.py", line 24, in _load_includes
    text = path.read_text()
  File "/Users/icaoberg/opt/anaconda3/lib/python3.8/pathlib.py", line 1235, in read_text
    with self.open(mode='r', encoding=encoding, errors=errors) as f:
  File "/Users/icaoberg/opt/anaconda3/lib/python3.8/pathlib.py", line 1221, in open
    return io.open(self, mode, buffering, encoding, errors, newline,
  File "/Users/icaoberg/opt/anaconda3/lib/python3.8/pathlib.py", line 1077, in _opener
    return self._accessor.open(self, flags, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/private/tmp/ingest-validation-tools/src/ingest_validation_tools/directory-schemas/nano.yaml'

From what file/list in code I need to remove nano.yaml?
How will the code know that nanoDESI assay type means validation with ims.yaml. Do I need to add it to a list/file?

cc @jswelling

hubmapconsortium / ingest-validation-tools

nanoDESI is now part of IMS #1059