usage: validate_upload.py [-h] --local_directory PATH
[--optional_fields FIELD [FIELD ...]]
[--no_url_checks] [--clear_cache]
[--ignore_deprecation]
[--dataset_ignore_globs GLOB [GLOB ...]]
[--upload_ignore_globs GLOB [GLOB ...]]
[--encoding ENCODING]
[--plugin_directory PLUGIN_DIRECTORY]
[--run_plugins] [--globus_token GLOBUS_TOKEN]
[--output {as_md,as_text,as_text_list,as_yaml}]
[--add_notes] [--save_report]
Validate a HuBMAP upload, both the metadata TSVs and the datasets.
If you only want to validate a TSV in isolation, look at validate_tsv.py.
optional arguments:
-h, --help show this help message and exit
--local_directory PATH
Local directory to validate
--optional_fields FIELD [FIELD ...]
The listed fields will be treated as optional. (But if
they are supplied in the TSV, they will be validated.)
--no_url_checks Skip URL checks (Spreadsheet Validator API checks
still run).
--clear_cache Clear cache of network check responses.
--ignore_deprecation Allow validation against deprecated versions of
metadata schemas.
--dataset_ignore_globs GLOB [GLOB ...]
Matching files in each dataset directory will be
ignored. Default: .*
--upload_ignore_globs GLOB [GLOB ...]
Matching files and subdirectories in the upload will
be ignored.
--encoding ENCODING Character-encoding to use for parsing TSVs. Default:
ascii. Work-in-progress:
https://github.com/hubmapconsortium/ingest-validation-
tools/issues/494
--plugin_directory PLUGIN_DIRECTORY
Directory of plugin tests.
--run_plugins Run plugin validation even if there are upstream
errors.
--globus_token GLOBUS_TOKEN
Token for URL checking using Entity API.
--output {as_md,as_text,as_text_list,as_yaml}
--add_notes Append a context note to error reports.
--save_report Save the report; Adding "--upload_ignore_globs
'report-*.txt'" is necessary to revalidate.
Typical usage:
--local_directory: Used by lab before upload, and on Globus after upload.
--local_directory + --dataset_ignore_globs + --upload_ignore_globs:
After the initial validation on Globus, the metadata TSVs are broken up,
and one-line TSVs are put in each dataset directory. This structure needs
extra parameters.
Exit status codes:
0: Validation passed
1: Unexpected bug
2: User error
3: Validation failed