Update validator for generic assay binary and categorical data #7973
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The changes look good. Thank you @dippindots! We can merge the PR.
| # (1) values defined in ALLOWED_VALUES | ||
| # (2) NA cell value is allowed; means value was not tested on a sample | ||
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| ALLOWED_VALUES = ['yes', 'no', 'true', 'false'] + GenericAssayWiseFileValidator.NULL_VALUES |
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Just a small question. Are the binary values fixed?
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Yes, in the RFC, we planned to have a controlled vocabulary for binary type: https://docs.google.com/document/d/1-6O16_j5b5LeHA5SnChnlEKQTYhcwNh4AEwCxB8FwC8/edit?disco=AAAAHCuNjcs.
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Right. We can extend the list if we have to introduce other binary values.
docs/File-Formats.md
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| ### Generic Assay meta file | ||
| The generic assay metadata file should contain the following fields: | ||
| ``` | ||
| cancer_study_identifier: Same value as specified in meta file of the study | ||
| genetic_alteration_type: GENERIC_ASSAY | ||
| generic_assay_type: <GENERIC_ASSAY_TYPE>, e.g., "TREATMENT_RESPONSE" or "MUTATIONAL_SIGNATURE" | ||
| datatype: LIMIT-VALUE | ||
| datatype: value from LIMIT-VALUE / CATEGORICAL / BINARY |
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Just to be consistent with how we define datatype in other profiles, can we update the line to datatype: LIMIT-VALUE, CATEGORICAL or BINARY?
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The failed tests seems to be not related to the changes in this PR. Can we merge?
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Yes, I think we can merge!
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Fix #7932
Only need to update validator for different data type, importer should use the same one.
GenericAssayContinuousValidatorbinaryandcategoricaldataFile-Formats.mdRef: RFC can be found here: #7920