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Simplifies the indexes on the published variants materialized view to speed up refresh jobs. Previously, the five indexes on this mv created large amounts of write overhead. Due to the nature of concurrent mv refreshes, this caused jobs to run for huge amounts of time with no sign of finishing. The single simpler unique index on only id fields of the table should result in much lower index maintenance overhead and much quicker mv refreshs.
To support all pillar project data sets, it is necessary to support score ranges without an explicit classification. This requires some changes to existing validation logic: - The wild type score is no longer required at all times. If you have provided a score range with `normal` classification, the wild type score is required and is required to be within this range. - If you do provide a wild type score, it is required you provide at least one `normal` classification. - Users may provide a new `Not Specified` classification, which comes free of normal and abnormal connotations. - All other validation restrictions remain in place and also apply to the new classification As part of these changes, a new file `utils.py` has been added to mavedb lib code. This file at present contains only one new function to help with string sanitization for score ranges, but should be used for other shared library utilities. At some point, we should make an effort to refactor shared utilities into it.
…cified-score-range Support for Score Ranges with an Unspecified Classification
…indices-on-published-variants-mv Simplify Published Variant MV Indexes
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Features / Enhancements
Closes #413: #414
Bugfixes
Fixes #409: #410
Maintenance
N/A