Release 2025.1.1 #406
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Release 2025.1.1 #406
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Modify tentivirus to lentivirus in alembic file.
…essary csv files.
…icodeDecodeError Debug UnicodeDecodeError problem and add a related test.
The previous version of these statistics endpoints featured code that was overly complex for the task at hand. This change refactors statistics code in a way that slightly increases duplicated code (mostly API decorators) while decreasing the complexity of shared functions and logic switches. The result is much clearer and concise endpoints for existing routes.
For historical data, we do not always have the genes that we mapped a target to. This script can be used to infer the mapped gene from the HGVS string of a mapped variant.
…tistics-endpoints Additional Statistics Endpoints and Statistics Router Refactor
…re-ranges-fix Fixes #358: Literal 'null' inserted for NULL score ranges.
Adds utilities for managing materialized and non-materialized views with SQLAlchemy. These ORM methods aren't perfect and will still require knowledge of the underlying view, but make accessing them easier and make their creation automated for test cases. Might also be useful for #89.
Adds refresh jobs for existing materialized views and invokes them: - Refreshes the published variants materialized view whenever a new score set is published. (We cannot delete a published score set, nor edit it's variants, so publication time is the only moment this view becomes outdated). - Refreshes all materialized views at 0300. Adds tests for newly placed publication view refresh. Clarifies connection -> inspector flow during mat view refresh. Opens #405.
Adds an additional two statistics routes for aggregate mapped variant data based on score sets. These routes make use of the new materialized view for published variants.
Materialized View Utilities for SQLAlchemy Models
…statistics-endpoints Additional Statistics Endpoints
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There's a known issue where our tests fail around 5 and 6 PM on here due to UTC time, which is what happened the first run. |
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Features / Enhancements
Closes #375: #397
Supports #375: #404 (don't worry, these routes can be found)
Closes #403: #402
Bug Fixes
Fixes #358: #399
Fixes #392: #393
Fixes #391: #396
Maintenance