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Rationale

Implement support for tables with BIGINT primary keys. E.g. RowId/ObjectId BIGSERIAL
Because of the large number of shared classes, utilities, services, etc, a lot of code was migrated to used Long. Code should now assume that an generic integer object key (as opposed to a known table PK), could be a Long.

This PR is aimed at a) Supporting ObjectID BIGSERIAL b) making it possible (but not automatic) to migrate tables that want to use RowId BIGSERIAL.

Related Pull Requests

Changes

New safer collection classes
class Int/LongHashMap
class Int/LongHashSet
explicit Class for key values in Map Objects returned by BaseSelector
Selector.getValueMap(Class key)
safe "cast" using asInteger or asLong, as opposed to (Integer) and (Long)

labkey-adam and others added 30 commits March 3, 2025 11:17
* Prefer bcftools/liftover

* Support tool to write 10x barcodes to file

* Correct argument

* Support SVType annotation

* Bugfix to UpdateSeuratPrototype

* Expose option to change strandedness threshold

* Auto-detect and remove '=' prefix on import

* Support new TCR components

* Bugfix to PoolImportPanel
… to use FileLike (#350)

* Update ValidateReadsetFilesAction and ImportReferenceSequencesAction to use FileLike
* Remove unused DownloadTempImageAction and ConvertTextToFileAction and its associated form classes.
* Minor auto-refactor code cleanup on a massive scale

* Remove unnecessary cast
* Disable scijava repository during server outage
* Disable scijava dependency during server outage
* Disable scijava repository during server outage
bbimber and others added 28 commits July 2, 2025 17:46
* Move `findUniqueFileName` from `AssayFileWriter` to `FileUtil`
* Bump schema version
bulk search/replace
@labkey-matthewb
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wrong branch

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10 participants