fix(GAT-9018): free-text linkage fallback + IndexElastic delta-row fixes - #1705
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fix(GAT-9018): free-text linkage fallback + IndexElastic delta-row fixes#1705calmacx wants to merge 3 commits into
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Fix async metadata extraction and Elasticsearch indexing on delta (patch)
version rows, whose raw `metadata` column is empty:
- Extract{Publications,Tools}FromMetadata: reconstruct the GWDM envelope via
DatasetService::getReconstructedMetadataEnvelope() rather than reading the
(empty) metadata column directly.
- IndexElastic / DatasetVersion: reconstruct the latest envelope for indexing
and gate indexing on GwdmMetadataHandler::supportsElasticIndexing().
- GwdmMetadataHandler: add supportsElasticIndexing() + toSearchableFields().
- V2 DatasetController: add ?view=metadataOnly on showActive.
Split out from the combined GAT-9018 branch; the unresolved-linkage fallback
now lives on fix/unresolved-linkages. The validateAllVersions() experiment is
dropped.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
indexElasticPublication, indexElasticDur and indexElasticCollections issued a Dataset::where(['id' => $id])->first() + latestVersion() query per linked dataset (and, for publications, a PublicationHasDatasetVersion lookup per row). Preload all datasets once via whereIn with their versions eager-loaded, resolve each latest version in memory (Dataset::latestVersion() ignores eager-loaded relations, so it can't be used here), and batch the publication link-type lookup with a single whereIn. Also adds a null-guard in indexElasticDur, which previously fataled on a missing dataset/version. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
getMaterialTypes() was duplicated in IndexElastic and DatasetHydrator, each branching on the GWDM version with an inline version_compare() — against the convention that only GwdmHandlerFactory may switch on schema version. - GwdmMetadataHandler: add getMaterialTypes() (base returns null). - Gwdm1xHandler: null (legacy has no tissuesSampleCollection). - Gwdm2xHandler: read + dedupe tissuesSampleCollection. - IndexElastic / DatasetHydrator: resolve the handler and delegate; the inline version_compare() branches (and IndexElastic's dead <2.0 $containsTissue path) are gone. Effective boundary shifts from 2.0 to 1.1 (the factory's split point): versions in [1.1, 2.0) now use the modern path. Locked in by GwdmHandlerMaterialTypesTest. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Stacked on feat/GAT-9018-2. Reinstates the fixes/features that were split out of PR2 because they're independent of the version-handler/DatasetService rearrangement — genuinely pre-existing bugs or new functionality, not caused by the refactor:
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