Enum Class GeoLibraryStrategy

java.lang.Object
java.lang.Enum<GeoLibraryStrategy>
ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
All Implemented Interfaces:
Serializable, Comparable<GeoLibraryStrategy>, Constable
public enum GeoLibraryStrategy extends Enum<GeoLibraryStrategy>
SRA's library_strategy controlled vocabulary, as GEO reports it in !Sample_library_strategy.

🛑 Completeness is the point, not tidiness. GeoFamilyParser THROWS on a value it does not recognize, and it does so deliberately: the alternative — folding the unknown into OTHER — would be unsafe, because OTHER is one of the three strategies GeoConverterImpl ALLOWS through as expression data. An unrecognized chromatin or genomic assay would then be imported as if it were RNA. So a missing constant costs an import failure, and the fix for that is to list the value, never to widen the fallback.

The vocabulary below is SRA's, plus the two single-cell spellings GEO adds on its own (scRNA-Seq, snRNA-Seq).

⚠️ Naming an assay here does not admit it. GeoConverterImpl accepts only RNA_SEQ, SSRNA_SEQ and OTHER (with libSource == TRANSCRIPTOMIC); everything else is recognized in order to be REFUSED with a reason rather than to crash.

⚠️ RIBO_SEQ will match fewer samples than its name suggests. Ribosome profiling is usually submitted as OTHER — GSE288755's samples are titled … Ribo-seq replicate #1 and … TCP-seq replicate 1 while their library_strategy reads OTHER — so the constant is here for series that DO declare it, not to reclassify the ones that do not.

Author:
gembro