Interface BioAssayMetadataService

All Known Implementing Classes:

BioAssayMetadataServiceImpl

public interface BioAssayMetadataService

Curator edits to the upstream-derived metadata on a sample: libraryStrategy, librarySelection and extractedMolecule.

Why this exists

GeoConverterImpl is the only other writer of these three columns, and it writes them once, at import, from what GEO declared. GEO under-declares: ribosome profiling is routinely submitted as OTHER, and GeoConverterImpl.effectiveLibStrategy only rescues the cases whose titles say so unambiguously. Everything it deliberately leaves alone — TRAP, polysome purification, the arms where GEO declared RNA-Seq outright — had no route to the column at all, so the alternative was direct SQL, which emits no audit event and validates nothing.

Validation

libraryStrategy and extractedMolecule are checked against closed vocabularies. 🛑 librarySelection is NOT, and deliberately so: GeoSample.librarySelection is kept as the submitter's raw string (cDNA, PCR, other) precisely so that normalizing to a closed set cannot drop values the enum does not know. It is trimmed and length-checked only.

Method Summary

Modifier and Type	Method	Description
Set<String>	getValidLibraryStrategies()	What setLibraryStrategy(ExpressionExperiment, Collection, String) will accept, for the 400 message and for callers that want to offer a menu.
Collection<BioAssay>	setExtractedMolecule(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set extractedMolecule on the given samples.
Collection<BioAssay>	setLibrarySelection(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set librarySelection on the given samples.
Collection<BioAssay>	setLibraryStrategy(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set libraryStrategy on the given samples.

Method Details

getValidLibraryStrategies

Set<String> getValidLibraryStrategies()

What setLibraryStrategy(ExpressionExperiment, Collection, String) will accept, for the 400 message and for callers that want to offer a menu.

setLibraryStrategy

Collection<BioAssay> setLibraryStrategy(ExpressionExperiment ee,
 Collection<BioAssay> bioAssays,
 @Nullable
 String value)

Set libraryStrategy on the given samples.

Parameters:

ee - the experiment the samples belong to; every assay must be one of its samples

bioAssays - the samples to change

value - a GeoLibraryStrategy constant name, MICROARRAY_ONE_COLOR or MICROARRAY_TWO_COLOR, or null to clear the field

Returns:

the samples actually changed; empty when every sample already held value

Throws:

IllegalArgumentException - if value is not a known strategy

setLibrarySelection

Collection<BioAssay> setLibrarySelection(ExpressionExperiment ee,
 Collection<BioAssay> bioAssays,
 @Nullable
 String value)

Set librarySelection on the given samples. Free text by design — see the class javadoc.

Parameters:

value - trimmed; null or blank clears the field

Returns:

the samples actually changed

Throws:

IllegalArgumentException - if value exceeds the column length

setExtractedMolecule

Collection<BioAssay> setExtractedMolecule(ExpressionExperiment ee,
 Collection<BioAssay> bioAssays,
 @Nullable
 String value)

Set extractedMolecule on the given samples.

Parameters:

value - an ExtractedMolecule constant name, or null to clear the field

Returns:

the samples actually changed

Throws:

IllegalArgumentException - if value is not a known molecule