Class GoldenPathFixtureRecorder

java.lang.Object

ubic.gemma.core.analysis.service.GoldenPathFixtureRecorder

@Tag("goldenPath") @Tag("slow")
public class GoldenPathFixtureRecorder
extends Object

One-shot capture utility that records every GoldenPathSequenceAnalysis.findAssociations(String, Long, Long, String, String, String, ThreePrimeDistanceMethod, ProbeMapperConfig) response for the gpl96.blatresults.psl.gz fixture against a live hg19 GoldenPath database, and writes a JSON fixture used by the fast mock variant of CompositeSequenceGeneMapperServiceTest.

Tagged goldenPath + slow so it is excluded from default mvn verify. Run only when refreshing the fixture, e.g.:

  mvn -pl gemma-core test \
      -Dtest='GoldenPathFixtureRecorder' \
      -DexcludedGroups= \
      -Dgemma.goldenpath.db.host=localhost \
      -Dgemma.goldenpath.db.user=root \
      -Dgemma.goldenpath.db.password=... \
      -Dgemma.goldenpath.db.human=hg19

Coordinate-system note: gpl96.blatresults.psl.gz was generated against hg19 (chromosome sizes match hg19). The fixture is only meaningful when captured from hg19. Running against hg38 would produce empty results for HSPA6 since the gene shifted assemblies. The gemma.goldenpath.db.human property must therefore be hg19 (overriding the hg38 default in default.properties).

Constructor Summary

Constructors

Constructor	Description
GoldenPathFixtureRecorder()

Method Summary

Modifier and Type	Method	Description
void	recordFixture()

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GoldenPathFixtureRecorder

public GoldenPathFixtureRecorder()

Method Details

recordFixture

@Test
public void recordFixture()
                   throws IOException

Throws:

IOException