Class SplitExperimentTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.core.analysis.preprocess.SplitExperimentTest

@ExtendWith(NetworkAvailableExtension.class)
public class SplitExperimentTest
extends BaseSpringContextTest5

Author:

paul

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
SplitExperimentTest()

Method Summary

Modifier and Type	Method	Description
void	teardown()
void	testSplitGivesEachNewExperimentAnAcl()	Every experiment a split produces must come out editable.
void	testSplitGSE123753ByCollectionOfMaterial()
void	testSplitGSE17183ByOrganismPart()

Methods inherited from class BaseSpringContextTest5

addTestAnalyses, countRowsInTable, deleteFromTables, getJdbcTemplate, getNewTestPersistentCompleteExpressionExperiment, getTaxon, getTestNonPersistentBioSequence, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentBasicExpressionExperiment, getTestPersistentBasicExpressionExperiment, getTestPersistentBibliographicReference, getTestPersistentBioAssay, getTestPersistentBioAssay, getTestPersistentBioMaterial, getTestPersistentBioMaterial, getTestPersistentBioSequence, getTestPersistentBioSequence, getTestPersistentBioSequence2GeneProducts, getTestPersistentBlatResult, getTestPersistentBlatResult, getTestPersistentCompleteExpressionExperiment, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentContact, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentExpressionExperiment, getTestPersistentExpressionExperiment, getTestPersistentGene, getTestPersistentGene, getTestPersistentGeneProduct, getTestPersistentQuantitationType, randomName, resetTestCollectionSize, runAsAdmin, runAsAgent, runAsAnonymous, runAsUser, runAsUser, setTestCollectionSize

Methods inherited from class BaseIntegrationTest5

setUpAuthentication, tearDownSecurityContext

Methods inherited from class Object

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

Constructor Details

SplitExperimentTest

public SplitExperimentTest()

Method Details

testSplitGSE17183ByOrganismPart

@Test
@Tag("slow")
@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testSplitGSE17183ByOrganismPart()
                                     throws Exception

Throws:

Exception

testSplitGSE123753ByCollectionOfMaterial

@Test
@Tag("slow")
@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testSplitGSE123753ByCollectionOfMaterial()
                                              throws Exception

Throws:

Exception

testSplitGivesEachNewExperimentAnAcl

@Test
public void testSplitGivesEachNewExperimentAnAcl()

Every experiment a split produces must come out editable.

A split child is created through eeWriteService.create, so its ACL is the responsibility of AclEventListener.onPostInsert — nothing in SplitExperimentService sets one up itself, and split is Propagation.NEVER so the insert happens in a transaction the method does not own. ExpressionExperiments 93287, 93288, 93289, 93433 and 93434 — splits made under Gemma 1.0, which had no such listener — reached production with no ACL at all and answer 403 on every update. This pins the 2.0 path: the ACL exists and grants edit.

Uses a synthetic single-platform experiment rather than a GEO series so it stays in the default suite; the two tests above are slow and need the network.

teardown

@AfterEach
public void teardown()
              throws Exception

Throws:

Exception