Class ArrayDesignSequenceProcessorFastacmdTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest

ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessorFastacmdTest

@ExtendWith(NetworkAvailableExtension.class)
public class ArrayDesignSequenceProcessorFastacmdTest
extends AbstractArrayDesignProcessingTest

Test exercises the fastacmd - requires executable.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
static final String	FASTA_CMD_CONFIG_NAME
static final String	FASTA_CMD_EXE

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
ArrayDesignSequenceProcessorFastacmdTest()

Method Summary

Modifier and Type	Method	Description
void	testProcessArrayDesignWithFastaCmdFetch()

Methods inherited from class AbstractArrayDesignProcessingTest

getAd, setupArrayDesign, tearDown

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

Field Details

FASTA_CMD_CONFIG_NAME

public static final String FASTA_CMD_CONFIG_NAME

See Also:

• Constant Field Values

FASTA_CMD_EXE

public static final String FASTA_CMD_EXE

Constructor Details

ArrayDesignSequenceProcessorFastacmdTest

public ArrayDesignSequenceProcessorFastacmdTest()

Method Details

testProcessArrayDesignWithFastaCmdFetch

@Test
@Tag("slow")
@NetworkAvailable(url="ftp://ftp.ncbi.nlm.nih.gov/geo/series/")
public void testProcessArrayDesignWithFastaCmdFetch()
                                             throws Exception

Throws:

Exception