Package ubic.gemma.core.loader.expression.arrayDesign

Class ArrayDesignSequenceProcessorFastacmdTest

java.lang.Object

org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

ubic.gemma.core.util.test.BaseTest

ubic.gemma.core.util.test.BaseIntegrationTest

ubic.gemma.core.util.test.BaseSpringContextTest

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

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

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

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
final NetworkAvailableRule	networkAvailableRule

Fields inherited from class ubic.gemma.core.util.test.BaseSpringContextTest

externalDatabaseService, log, persisterHelper, rule, taxonService, testHelper

Fields inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

applicationContext, logger

Constructor Summary

Constructors

Constructor	Description
ArrayDesignSequenceProcessorFastacmdTest()

Method Summary

Modifier and Type	Method	Description
void	testProcessArrayDesignWithFastaCmdFetch()

Methods inherited from class ubic.gemma.core.loader.expression.arrayDesign.AbstractArrayDesignProcessingTest

getAd, setupArrayDesign, tearDown

Methods inherited from class ubic.gemma.core.util.test.BaseSpringContextTest

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 ubic.gemma.core.util.test.BaseIntegrationTest

setUpAuthentication, tearDownSecurityContext

Methods inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

setApplicationContext

Methods inherited from class java.lang.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

networkAvailableRule

public final NetworkAvailableRule networkAvailableRule

Constructor Details

ArrayDesignSequenceProcessorFastacmdTest

public ArrayDesignSequenceProcessorFastacmdTest()

Method Details

testProcessArrayDesignWithFastaCmdFetch

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

Throws:

Exception