Package ubic.gemma.core.util

Class AbstractCLIContextCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractSpringAwareCLI

ubic.gemma.core.util.AbstractCLIContextCLI

All Implemented Interfaces:

CLI

Direct Known Subclasses:

ArrayDesignAlternativePopulateCli, ArrayDesignSequenceManipulatingCli, BibRefUpdaterCli, BlacklistCli, CountObsoleteTermsCli, DatabaseViewGeneratorCLI, DeleteEvidenceCLI, EvidenceImporterAbstractCLI, ExperimentalDesignImportCli, ExperimentalDesignViewCli, ExpressionExperimentManipulatingCLI, ExternalDatabaseAdderCli, ExternalDatabaseEvidenceImporterAbstractCLI, ExternalFileGeneLoaderCLI, GenericGenelistDesignGenerator, GeoGrabberCli, LoadEvidenceForClassifier, LoadExpressionDataCli, LoadSimpleExpressionDataCli, MultifunctionalityCli, NCBIGene2GOAssociationLoaderCLI, NcbiGeneLoaderCLI, PubMedLoaderCli, PubMedSearcher, TaxonLoaderCli, UpdatePubMedCli

public abstract class AbstractCLIContextCLI
extends AbstractSpringAwareCLI

Spring configuration for CLI.

Author:

anton date: 18/02/13

Field Summary

Fields inherited from class ubic.gemma.core.util.AbstractSpringAwareCLI

auditEventService, auditTrailService

Fields inherited from class ubic.gemma.core.util.AbstractCLI

AUTO_OPTION_NAME, autoSeek, autoSeekEventType, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, host, log, mDate, numThreads, port, SUCCESS, THREADS_OPTION

Constructor Summary

Constructors

Constructor	Description
AbstractCLIContextCLI()

Method Summary

Modifier and Type	Method	Description
protected ubic.gemma.model.expression.arrayDesign.ArrayDesign	locateArrayDesign(String name, ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService arrayDesignService)
protected static List<String>	readListFileToStrings(String fileName)	may be tab-delimited, only first column used, commented (#) lines are ignored.
protected ubic.gemma.model.genome.Taxon	setTaxonByName(org.apache.commons.cli.CommandLine commandLine, ubic.gemma.persistence.service.genome.taxon.TaxonService taxonService)

Methods inherited from class ubic.gemma.core.util.AbstractSpringAwareCLI

executeBatchTasks, getBean, getBean, getPersisterHelper, getShortDesc, noNeedToRun, processStandardOptions, requireLogin

Methods inherited from class ubic.gemma.core.util.AbstractCLI

addAutoOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addHostAndPortOptions, addSuccessObject, addSuccessObject, addThreadsOption, buildOptions, buildStandardOptions, doWork, executeCommand, getDoubleOptionValue, getDoubleOptionValue, getFileNameOptionValue, getFileNameOptionValue, getIntegerOptionValue, getIntegerOptionValue, getLimitingDate, printHelp, processOptions

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.util.CLI

getCommandGroup, getCommandName

Constructor Detail

AbstractCLIContextCLI

public AbstractCLIContextCLI()

Method Detail

readListFileToStrings

protected static List<String> readListFileToStrings(String fileName)
                                             throws IOException

may be tab-delimited, only first column used, commented (#) lines are ignored.

Parameters:

fileName - the file name

Returns:

list of ee identifiers

Throws:

IOException - in case there is an IO error while reading the file

setTaxonByName

protected ubic.gemma.model.genome.Taxon setTaxonByName(org.apache.commons.cli.CommandLine commandLine,
                                                       ubic.gemma.persistence.service.genome.taxon.TaxonService taxonService)

locateArrayDesign

protected ubic.gemma.model.expression.arrayDesign.ArrayDesign locateArrayDesign(String name,
                                                                                ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService arrayDesignService)

Parameters:

name - of the array design to find.

arrayDesignService - the arrayDesignService to use for the AD retrieval

Returns:

an array design, if found. Bails otherwise with an error exit code