Package ubic.gemma.core.loader.association.phenotype

Class EvidenceImporterCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI

ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI

All Implemented Interfaces:

CLI

public class EvidenceImporterCLI
extends EvidenceImporterAbstractCLI

Class used to load evidence into Phenocarta. The file used to import the evidence must have at least those columns: (GeneSymbol, GeneId, EvidenceCode, Comments, IsNegative, Phenotypes) The order of the column is not important, EvidenceImporterAbstractCLI contain the naming rules of those colunms

Author:

nicolas

Field Summary

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

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
EvidenceImporterCLI()

Method Summary

Modifier and Type	Method	Description
protected void	doWork()	Command line implementation.
int	executeCommand(String[] args)	Execute the given command given CLI arguments.
GemmaCLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
String	getCommandName()	A short memorable name for the command that can be used to locate this class.
String	getShortDesc()	Obtain a short description for this command explaining what it does.

Methods inherited from class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI

buildOptions, createWriteFolder, findTypeOfEvidence, processOptions

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

executeBatchTasks, processStandardOptions, requireLogin

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

addAutoOption, addAutoOption, addBatchOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, buildStandardOptions, getAutoSeekEventType, getBean, getBean, getLimitingDate, getNumThreads, getOptions, isAutoSeek, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object

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

Constructor Detail

EvidenceImporterCLI

public EvidenceImporterCLI()

Method Detail

executeCommand

public int executeCommand(String[] args)

Description copied from class: AbstractCLI

Execute the given command given CLI arguments.

Parse and process CLI arguments, invoke the command AbstractCLI.doWork() implementation, and print basic statistics about time usage.

Any exception raised by doWork results in a value of AbstractCLI.FAILURE, and any error set in the internal error objects will result in a value of AbstractCLI.FAILURE_FROM_ERROR_OBJECTS.

Specified by:

executeCommand in interface CLI

Overrides:

executeCommand in class AbstractCLI

Returns:

an exit code

getCommandName

public String getCommandName()

Description copied from interface: CLI

A short memorable name for the command that can be used to locate this class.

Returns:

name; if null or blank, this will not be available as a shortcut command.

doWork

protected void doWork()
               throws Exception

Description copied from class: AbstractCLI

Command line implementation.

This is called after AbstractCLI.buildOptions(Options) and AbstractCLI.processOptions(CommandLine), so the implementation can assume that all its arguments have already been initialized.

Specified by:

doWork in class AbstractCLI

Throws:

Exception - in case of unrecoverable failure, an exception is thrown and will result in a AbstractCLI.FAILURE exit code, otherwise use AbstractCLI.addErrorObject(java.lang.Object, java.lang.String, java.lang.Throwable) to indicate an error and resume processing

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command group for this CLI.

Specified by:

getCommandGroup in interface CLI

Overrides:

getCommandGroup in class EvidenceImporterAbstractCLI

getShortDesc

public String getShortDesc()

Description copied from interface: CLI

Obtain a short description for this command explaining what it does.