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

Class EvidenceImporterAbstractCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

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

All Implemented Interfaces:

CLI

Direct Known Subclasses:

EvidenceImporterCLI

@Deprecated
public abstract class EvidenceImporterAbstractCLI
extends AbstractAuthenticatedCLI

Deprecated.

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
EvidenceImporterAbstractCLI()	Deprecated.

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Deprecated. Build option implementation.
protected void	createWriteFolder()	Deprecated.
protected String	findTypeOfEvidence()	Deprecated. Look at all Headers and identify them to determine the type of evidence
GemmaCLI.CommandGroup	getCommandGroup()	Deprecated. Obtain the command group for this CLI.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Deprecated. Process command line options.

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, doWork, executeCommand, 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

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

getCommandName, getShortDesc

Constructor Detail

EvidenceImporterAbstractCLI

public EvidenceImporterAbstractCLI()

Deprecated.

Method Detail

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Deprecated.

Description copied from interface: CLI

Obtain the command group for this CLI.

buildOptions

protected void buildOptions(org.apache.commons.cli.Options options)

Deprecated.

Description copied from class: AbstractCLI

Build option implementation.

Implement this method to add options to your command line, using the OptionBuilder.

This is called right after AbstractCLI.buildStandardOptions(Options) so the options will be added after standard options.

Specified by:

buildOptions in class AbstractCLI

processOptions

protected void processOptions(org.apache.commons.cli.CommandLine commandLine)

Deprecated.

Description copied from class: AbstractCLI

Process command line options.

Implement this to provide processing of options. It is called after AbstractCLI.buildOptions(Options) and right before AbstractCLI.doWork().

Specified by:

processOptions in class AbstractCLI

createWriteFolder

protected void createWriteFolder()
                          throws Exception

Deprecated.

Throws:

Exception

findTypeOfEvidence

protected String findTypeOfEvidence()
                             throws Exception

Deprecated.

Look at all Headers and identify them to determine the type of evidence

Returns:

type

Throws:

Exception - IO problems