Package ubic.gemma.core.apps

Class ExpressionExperimentManipulatingCLI

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

All Implemented Interfaces:

CLI

Direct Known Subclasses:

AffyDataFromCelCli, BatchEffectPopulationCli, DeleteDiffExCli, DeleteExperimentsCli, DifferentialExpressionAnalysisCli, ExperimentalDesignWriterCLI, ExpressionDataCorrMatCli, ExpressionDataMatrixWriterCLI, ExpressionExperimentDataFileGeneratorCli, ExpressionExperimentPlatformSwitchCli, ExpressionExperimentPrimaryPubCli, GeeqCli, LinkAnalysisCli, MakeExperimentPrivateCli, MakeExperimentsPublicCli, OrderVectorsByDesignCli, ProcessedDataComputeCLI, RefreshExperimentCli, ReplaceDataCli, RNASeqBatchInfoCli, RNASeqDataAddCli, SplitExperimentCli, SVDCli, VectorMergingCli

public abstract class ExpressionExperimentManipulatingCLI
extends AbstractAuthenticatedCLI

Base class for CLIs that needs one or more expression experiment as an input. It offers the following ways of reading them in:

• All EEs (if -all is supplied)
• All EEs for a particular taxon.
• A specific ExpressionExperimentSet, identified by name
• A comma-delimited list of one or more EEs identified by short name given on the command line
• From a file, with one short name per line.
• EEs matching a query string (e.g., 'brain')
• (Optional) 'Auto' mode, in which experiments to analyze are selected automatically based on their workflow state. This can be enabled and modified by subclasses who override the "needToRun" method.
• All EEs that were last processed after a given date, similar to 'auto' otherwise.

Some of these options can be (or should be) combined, and modified by a (optional) "force" option, and will have customized behavior.

In addition, EEs can be excluded based on a list given in a separate file.

Author:

Paul

Field Summary

Fields

Modifier and Type	Field	Description
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService	auditEventService
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService	auditTrailService
protected ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService	eeService
protected Set<ubic.gemma.model.expression.experiment.BioAssaySet>	expressionExperiments
protected boolean	force	Force processing of EEs regardless of their troubled status.

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

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentManipulatingCLI()

Method Summary

Modifier and Type	Method	Description
protected void	addForceOption(org.apache.commons.cli.Options options)
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
GemmaCLI.CommandGroup	getCommandGroup()	Obtain the command group for this CLI.
protected boolean	noNeedToRun(ubic.gemma.model.common.auditAndSecurity.Auditable auditable, Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType> eventClass)
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.
protected void	refreshExpressionExperimentFromGemmaWeb(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, boolean refreshVectors, boolean refreshReports)	Refresh a dataset for Gemma Web.
protected void	setUseReferencesIfPossible(boolean useReferencesIfPossible)	Set this to true to allow reference to be retrieved instead of actual entities.

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

createBatchTaskExecutorService, getGemmaRestApiClient, processStandardOptions, requireLogin

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

addAutoOption, addAutoOption, addBatchOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, buildStandardOptions, doWork, executeBatchTasks, executeCommand, getAutoSeekEventType, getBatchTaskExecutor, 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

Field Detail

eeService

@Autowired
protected ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService eeService

auditTrailService

@Autowired
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService auditTrailService

auditEventService

@Autowired
protected ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService auditEventService

expressionExperiments

protected final Set<ubic.gemma.model.expression.experiment.BioAssaySet> expressionExperiments

force

protected boolean force

Force processing of EEs regardless of their troubled status.

Constructor Detail

ExpressionExperimentManipulatingCLI

public ExpressionExperimentManipulatingCLI()

Method Detail

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command group for this CLI.

buildOptions

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

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)
                       throws org.apache.commons.cli.ParseException

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

Throws:

org.apache.commons.cli.ParseException - in case of unrecoverable failure (i.e. missing option or invalid value), an exception can be raised and will result in an exit code of AbstractCLI.FAILURE.

addForceOption

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

noNeedToRun

protected boolean noNeedToRun(ubic.gemma.model.common.auditAndSecurity.Auditable auditable,
                              Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType> eventClass)

Parameters:

auditable - auditable

eventClass - can be null

Returns:

boolean

refreshExpressionExperimentFromGemmaWeb

protected void refreshExpressionExperimentFromGemmaWeb(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                       boolean refreshVectors,
                                                       boolean refreshReports)
                                                throws Exception

Refresh a dataset for Gemma Web.

Throws:

Exception

setUseReferencesIfPossible

protected void setUseReferencesIfPossible(boolean useReferencesIfPossible)

Set this to true to allow reference to be retrieved instead of actual entities.

This only works for entities retrieved by ID.

When this is enabled, do not access anything but ExpressionExperiment.getId(), or else proxy-initialization will be triggered, and you will have to deal with a LazyInitializationException.

The default is false.