Package ubic.gemma.apps

Class ExpressionExperimentManipulatingCLI

java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.cli.util.AbstractAuthenticatedCLI
ubic.gemma.cli.util.AbstractAutoSeekingCLI<ubic.gemma.model.expression.experiment.ExpressionExperiment>
ubic.gemma.apps.ExpressionExperimentManipulatingCLI
All Implemented Interfaces:
org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI
Direct Known Subclasses:
AffyDataFromCelCli, BatchEffectPopulationCli, DeleteDiffExCli, DeleteExperimentsCli, DifferentialExpressionAnalysisCli, DifferentialExpressionAnalysisWriterCli, ExperimentalDesignImportCli, ExperimentalDesignWriterCLI, ExpressionDataCorrMatCli, ExpressionDataMatrixWriterCLI, ExpressionExperimentDataFileGeneratorCli, ExpressionExperimentDataUpdaterCli, ExpressionExperimentMetadataChangelogEntryAdderCli, ExpressionExperimentMetadataChangelogViewerCli, ExpressionExperimentMetadataFileAdderCli, ExpressionExperimentPlatformSwitchCli, ExpressionExperimentPrimaryPubCli, ExpressionExperimentVectorsManipulatingCli, GeeqCli, LinkAnalysisCli, LockExpressionDataFileCli, MakeExperimentPrivateCli, MakeExperimentsPublicCli, OrderVectorsByDesignCli, ProcessedDataComputeCLI, RefreshExperimentCli, ReplaceDataCli, RNASeqBatchInfoCli, RNASeqDataAddCli, SingleCellCellTypeFactorCreatorCli, SingleCellDataLoaderCli, SingleCellSparsityMetricsUpdaterCli, SplitExperimentCli, SVDCli, UpdateEe2AdCli, UpdateEE2CCli, VectorMergingCli
public abstract class ExpressionExperimentManipulatingCLI extends AbstractAutoSeekingCLI<ubic.gemma.model.expression.experiment.ExpressionExperiment>
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 Details

    • 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

    • entityLocator

      @Autowired protected EntityLocator entityLocator

    • entityUrlBuilder

      @Autowired protected ubic.gemma.persistence.util.EntityUrlBuilder entityUrlBuilder

  • Constructor Details

    • ExpressionExperimentManipulatingCLI

      protected ExpressionExperimentManipulatingCLI()

  • Method Details

    • getCommandGroup

      public CLI.CommandGroup getCommandGroup()
      Description copied from interface: CLI
      Obtain the command group for this CLI.
      Specified by:
      getCommandGroup in interface CLI
      Overrides:
      getCommandGroup in class AbstractCLI

    • addSingleExperimentOption

      protected void addSingleExperimentOption(org.apache.commons.cli.Options options, org.apache.commons.cli.Option option)
      Add an option that is only available in single-experiment mode.

    • addSingleExperimentOption

      protected void addSingleExperimentOption(org.apache.commons.cli.Options options, String opt, String longOpt, boolean hasArg, String description)
      Add an option that is only available in single-experiment mode.

    • addSingleExperimentAutoOption

      protected void addSingleExperimentAutoOption(org.apache.commons.cli.Options options, String opt, String longOpt, String description, String noOpt, String longNoOpt, String noDescription)
      Add an auto option that is only available in single-experiment mode.
      See Also:

    • addSingleExperimentEnumOption

      protected <T extends Enum<T>> void addSingleExperimentEnumOption(org.apache.commons.cli.Options options, String opt, String longOpt, String description, Class<T> enumClass, EnumMap<T,org.springframework.context.MessageSourceResolvable> descriptions)
      Add an enumerated option that is only available in single-experiment mode.
      See Also:

    • addDataFileOptions

      protected void addDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation)
      See Also:

    • addDataFileOptions

      protected void addDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, boolean allowFile, boolean allowDirectory, boolean allowCurrentDirectory, boolean allowStdout)
      See Also:

    • addExpressionDataFileOptions

      protected void addExpressionDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation)
      See Also:

    • addSingleCellExpressionDataFileOptions

      protected void addSingleCellExpressionDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation)

    • addDesignFileOptions

      protected void addDesignFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation)
      See Also:

    • addCellMetadataFileOptions

      protected void addCellMetadataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation)
      See Also:

    • getDataFileOptionValue

      protected DataFileOptionValue getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • getDataFileOptionValue

      protected DataFileOptionValue getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, boolean allowStdout, boolean allowCurrentDirectory) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • getExpressionDataFileOptionValue

      protected ExpressionDataFileOptionValue getExpressionDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • getSingleCellExpressionDataFileOptionValue

      protected SingleCellExpressionDataFileOptionValue getSingleCellExpressionDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • getDesignFileOptionValue

      protected DesignFileOptionValue getDesignFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • getCellMetadataFileOptionValue

      protected CellMetadataFileOptionValue getCellMetadataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • buildOptions

      protected final 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.

      Overrides:
      buildOptions in class AbstractCLI

    • buildExperimentOptions

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

    • processOptions

      protected final 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().

      Overrides:
      processOptions in class AbstractAutoSeekingCLI<ubic.gemma.model.expression.experiment.ExpressionExperiment>
      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.

    • processExperimentOptions

      protected void processExperimentOptions(org.apache.commons.cli.CommandLine commandLine) throws org.apache.commons.cli.ParseException
      Throws:
      org.apache.commons.cli.ParseException

    • doAuthenticatedWork

      protected void doAuthenticatedWork() throws Exception
      Specified by:
      doAuthenticatedWork in class AbstractAuthenticatedCLI
      Throws:
      Exception

    • preprocessExpressionExperiments

      protected Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> preprocessExpressionExperiments(Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> expressionExperiments)
      Preprocess the set of ExpressionExperiment before invoking processExpressionExperiments(Collection) or processExpressionExperiment(ExpressionExperiment).

      This can be an opportunity to filter or modify the set of experiments.

    • processAllExpressionExperiments

      protected void processAllExpressionExperiments()
      Process all ExpressionExperiment.

      This is only called when -all and the CLI is configured to treat it lazily with setAllIsLazy().

    • processExpressionExperiments

      protected void processExpressionExperiments(Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> expressionExperiments)
      Process multiple ExpressionExperiment.

      This only called if more than one experiment was found.

    • processExpressionExperiment

      protected void processExpressionExperiment(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment) throws Exception
      Process an ExpressionExperiment.
      Throws:
      Exception

    • postprocessExpressionExperiments

      protected void postprocessExpressionExperiments(Collection<ubic.gemma.model.expression.experiment.ExpressionExperiment> expressionExperiments)
      Post-process ExpressionExperiments that were processed by the CLI.

    • toBatchObject

      protected final Serializable toBatchObject(@Nullable ubic.gemma.model.expression.experiment.ExpressionExperiment object)
      Description copied from class: AbstractAutoSeekingCLI
      Convert the given object to a serializable object for batch processing.
      Specified by:
      toBatchObject in class AbstractAutoSeekingCLI<ubic.gemma.model.expression.experiment.ExpressionExperiment>

    • refreshExpressionExperimentFromGemmaWebSilently

      protected void refreshExpressionExperimentFromGemmaWebSilently(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, boolean refreshVectors, boolean refreshReports)
      A silent version of refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment, boolean, boolean) that produces a warning via AbstractCLI.addWarningObject(Serializable, String, Throwable) instead of throwing an exception.
      See Also:

    • refreshExpressionExperimentFromGemmaWeb

      protected void refreshExpressionExperimentFromGemmaWeb(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, boolean refreshVectors, boolean refreshReports) throws Exception
      Refresh a dataset for Gemma Web.
      Parameters:
      refreshVectors - if true, refresh vectors from the caches, that include raw, single-cell, processed and also cached processed vectors in the form of DataVectorValueObject.
      Throws:
      Exception

    • setSingleExperimentMode

      protected void setSingleExperimentMode()
      Enable the single-experiment mode.

    • setDefaultToAll

      public void setDefaultToAll()
      Default to all datasets if no options are provided.

      This is a very dangerous setting that should be combined with useReferencesIfPossible.

    • setAllIsLazy

      public void setAllIsLazy()
      Enable the "all is lazy" mode.

      When -all is set, no experiments are actually loaded and processAllExpressionExperiments() is called instead.

    • setUseReferencesIfPossible

      protected void setUseReferencesIfPossible()
      Set this 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.

    • isAbortOnError

      public boolean isAbortOnError()
      Indicate if this CLI should abort on error or move on to the next experiment.

    • setAbortOnError

      protected void setAbortOnError()
      Set this to stop processing experiments if an error occurs.

    • formatExperiment

      protected String formatExperiment(ubic.gemma.model.expression.experiment.ExpressionExperiment bas)
      Render an experiment to string, with special handling in case of an uninitialized proxy.

      Use this for printing datasets if useReferencesIfPossible is set to prevent LazyInitializationException.

    • noNeedToRun

      protected boolean noNeedToRun(ubic.gemma.model.expression.experiment.ExpressionExperiment auditable, @Nullable Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType> eventClass)
      Description copied from class: AbstractAutoSeekingCLI
      Check if the given auditable can be skipped.
      Overrides:
      noNeedToRun in class AbstractAutoSeekingCLI<ubic.gemma.model.expression.experiment.ExpressionExperiment>
      Parameters:
      auditable - auditable
      eventClass - can be null
      Returns:
      boolean

    • readChangelogEntryFromConsole

      protected String readChangelogEntryFromConsole(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, @Nullable String defaultText) throws IOException, InterruptedException
      Read a changelog entry from the console.
      Parameters:
      defaultText - a default text to be shown in the editor, or null to keep the file empty
      Throws:
      IOException
      InterruptedException