Package ubic.gemma.cli.util

Class AbstractAutoSeekingCLI<T extends Auditable>

java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.cli.util.AbstractAuthenticatedCLI
ubic.gemma.cli.util.AbstractAutoSeekingCLI<T>
Type Parameters:
T - the type of entity being seeked
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:
ArrayDesignSequenceManipulatingCli, ExpressionExperimentManipulatingCLI
public abstract class AbstractAutoSeekingCLI<T extends Auditable> extends AbstractAuthenticatedCLI
Provide auto-seeking capabilities to a CLI.

This allows CLIs to process entities that lack certain AuditEvent or that haven't been updated since a certain date.

  • Field Details

  • Constructor Details

    • AbstractAutoSeekingCLI

      protected AbstractAutoSeekingCLI(Class<T> entityClass)

  • Method Details

    • addAutoOption

      protected void addAutoOption(org.apache.commons.cli.Options options)
      Add the -auto option.

      The auto option value can be retrieved with isAutoSeek().

    • addAutoOption

      protected void addAutoOption(org.apache.commons.cli.Options options, Class<? extends AuditEventType> autoSeekEventType)
      Add the -auto option for a specific AuditEventType.

      The event type can be retrieved with getAutoSeekEventType().

    • addLimitingDateOption

      protected void addLimitingDateOption(org.apache.commons.cli.Options options)
      Add the -mdate option.

      The limiting date can be retrieved with getLimitingDate().

    • addForceOption

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

    • addForceOption

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

    • isAutoSeek

      protected boolean isAutoSeek()
      Indicate if auto-seek is enabled.

    • getAutoSeekEventType

      protected Class<? extends AuditEventType> getAutoSeekEventType()
      Indicate the event to be used for auto-seeking.

    • getLimitingDate

      @Nullable protected Date getLimitingDate()
      Obtain the limiting date (i.e. starting date at which entities should be processed).

    • isForce

      protected boolean isForce()
      Check if forcing is enabled.

    • setForce

      protected void setForce()
      Enable the forcing mode.

    • processOptions

      @OverridingMethodsMustInvokeSuper 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().

      Overrides:
      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.

    • addSuccessObject

      protected final void addSuccessObject(T successObject, String message)

    • addSuccessObject

      protected final void addSuccessObject(T successObject)

    • addWarningObject

      protected final void addWarningObject(@Nullable T warningObject, String message)

    • addWarningObject

      protected final void addWarningObject(@Nullable T warningObject, String message, Throwable throwable)

    • addErrorObject

      protected final void addErrorObject(@Nullable T errorObject, String message, Throwable throwable)

    • addErrorObject

      protected final void addErrorObject(@Nullable T errorObject, String message)

    • addErrorObject

      protected final void addErrorObject(@Nullable T errorObject, Exception exception)

    • toBatchObject

      protected abstract Serializable toBatchObject(@Nullable T object)
      Convert the given object to a serializable object for batch processing.

    • noNeedToRun

      protected boolean noNeedToRun(T auditable, @Nullable Class<? extends AuditEventType> eventClass)
      Check if the given auditable can be skipped.
      Parameters:
      auditable - auditable
      eventClass - can be null
      Returns:
      boolean