Package ubic.gemma.cli.options

Class DataFileOptionValue

java.lang.Object
ubic.gemma.cli.options.DataFileOptionValue
Direct Known Subclasses:
CellMetadataFileOptionValue, DesignFileOptionValue, ExpressionDataFileOptionValue
public class DataFileOptionValue extends Object
Shared option values for commands that write data files.
Author:
poirigui

  • Field Details

    • standardLocation

      protected final boolean standardLocation
      Write the file to the standard location in the ${gemma.appdata.home}/dataFiles directory.

    • standardOutput

      protected final boolean standardOutput
      Write the file to standard output.

    • outputFile

      @Nullable protected final Path outputFile
      Write the file to the given output file.

    • outputDir

      @Nullable protected final Path outputDir
      Write the file to the given output directory.

  • Constructor Details

    • DataFileOptionValue

      public DataFileOptionValue(boolean standardLocation, boolean standardOutput, @Nullable Path outputFile, @Nullable Path outputDir, @Nullable String forceOption, boolean force)
      Creates a new DataFileOptionValue instance.
      Parameters:
      standardLocation - Write the file to the standard location in the ${gemma.appdata.home}/dataFiles directory.
      standardOutput - Write the file to standard output.
      outputFile - Write the file to the given output file.
      outputDir - Write the file to the given output directory.
      forceOption - Name of the force option.
      force - Indicate if existing files should be overwritten.

  • Method Details

    • getOutputFile

      public Path getOutputFile(String filenameToUseIfDirectory)
      Parameters:
      filenameToUseIfDirectory - if the output directory is set, this filename will be used to create the output file. Use utilities in ExpressionDataFileUtils to generate the filename.

    • isStandardLocation

      public boolean isStandardLocation()
      Write the file to the standard location in the ${gemma.appdata.home}/dataFiles directory.

    • isStandardOutput

      public boolean isStandardOutput()
      Write the file to standard output.

    • getOutputFile

      @Nullable public Path getOutputFile()
      Write the file to the given output file.

    • getOutputDir

      @Nullable public Path getOutputDir()
      Write the file to the given output directory.

    • getForceOption

      @Nullable public String getForceOption()
      Name of the force option.

    • isForce

      public boolean isForce()
      Indicate if existing files should be overwritten.