Field Detail

• interactive

  protected boolean interactive

Constructor Detail

• Metadata

  public Metadata()

  Constructor for Metadata.

Method Detail

• init

  public ReturnValue init()

  Plugin initialization code goes here. This is the first phase of the plugin lifecycle run. Might do things here like set up database access, create temp files, define defaults, etc. Preprocessing can be done here, although normally processing should be done by/during do_run(). The SEQWARE_SETTINGS file contents is passed in here.

  Returns:

• do_test

  public ReturnValue do_test()

  Perform any active system testing here. Use to make sure a DB is available, that a command line tools can be run, etc. You can even write functional tests that run the program you're wrapping on a small known good and then verify the output.

  Returns:

• do_run

  public ReturnValue do_run()

  Performs the main tasks for the plugin. This is where you actually execute your task and where the bulk of your implementation will go.

  Returns:

• listFields

  protected ReturnValue listFields(String table)

  list the fields available to set

  Parameters:

  table -

  Returns:

• addWorkflow

  protected ReturnValue addWorkflow()

  Returns:

  ReturnValue

• addWorkflowRun

  protected ReturnValue addWorkflowRun()

  Returns:

  ReturnValue

• addFile

  protected ReturnValue addFile()

  Returns:

  ReturnValue

• addStudy

  protected ReturnValue addStudy()

  Returns:

  ReturnValue

• addExperiment

  protected ReturnValue addExperiment()

  Returns:

  ReturnValue

• addSample

  protected ReturnValue addSample()

  Returns:

  ReturnValue

• addSequencerRun

  protected ReturnValue addSequencerRun()

  Returns:

  ReturnValue

• addLane

  protected ReturnValue addLane()

• addIUS

  protected ReturnValue addIUS()

• print

  public void print(String string)

  print.

  Overrides:

  print in class Plugin

  Parameters:

  string -

• parseFields

  protected ReturnValue parseFields()

  Returns:

  ReturnValue

• parseFiles

  protected ReturnValue parseFiles()

• parseParentAccessions

  protected int[] parseParentAccessions()

• clean_up

  public ReturnValue clean_up()

  Perform post-task clean-up here. Use to remove temporary files and directories, flush buffers and close db connections, etc.

  Returns:

• get_description

  public String get_description()

  Generates a short description of the plugin, preferably one line.

  Specified by:

  get_description in interface PluginInterface

  Overrides:

  get_description in class Plugin

  Returns:

• closeBufferWriter

  protected void closeBufferWriter()

• checkFields

  public boolean checkFields(String[] fs)

• promptForStudy

  protected void promptForStudy(String[] necessaryFields)

• promptForSample

  protected void promptForSample(String[] necessaryFields)

• promptForSequencerRun

  protected void promptForSequencerRun(String[] necessaryFields)

• promptForExperiment

  protected void promptForExperiment(String[] necessaryFields)

• promptForLane

  protected void promptForLane(String[] necessaryFields)

• promptForIUS

  protected void promptForIUS(String[] necessaryFields)

• promptForFields

  protected void promptForFields(String[] fs)

• promptString

  protected String promptString(String string,
                    String deflt)

• promptInteger

  protected Integer promptInteger(String string,
                      Integer deflt)

• promptBoolean

  protected Boolean promptBoolean(String string,
                      Boolean deflt)

• fieldsConfirmed

  protected boolean fieldsConfirmed(String[] necessaryFields)

• fileString2FileMetadata

  public static FileMetadata fileString2FileMetadata(String fileString)