Field Detail

• WORKFLOW_RUN_ACCESSION

  public static final String WORKFLOW_RUN_ACCESSION

  See Also:

  Constant Field Values

Constructor Detail

• WorkflowStatusChecker

  public WorkflowStatusChecker()

  Constructor for WorkflowStatusChecker.

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:

• 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:

• getMetadata

  protected Metadata getMetadata()

• stripInvalidXmlCharacters

  public static String stripInvalidXmlCharacters(String input)

  Stolen from https://stackoverflow.com/questions/93655/stripping-invalid-xml-characters-in-java/9635310#9635310

  Parameters:

  input -

  Returns:

• extractStdErr

  public static String extractStdErr(WorkflowRun wr,
                     Set<String> set)

  Extract stderr from a workflow run

  Parameters:

  wr -

  set - filter SGE results using a particular id

  Returns:

• extractStdOut

  public static String extractStdOut(WorkflowRun wr,
                     Set<String> set)

  Extract stdout from a workflow run

  Parameters:

  wr -

  set - filter SGE results using a particular id

  Returns: