Constructor Detail

• AbstractWorkflowDataModel

  public AbstractWorkflowDataModel()

Method Detail

• prepare

  public static void prepare(AbstractWorkflowDataModel model)

  Validates and potentially modifies the specified model in preparation for launching.

  Parameters:

  model -

• setupDirectory

  public void setupDirectory()

  to be Overridden by the workflow author. Called via reflection in WorkflowDataModelFactory

• setupWorkflow

  public void setupWorkflow()

  to be Overridden by the workflow author you generally don't call this as the workflow author since it promotes hardcoding this will typically be filled in by maven Called via reflection in WorkflowDataModelFactory

• setupEnvironment

  public void setupEnvironment()

  to be Overridden by the workflow author generally people don't override this. Called via reflection in WorkflowDataModelFactory

• setupFiles

  public Map<String,SqwFile> setupFiles()

  to be Overridden by the workflow author the place to specify inputs and outputs to the program also, a user can specify inputs and outputs on jobs directly in which case they are still provisioned properly with respect to the job (inputs before, outputs after) when you define inputs/outputs here they are provisioned before all jobs and after all jobs respectively

  Returns:

• buildWorkflow

  public abstract void buildWorkflow()

  to be Overridden by the workflow author Called via reflection in WorkflowDataModelFactory

• wrapup

  public void wrapup()

  to be Overridden by the workflow author Called via reflection in WorkflowDataModelFactory

• getDate

  public String getDate()

  Returns:

  pre-defined date variable

• setDate

  public void setDate(String date)

  set the pre-defined date variable

  Parameters:

  date -

• getRandom

  public String getRandom()

  Returns:

  the pre-defined random variable

• setRandom

  public void setRandom(String random)

  set the pre-defined random variable

  Parameters:

  random -

• getWorkflowBundleDir

  public String getWorkflowBundleDir()

  Returns:

  the workflow bundle Dir

• setWorkflowBundleDir

  public void setWorkflowBundleDir(String dir)

• getName

  public String getName()

  Returns:

  current workflow name

• setName

  public void setName(String name)

  set the workflow name

  Parameters:

  name -

• getWorkflow

  public Workflow getWorkflow()

  Returns:

  pre-defined workflow object;

• isMetadataWriteBack

  public boolean isMetadataWriteBack()

  need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line

  Returns:

• setMetadataWriteBack

  public void setMetadataWriteBack(boolean b)

  need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line

  Parameters:

  b -

• getConfigs

  public Map<String,String> getConfigs()

  Returns:

  the key-value properties from INI files

• setConfigs

  public void setConfigs(Map<String,String> configs)

  set the key-value properties for workflow

  Parameters:

  configs -

• getVersion

  public String getVersion()

  Returns:

  workflow version

• setVersion

  public void setVersion(String version)

  set workflow version

  Parameters:

  version -

• getFiles

  public Map<String,SqwFile> getFiles()

  Returns:

  user defined files

• getWorkflowBaseDir

  public String getWorkflowBaseDir()

  Returns:

  ${workflow_bundle_dir}/Workflow_Bundle_${workflow-directory-name}/${version}

• getTags

  public Map<String,String> getTags()

  the key-value from metadata.xml

  Returns:

• setTags

  public final void setTags(Map<String,String> tags)

  set the key-value properties from metadata.xml

  Parameters:

  tags -

• getEnv

  public Environment getEnv()

  Returns:

  workflow environment

• addDirectory

  public void addDirectory(String name)

  create a user defined directory before all jobs started

  Parameters:

  name - : directory name

• getDirectories

  public Collection<String> getDirectories()

  Returns:

  user defined directories

• createFile

  public SqwFile createFile(String name)

  Creates a sqwfile attached to the workflow as a whole for provisioning.

  Parameters:

  name -

  Returns:

  the created sqwfile

• getParentAccessions

  public Collection<String> getParentAccessions()

  Returns:

  parent_accessions separated by ","

• getWorkflow_accession

  public String getWorkflow_accession()

  Returns:

  a workflow_accession number

• getWorkflow_run_accession

  public String getWorkflow_run_accession()

  Returns:

  workflow run accession number

• getMetadata_output_file_prefix

  public String getMetadata_output_file_prefix()

  Returns:

  output file prefix

• getMetadata_output_dir

  public String getMetadata_output_dir()

• getWorkflow_engine

  public String getWorkflow_engine()

  Returns:

  engine that workflow will run on, default is pegasus

• setWorkflow_engine

  public void setWorkflow_engine(String workflow_engine)

  default is pegasus

  Parameters:

  workflow_engine -

• getProperty

  public String getProperty(String key)
                     throws Exception

  get the user defined INI files properties

  Parameters:

  key -

  Returns:

  value of the key.

  Throws:

  Exception

• hasProperty

  public boolean hasProperty(String key)

• hasPropertyAndNotNull

  public boolean hasPropertyAndNotNull(String key)

• getWorkflow_directory_name

  public String getWorkflow_directory_name()

• getSeqware_version

  public String getSeqware_version()

• getBundle_version

  public String getBundle_version()