Constructor Detail

• SqwFile

  public SqwFile()

Method Detail

• getType

  public String getType()

• setType

  public void setType(String type)

• getSourcePath

  public String getSourcePath()

• setSourcePath

  public void setSourcePath(String location)

• getOutputPath

  public String getOutputPath()

• setOutputPath

  public void setOutputPath(String location)

• isOutput

  public boolean isOutput()

  is an output file?

  Returns:

• isInput

  public boolean isInput()

  is an input file?

  Returns:

• setIsInput

  public void setIsInput(boolean isInupt)

  isInput = @param isInput isOutput = !@param isInput

  Parameters:

  isInupt -

• setIsOutput

  public void setIsOutput(boolean isOutput)

  isInput = !@param isOutput isOutput = @param isOutput

  Parameters:

  isOutput -

• equals

  public boolean equals(Object obj)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object

• isForceCopy

  public boolean isForceCopy()

• setForceCopy

  public void setForceCopy(boolean forceCopy)

  when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob

  Parameters:

  forceCopy -

• getProvisionedPath

  public String getProvisionedPath()

  Returns:

  the file path after provisioned.

• getUniqueDir

  public String getUniqueDir()

  return the unique dir associate with the file if the file type is input, the provisioned file will be output to provisionfiles/uniquedir + filename

  Returns:

• setParentAccessions

  public void setParentAccessions(Collection<String> parentAccessions)

  set the parent accessions for provision file job

  Parameters:

  parentAccessions -

• getParentAccessions

  public Collection<String> getParentAccessions()

• isAttached

  public boolean isAttached()

  Returns:

  the attached

• setAttached

  public void setAttached(boolean attached)

  Parameters:

  attached - the attached to set

• isSkipIfMissing

  public boolean isSkipIfMissing()

  Returns:

  the skipIfMissing

• setSkipIfMissing

  public void setSkipIfMissing(boolean skipIfMissing)

  Parameters:

  skipIfMissing - only relevant for provision output, this sets the skip if missing parameter of the provision files module allowing for the additional of optional files

• getAnnotations

  public Map<String,String> getAnnotations()

  Set arbitrary key-value annotations on provisioned files.

  Returns: