Extend PipelineTasks to facilitate creating directories and moving/copying files

[pjbriggs]

Proposal to extend the PipelineTask class in the pipeliner module to make it easier to create directories, and move or copy files created by the task. These would be most useful for removing boilerplate code from the task-specific finish methods, where often it seems necessary to know explicitly where files have been created by the task.

For example, something like:

if not os.path.exists(self.args.out_dir):
    os.makedirs(self.args.out_dir)

could be replaced by:

self.makedirs(self.args.out_dir)

which could provide a consistent interface and wrap all the required checks.

Another example:

for output in expected_outputs:
    f = "%s.%s" % (self.args.name,output)
    if os.path.exists(os.path.join(self.args.out_dir,f)):
        continue
    else:
        if os.path.exists(f):
            shutil.copy(f,self.args.out_dir)

could be replaced by something like:

for output in expected_outputs:
   self.export_file("%s.%s" % (self.args.name,output),self.args.out_dir)

By convention, relative paths would be considered to be within the task working directory (absolute paths would be used as-is). It might also be useful if the pipeline infrastructure was extended to run each job in a dedicated working directory.

Additional optional arguments could be provided e.g. to avoid overwriting existing files etc.

Other potentially useful methods might be to check for the existence of files.