cwltool.cwlprov.provenance_profile
==================================

.. py:module:: cwltool.cwlprov.provenance_profile


Attributes
----------

.. autoapisummary::

   cwltool.cwlprov.provenance_profile.CWLArtifact


Classes
-------

.. autoapisummary::

   cwltool.cwlprov.provenance_profile.ProvenanceProfile


Functions
---------

.. autoapisummary::

   cwltool.cwlprov.provenance_profile.copy_job_order


Module Contents
---------------

.. py:data:: CWLArtifact

.. py:function:: copy_job_order(job, job_order_object)

   Create copy of job object for provenance.


.. py:class:: ProvenanceProfile(research_object, full_name, host_provenance, user_provenance, orcid, fsaccess, run_uuid = None)

   Provenance profile.

   Populated as the workflow runs.


   .. py:attribute:: fsaccess


   .. py:attribute:: orcid


   .. py:attribute:: research_object


   .. py:attribute:: folder


   .. py:attribute:: document


   .. py:attribute:: host_provenance


   .. py:attribute:: user_provenance


   .. py:attribute:: engine_uuid


   .. py:attribute:: add_to_manifest


   .. py:attribute:: full_name


   .. py:attribute:: workflow_run_uuid


   .. py:attribute:: workflow_run_uri
      :value: 'urn:uuid:'



   .. py:method:: __str__()

      Represent this Provenvance profile as a string.



   .. py:method:: generate_prov_doc()

      Add basic namespaces.



   .. py:method:: evaluate(process, job, job_order_object, research_obj)

      Evaluate the nature of job.



   .. py:method:: record_process_start(process, job, process_run_id = None)


   .. py:method:: start_process(process_name, when, process_run_id = None)

      Record the start of each Process.



   .. py:method:: record_process_end(process_name, process_run_id, outputs, when)


   .. py:method:: declare_file(value)

      Construct a FileEntity for the given CWL File object.



   .. py:method:: declare_directory(value)

      Register any nested files/directories.



   .. py:method:: declare_string(value)

      Save as string in UTF-8.



   .. py:method:: declare_artefact(value)

      Create data artefact entities for all file objects.



   .. py:method:: used_artefacts(job_order, process_run_id, name = None)

      Add used() for each data artefact.



   .. py:method:: generate_output_prov(final_output, process_run_id, name)

      Call wasGeneratedBy() for each output,copy the files into the RO.



   .. py:method:: prospective_prov(job)

      Create prospective prov recording as wfdesc prov:Plan.



   .. py:method:: activity_has_provenance(activity, prov_ids)

      Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files.



   .. py:method:: finalize_prov_profile(name)

      Transfer the provenance related files to the RO.