==============
Pipeliner Jobs
==============

Pipeliner jobs
--------------

.. automodule:: pipeliner.pipeliner_job
    :members:
    :undoc-members:
    :show-inheritance:

Display tools
-------------

Use these methods to create ``ResultsDisplayObject``
used by the pipeliner GUI Doppio to create graphical
outputs for each job.

.. automodule:: pipeliner.display_tools
    :members:
    :undoc-members:
    :show-inheritance:

ResultsDisplay Objects
----------------------
These objects generally should not be instantiated directly
they should instead be created using the functions above.

.. automodule:: pipeliner.results_display_objects
    :members:
    :undoc-members:
    :show-inheritance:


Deposition Objects
------------------
Lists of ``DepositionObject`` are returned by a ``PipelinerJob``.
The ``prepare_emdb_deposition_data`` and ``prepare_empiar_deposition_data`` functions
are used to prepare automated depositions to the EMDB, and EMPIAR.

.. automodule:: pipeliner.deposition_tools.deposition_tools
    :members:
    :undoc-members:
    :show-inheritance:

Functions that support these methods are:

*EMPIAR DepositionObjects*

.. automodule:: pipeliner.deposition_tools.empiar_deposition_objects
    :members:
    :undoc-members:
    :show-inheritance:

.. automodule:: pipeliner.deposition_tools.empiar_deposition
    :members:
    :undoc-members:
    :show-inheritance:

*EMDB DepositionObjects*

EMDB Deposition objects correspond to the schema
here: http://ftp.ebi.ac.uk/pub/databases/emdb/doc/XML-schemas/emdb-schemas/v3/current_v3/doc/Untitled.html

.. automodule:: pipeliner.deposition_tools.emdb_deposition_objects
    :members:
    :undoc-members:
    :show-inheritance:

.. automodule:: pipeliner.deposition_tools.emdb_deposition
    :members:
    :undoc-members:
    :show-inheritance:

*PDB deposition objects*

PDB depositions are not currently supported