Metadata-Version: 2.1
Name: pyUSIrest
Version: 0.2.1
Summary: Python USI submission REST API contain all methods to interact with EMBL-EBI Unified Submissions Interface
Home-page: https://github.com/cnr-ibba/pyUSIrest
Author: Paolo Cozzi
Author-email: cozzi@ibba.cnr.it
License: GNU General Public License v3
Keywords: pyUSIrest
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Requires-Dist: python-jwt
Requires-Dist: requests
Requires-Dist: url-normalize

==============================
Python USI submission REST API
==============================


.. image:: https://img.shields.io/pypi/v/pyUSIrest.svg
        :target: https://pypi.python.org/pypi/pyUSIrest

.. image:: https://img.shields.io/travis/cnr-ibba/pyUSIrest.svg
        :target: https://travis-ci.org/cnr-ibba/pyUSIrest

.. image:: https://readthedocs.org/projects/pyusirest/badge/?version=latest
        :target: https://pyusirest.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. image:: https://coveralls.io/repos/github/cnr-ibba/pyUSIrest/badge.svg?branch=master
        :target: https://coveralls.io/github/cnr-ibba/pyUSIrest?branch=master



Python USI submission REST API contain all methods to interact with EMBL-EBI
Unified Submissions Interface

* Free software: GNU General Public License v3
* Documentation: https://pyusirest.readthedocs.io.


Features
--------

* Deal with EBI AAP_  (Authentication, Authorisation and Profile) service,
  generating tokens and dealing with User and Groups
* Interact with EBI USI (Unified Submission Interface) in order to submit data to
  biosample as described by this guide_. In details:

  * Getting `USI API root`_
  * Selecting a Team_
  * Creating a Submission_
  * Adding `items to Submission`_
  * Checking Biosample `Validation`_
  * Finalising_ a Submission

.. _AAP: https://explore.api.aai.ebi.ac.uk/docs/
.. _guide: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html
.. _`USI API root`: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html#_start_from_the_root
.. _Team: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html#_pick_a_team
.. _Submission: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html#_creating_a_submission
.. _`items to Submission`: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html#_adding_documents_to_a_submission
.. _Validation: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html#_validation
.. _Finalising: https://submission-test.ebi.ac.uk/api/docs/guide_getting_started.html#_finalising_your_submission

Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.2.1-dev
---------

TODO
^^^^

Features
^^^^^^^^

* test for an empty submission (no samples)
* updated `root.json`, `userSubmission.json` test data
* submissionStatus is no longer an attribute, when feching submission by name
  is present when getting user submissions
* follow submissionStatus link (if necessary)
* update submission status after create a new submission
* update submission status after ``get_submission_by_name``
* update submission status after reload a just finalized submission
* ``Domain.users`` returns ``User`` objects in a list
* improved ``Submission.get_samples`` method

0.2.0 (2018-10-23)
------------------

Features
^^^^^^^^

* Fetch submission by name
* changed library name to ``pyUSIrest``
* published to pypi
* Finalize submission with *PUT*

0.1.0 (2018-10-17)
------------------

Features
^^^^^^^^

* submit into biosample with python methods


