Metadata-Version: 1.1
Name: apollo
Version: 4.2.4
Summary: Apollo API library
Home-page: https://github.com/galaxy-genome-annotation/python-apollo
Author: Helena Rasche;Anthony Bretaudeau;Nathan Dunn
Author-email: hxr@hx42.org
License: MIT
Description: Apollo API Library
        ==================
        
        .. image:: https://travis-ci.org/galaxy-genome-annotation/python-apollo.svg?branch=master
            :target: https://travis-ci.org/galaxy-genome-annotation/python-apollo
        
        .. image:: https://readthedocs.org/projects/python-apollo/badge/?version=latest
            :target: http://python-apollo.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        Apollo is a Python library for interacting with
        `Apollo <https://github.com/gmod/apollo/>`__. Arrow is its companion CLI tool.
        
            `for the record <https://gitter.im/galaxy-genome-annotation/Lobby?at=5ebee6c049a1b7318479380d>`__ ... arrow makes working with Apollo SOOO much easier
            — Nathan Dunn, Apollo Developer
        
        
        Installation
        ------------
        
        .. code-block:: shell
        
            pip install apollo
        
        Examples
        --------
        
        Example code to create a new organism and add yourself in the permission list:
        
        .. code:: python
        
            from apollo import ApolloInstance
            wa = ApolloInstance('https://fqdn/apollo', 'jane.doe@fqdn.edu', 'password')
        
            orgs = wa.organisms.add_organism(
                "Yeast",
                "/path/to/jbrowse/data",
                genus='Saccharomyces',
                species='cerevisiae',
                public=False
            )
        
            # Give Apollo a second to process the uploaded organism.
            time.sleep(1)
        
            # Then add yourself to permission list
            data = wa.users.update_organism_permissions(
                "jane.doe@fqdn.edu",
                "Yeast",
                write=True,
                export=True,
                read=True,
            )
        
        If you have already created an Arrow config file (with command `arrow init`),
        you can also get an ApolloInstance without writing credentials explicitely:
        
        .. code:: python
        
            from arrow.apollo import get_apollo_instance
            wa = get_apollo_instance()
        
        Or with the Arrow client:
        
        .. code-block:: shell
        
            $ arrow groups create_group university
            {
                "publicGroup": false,
                "class": "org.bbop.apollo.UserGroup",
                "name": "university",
                "users": null,
                "id": 558319
            }
            # THEN
            $ arrow users get_users | \
                jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
                xargs -n1 arrow users add_to_group university
            # OR
            $ arrow users get_users | \
                jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
                paste -s -d',' | \
                xargs arrow group update_membership 558319 --users
        
        History
        -------
        
        - 4.2.4
            - Remove unused dependency
        - 4.2.3
            - Fixed `load_gff3` to more accurately load transcripts including the CDS as well as handle non-coding types more accurately.
        - 4.2.2
            - Drastically speed up load_gff3
            - `load_gff3` now uses the Apollo `add_transcript` method if it is a gene or mRNA type
            - Added support for all of the current Apollo coding and non-coding types
            - Drop support for Python 2.7
        - 4.2.1
            - Fix getting groups by name
            - Add tests for group api
        - 4.2
            - Improve user update method
            - Add tests for user api
        - 4.1
            - Fix loading attributes from gff3
            - Better handling of genome sequence update, with or without the no_reload_sequences option
        - 4.0.1
            - Fix missing file in pypi package, no code change
        - 4.0
            - Added support for remote creation/update/deletion of organisms/tracks
            - Added support for adding GFF3 in the annotation track
            - Added tests
        - 3.1
            - Added user activate/inactivate
            - Added get_creator for user, group and organisms
            - Added omitEmptyOrganisms to get_users
            - Added support for group admins
            - Added support for bulk group creation/deletion
            - Repaired GFF3/Fasta downloading
        - 3.0.4
            - `Fixed bug <https://github.com/galaxy-genome-annotation/python-apollo/issues/4>`__ in deleteFeatures (Thanks `@NeillGibson <https://github.com/NeillGibson>`__)
        - 3.0.3
            - findAllOrganisms works correctly, client side filtering no longer necessary.
        - 3.0.2
            - Patch a bug discovered in io.write, thanks Morgan!
        - 3.0
            - "Arrow" CLI utility
            - More pythonic API and many workarounds for Apollo bugs or oddities
            - Complete package restructure
            - Nearly all functions renamed
        - 2.0
            - Galaxy Functions
            - TTL Cache to work around Galaxy's behaviour
            - Status and Canned* Clients from `@abretaud <https://github.com/abretaud>`__
        - 1.0
            - Initial release
        
        
        Development
        -----------
        
        The content of docs and arrow directories is automatically generated from the code in the apollo directory.
        To regenerate it, install the latest version of the code, then run:
        
        
        .. code-block:: shell
        
            make rebuild
        
        
        License
        -------
        
        Available under the MIT License
        
        
        
        Support
        -------
        
        This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
