apollo

Python library for talking to Apollo API

https://github.com/galaxy-genome-annotation/python-apollo

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
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3 of 9 committers (33.3%) from academic institutions
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Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary

Keywords

apollo jbrowse python

Keywords from Contributors

usegalaxy bioinformatics dna genomics ngs sequencing workflow-engine cloudman

Last synced: 6 months ago · JSON representation

Repository

Python library for talking to Apollo API

Basic Info

Host: GitHub
Owner: galaxy-genome-annotation
License: mit
Language: Python
Default Branch: master
Homepage:
Size: 798 KB

Statistics

Stars: 10
Watchers: 4
Forks: 11
Open Issues: 7
Releases: 0

Topics

apollo jbrowse python

Created about 10 years ago · Last pushed about 2 years ago

Metadata Files

Readme License

README.rst

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 `__. Arrow is its companion CLI tool.

    `for the record `__ ... 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
-------

- 4.2.13
    - Relax biopython requirements
- 4.2.12
    - Do not filter out username from api responses
- 4.2.11
    - Updated wrong version number
- 4.2.10
    - Bugfix handling Shine-Dalgarno sequences (https://github.com/galaxy-genome-annotation/python-apollo/issues/48)
- 4.2.9
    - Bugfix to  update_organism when using suppress_output
- 4.2.8
    - Added --suppress_output to update_organism
- 4.2.7
    - Renamed --return_all option to --suppress_output
- 4.2.6
    - Added --return_all option to add_organism and delete_organism methods
- 4.2.5
    - Prevent from displaying login/password in the logs
- 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 `__ in deleteFeatures (Thanks `@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 `__
- 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)

Owner

Name: Galaxy Genome Annotation
Login: galaxy-genome-annotation
Kind: organization

Website: https://galaxy-genome-annotation.github.io/
Repositories: 17
Profile: https://github.com/galaxy-genome-annotation

Galaxy tools, infrastructure, and related materials focused on Genome Annotation

GitHub Events

Total

Issues event: 1
Watch event: 1
Issue comment event: 1
Fork event: 1

Last Year

Issues event: 1
Watch event: 1
Issue comment event: 1
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 304
Total Committers: 9
Avg Commits per committer: 33.778
Development Distribution Score (DDS): 0.582

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Anthony Bretaudeau	a**u@i**r	127
Eric Rasche	r**c@g**m	88
Nathan Dunn	n**n@m**m	42
E Rasche	h**r@h**g	30
Cory Maughmer	c**r@t**u	6
Luke Sargent	l**t@g**m	5
Nathan Dunn	n**n@l**v	3
mboudet	m**t@i**r	2
Cory Maughmer	c**r@g**m	1

Committer Domains (Top 20 + Academic)

irisa.fr: 1 lbl.gov: 1 tamu.edu: 1 hx42.org: 1 me.com: 1 inria.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 18
Total pull requests: 46
Average time to close issues: 3 months
Average time to close pull requests: 23 days
Total issue authors: 12
Total pull request authors: 6
Average comments per issue: 3.28
Average comments per pull request: 1.76
Merged pull requests: 40
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: 6 days
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 2.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

mpoelchau (3)
nathandunn (3)
jaspwn (2)
hexylena (2)
epaule (1)
MoffMade (1)
luke-c-sargent (1)
NeillGibson (1)
AlexanderThomasJulian (1)
buerklem (1)
pwilx666 (1)
RenanFerreira0412 (1)

Pull Request Authors

abretaud (22)
nathandunn (14)
hexylena (6)
MoffMade (3)
luke-c-sargent (2)
mboudet (1)

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Packages

Total packages: 1
Total downloads:
- pypi 427 last-month
Total docker downloads: 9

Total dependent packages: 1
Total dependent repositories: 5
Total versions: 25
Total maintainers: 3

pypi.org: apollo

Apollo API library

Homepage: https://github.com/galaxy-genome-annotation/python-apollo
Documentation: https://apollo.readthedocs.io/
License: MIT
Latest release: 4.2.13
published over 4 years ago

Versions: 25
Dependent Packages: 1
Dependent Repositories: 5
Downloads: 427 Last month
Docker Downloads: 9

Rankings

Docker downloads count: 4.2%

Dependent repos count: 6.6%

Dependent packages count: 10.0%

Average: 10.3%

Forks count: 10.5%

Downloads: 12.6%

Stargazers count: 17.7%

Maintainers (3)

abretaud erasche nathandunn

Last synced: 6 months ago

Dependencies

requirements.txt pypi

bcbio-gff >=0.6.6
biopython >=1.77
cachetools <4
click >=6.7
decorator *
pyyaml *
requests *
wrapt *

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apollo

Science Score: 10.0%

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README.rst

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