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Apollo API library

Project description

https://travis-ci.org/galaxy-genome-annotation/python-apollo.svg?branch=master Documentation Status

Apollo is a Python library for interacting with Apollo

Installation

pip install apollo

Examples

Example code to create a new organism and add yourself in the permission list:

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:

from arrow.apollo import get_apollo_instance
wa = get_apollo_instance()

Or with the Arrow client:

$ 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

  • 4.2.1
    • 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
  • 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

License

Available under the MIT License

Support

This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)

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