apollo 4.1

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

• 4.1

  • 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

License

Available under the MIT License

Support

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