apollo 3.0.2

WebApollo API library

Apollo is a Python library for interacting with WebApollo

Examples

from apollo import WebApolloInstance
wa = WebApolloInstance('https://fqdn/apollo', '[e-mail]', 'password')

orgs = wa.organisms.add_organism(
    "Yeast",
    "/path/to/jbrowse/data",
    genus='Saccharomyces',
    species='cerevisiae',
    public=False
)

# Give webapollo a second to process the uploaded organism.
time.sleep(1)

# Then add yourself to permission list
data = wa.users.update_organism_permissions(
    "[e-mail]",
    "Yeast",
    write=True,
    export=True,
    read=True,
)

Or with the new 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

• 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

License

Available under the MIT License

Support

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