Apollo API library
Project description
Apollo is a Python library for interacting with Apollo
Examples
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,
)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 --usersHistory
- 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)
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