apollo 4.2.13

Description:

apollo 4.2.13

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
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', '[email protected]', '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(
"[email protected]",
"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


4.2.13

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:
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)