#!/usr/bin/env python
import json
import argparse
from webapollo import WAAuth, WebApolloInstance, AssertUser, accessible_organisms
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="List all organisms available in an Apollo instance")
WAAuth(parser)
parser.add_argument("email", help="User Email")
args = parser.parse_args()
wa = WebApolloInstance(args.apollo, args.username, args.password)
gx_user = AssertUser(wa.users.loadUsers(email=args.email))
all_orgs = wa.organisms.findAllOrganisms()
orgs = accessible_organisms(gx_user, all_orgs)
cleanedOrgs = []
for organism in all_orgs:
org = {
"name": organism["commonName"],
"id": organism["id"],
"annotations": organism["annotationCount"],
"sequences": organism["sequences"],
}
cleanedOrgs.append(org)
print(json.dumps(cleanedOrgs, indent=2))
OrgOrGuess(parser)
args = parser.parse_args()
wa = WebApolloInstance(args.apollo, args.username, args.password)
# User must have an account
gx_user = AssertUser(wa.users.loadUsers(email=args.email))
# Get organism
org_cn = GuessOrg(args, wa)[0]
# Fetch all organisms
all_orgs = wa.organisms.findAllOrganisms()
# Figure out which are accessible to the user
# filter out common names
orgs = [d[0] for d in accessible_organisms(gx_user, all_orgs)]
# This user MUST be allowed to access an organism before they can
# modify permissions on it.
assert org_cn in orgs
org = wa.organisms.findOrganismByCn(org_cn)
# The other person must already be an apollo user
other_user = AssertUser(
wa.users.loadUsers(email=args.share_with.replace("__at__", "@")))
wa.users.updateOrganismPermission(
other_user,
org_cn,
administrate=False,