try:
org = wa.organisms.show_organism(org_cn)
except Exception:
org = None
if org and 'error' not in org:
old_directory = org['directory']
all_orgs = wa.organisms.get_organisms()
if 'error' in all_orgs:
all_orgs = []
all_orgs = [x['commonName'] for x in all_orgs]
if org_cn not in all_orgs:
raise Exception("Could not find organism %s" % org_cn)
orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
if not orgs:
raise Exception("Naming Conflict. You do not have write permission on this organism. Either request permission from the owner, or choose a different name for your organism.")
log.info("\tUpdating Organism")
if IsRemote():
with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
with tarfile.open(archive.name, mode="w:gz") as tar:
dataset_data_dir = args.jbrowse_src
for file in glob.glob(dataset_data_dir):
tar.add(file, arcname=file.replace(dataset_data_dir, './'))
if IsBlatEnabled():
tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
data = wa.remote.update_organism(
org['id'],
archive,
org_cns, seqs = GuessCn(args, wa)
if not isinstance(org_cns, list):
org_cns = [org_cns]
all_orgs = wa.organisms.get_organisms()
if 'error' in all_orgs:
all_orgs = []
all_orgs = [org['commonName'] for org in all_orgs]
org_data = []
for org_cn in org_cns:
if org_cn not in all_orgs:
raise Exception("Could not find organism %s" % org_cn)
orgs = accessible_organisms(gx_user, [org_cn], 'READ')
if not orgs:
raise Exception("You do not have read permission on organism %s" % org_cn)
org = wa.organisms.show_organism(org_cn)
uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs)
if 'error' in uuid_gff or 'uuid' not in uuid_gff:
raise Exception("Apollo failed to prepare the file for download: %s" % uuid_gff)
args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
time.sleep(1)
uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
raise Exception("Apollo failed to prepare the file for download: %s" % uuid_vcf)
#!/usr/bin/env python
from __future__ import print_function
import argparse
import json
from apollo import accessible_organisms
from arrow.apollo import get_apollo_instance
from webapollo import UserObj, handle_credentials
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance')
parser.add_argument('email', help='User Email')
args = parser.parse_args()
wa = get_apollo_instance()
gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
handle_credentials(gx_user)
all_orgs = wa.organisms.get_organisms()
orgs = accessible_organisms(gx_user, all_orgs)
print(json.dumps(orgs, indent=2))