def annotation_start():
"""Selects a gene in MongoDB and imports it in the Annotation track
Returns
-------
json
url: url for the apollo window, centered on the gene position
attributes: chromosome on which the gene is
"""
DataInstance = Data(ca, session)
current_gene = DataInstance.get_current_annotation(
session["user"]["username"])
if not current_gene:
all_positions = DataInstance.get_all_positions()
level = DataInstance.get_user_level(session["user"]["username"])
restrict_positions = DataInstance.select_genes(level, all_positions)
# FIXME error if no gene in db
selected_item = Utils.get_random_items(1, restrict_positions)[0]
ca.logger.info("Selected gene: {}".format(selected_item))
db = ca.mongo.db
fs = gridfs.GridFS(
db, collection="genes"
) # FIXME not sure we really need gridfs (small chunks of gff)
gff_file = fs.get(selected_item["_id"])
gff_str = StringIO()
gff_str.write(gff_file.read().decode())
gff_str.seek(0)
ca.logger.info("Loading gff: {}".format(gff_str.read()))
gff_str.seek(0)
apollo = ApolloInstance(ca.apollo_url, ca.apollo_admin_email,
ca.apollo_admin_password)
apollo.annotations.load_gff3(
"%s_%s" % (ca.apollo_org_id, session["user"]["email"]), gff_str)
time.sleep(1)
url = "%s/annotator/loadLink?loc=%s:%s..%s&organism=%s_%s" % (
ca.apollo_url_ext, selected_item["chromosome"],
selected_item["start"], selected_item["end"], ca.apollo_org_id,
session["user"]["email"])
DataInstance.update_current_annotation(session["user"]["username"],
selected_item)
else:
selected_item = DataInstance.get_current_annotation(
session["user"]["username"])
url = "%s/annotator/loadLink?loc=%s:%s..%s&organism=%s_%s" % (
ca.apollo_url_ext, selected_item["chromosome"],
selected_item["start"], selected_item["end"], ca.apollo_org_id,
session["user"]["email"])
return {'url': url}
def cli(ctx, url=None, api_key=None, admin=False, **kwds):
"""Help initialize global configuration (in home directory)
"""
# TODO: prompt for values someday.
click.echo("""Welcome to Apollo's Arrow!""")
if os.path.exists(config.global_config_path()):
info(
"Your arrow configuration already exists. Please edit it instead: %s"
% config.global_config_path())
return 0
while True:
apollo_url = click.prompt("Please entry your Apollo's URL")
apollo_username = click.prompt("Please entry your Apollo Username")
apollo_password = click.prompt("Please entry your Apollo Password",
hide_input=True)
info("Testing connection...")
try:
ai = ApolloInstance(apollo_url, apollo_username, apollo_password)
try:
ai.metrics.get_metrics()
# Ok, success
info("Ok! Everything looks good.")
break
except Exception as e:
print(e)
warn(
"Error, we could not access the configuration data for your instance."
)
should_break = click.prompt(
"Continue despite inability to contact this Apollo Instance? [y/n]"
)
if should_break in ('Y', 'y'):
break
except Exception as e:
warn(
"Error, we could not access the configuration data for your instance."
)
should_break = click.prompt(
"Continue despite inability to contact this Apollo Instance? [y/n]"
)
if should_break in ('Y', 'y'):
break
config_path = config.global_config_path()
if os.path.exists(config_path):
warn("File %s already exists, refusing to overwrite." % config_path)
return -1
with open(config_path, "w") as f:
f.write(
CONFIG_TEMPLATE % {
'url': apollo_url,
'username': apollo_username,
'password': apollo_password,
})
info(SUCCESS_MESSAGE)
def validation():
"""Selects a gene from the answers and imports it in the Annotation track
Returns
-------
json
url: url for the apollo window, centered on the gene position
attributes: chromosome on which the gene is
gene_id : current gene id
"""
DataInstance = Data(ca, session)
all_positions = DataInstance.get_not_validated()
# FIXME error if no gene in db
selected_item = all_positions[0]
ca.logger.info("Selected gene: {}".format(selected_item))
db = ca.mongo.db
fs = gridfs.GridFS(
db, collection="answers"
) # FIXME not sure we really need gridfs (small chunks of gff)
gff_file = fs.get(selected_item["_id"])
gff_str = StringIO()
gff_str.write(gff_file.read().decode())
gff_str.seek(0)
ca.logger.info("Loading gff: {}".format(gff_str.read()))
gff_str.seek(0)
apollo = ApolloInstance(ca.apollo_url, ca.apollo_admin_email,
ca.apollo_admin_password)
apollo.organisms.delete_features(
"%s_%s" % (ca.apollo_org_id, session["user"]["email"]))
apollo.annotations.load_gff3(
"%s_%s" % (ca.apollo_org_id, session["user"]["email"]), gff_str)
time.sleep(1)
url = "%s/annotator/loadLink?loc=%s:%s..%s&organism=%s_%s" % (
ca.apollo_url_ext, selected_item["chromosome"], selected_item["start"],
selected_item["end"], ca.apollo_org_id, session["user"]["email"])
DataInstance.update_current_annotation(session["user"]["username"],
selected_item)
return {'url': url, 'gene_id': selected_item["_id"]}
class Config(object):
if not (os.environ.get('APOLLO_USER') and os.environ.get('APOLLO_PASSWORD')
and os.environ.get('APOLLO_URL')):
raise Exception(
"Missing either APOLLO_USER, APOLLO_PASSWORD or APOLLO_URL env variable"
)
APOLLO_USER = os.environ.get('APOLLO_USER')
APOLLO_PASSWORD = os.environ.get('APOLLO_PASSWORD')
APOLLO_URL = os.environ.get('APOLLO_URL')
PROXY_HEADER = os.environ.get("PROXY_HEADER", "REMOTE_USER")
USER_AUTOCOMPLETE = os.environ.get('USER_AUTOCOMPLETE', "FALSE")
CRON_SYNC = os.environ.get('CRON_SYNC', "FALSE")
PROXY_PREFIX = os.environ.get('PROXY_PREFIX')
APOLLO_INSTANCE = ApolloInstance(APOLLO_URL, APOLLO_USER, APOLLO_PASSWORD)
SECRET_KEY = os.urandom(32)
CACHE_TYPE = "simple"
CACHE_DEFAULT_TIMEOUT = 3600
def get_permissions(self):
ai = ApolloInstance(os.environ['APOLLO_URL'],
os.environ['APOLLO_USER'],
os.environ['APOLLO_PASS'])
groups = ai.groups.get_groups()
orgs_by_user = {}
for group in groups:
for org in group['organismPermissions']:
for group_user in group['users']:
if self.split_users:
user_name = re.sub(r"^(.+)@[a-zA-Z0-9]+$", r"\1",
group_user['email'])
else:
user_name = group_user['email']
if user_name not in orgs_by_user:
orgs_by_user[user_name] = []
orgs_by_user[user_name].append(org['organism'])
return orgs_by_user
def annotation_end():
"""gets the new annotation and saves it in mongodb"""
DataInstance = Data(ca, session)
current_gene = DataInstance.get_current_annotation(
session["user"]["username"])
apollo = ApolloInstance(ca.apollo_url, ca.apollo_admin_email,
ca.apollo_admin_password)
features = apollo.annotations.get_features(
organism="%s_%s" % (ca.apollo_org_id, session["user"]["email"]),
sequence=current_gene["chromosome"])["features"]
gff_file = apollo.annotations.get_gff3(
features[0]["uniquename"],
"%s_%s" % (ca.apollo_org_id, session["user"]["email"]))
DataInstance.store_answers_from_user(session["user"]["username"], gff_file)
apollo.organisms.delete_features(
"%s_%s" % (ca.apollo_org_id, session["user"]["email"]))
return {'error': False, 'errorMessage': 'no error'}
def __init__(self):
self.wa = ApolloInstance(ca.apollo_url, ca.apollo_admin_email,
ca.apollo_admin_password)
def get_apollo_instance(instance_name=None):
conf = get_instance(instance_name=instance_name)
return ApolloInstance(conf['url'], conf['username'], conf['password'])
other_id = "%s %s %s %s %s %s" % (f.qualifiers['Name'][0], f.type,
rec.id, feat_strand,
f.location.start, f.location.end)
if other_id in other_attrs:
print(
"Found multiple other feat with same id '%s'!! Aborting" %
other_id)
sys.exit()
other_attrs[other_id] = {'gene': f.qualifiers}
#print(mrnas_attrs)
#print(other_attrs)
org_common_name = "genus_species"
wa = ApolloInstance('http://*****:*****@xxxxxxxxxx', 'password...')
def apply_attrs(feature_id, attrs):
if 'symbol' in attrs:
wa.annotations.set_symbol(feature_id, attrs['symbol'][0])
if 'description' in attrs:
wa.annotations.set_description(feature_id, attrs['description'][0])
if 'Name' in attrs:
wa.annotations.set_name(feature_id, attrs['Name'][0])
if 'Dbxref' in attrs:
for dbx in attrs['Dbxref']:
dbx = dbx.split(':')
if len(dbx) == 2:
wa.annotations.add_dbxref(feature_id, dbx[0], dbx[1])
if 'Note' in attrs:
from __future__ import print_function
import os
import random
import re
import string
import sys
import time
from apollo import ApolloInstance
import ldap
wa = ApolloInstance(os.environ['APOLLO_URL'], os.environ['APOLLO_ADMIN'],
os.environ['APOLLO_PASSWORD'])
admin_users = [os.environ['APOLLO_ADMIN']]
fake_email = os.environ['FAKE_EMAIL']
use_fake_email = fake_email and fake_email.startswith('@')
default_group = os.environ['DEFAULT_GROUP']
ldap_user_filter = '(mail=*)'
if 'LDAP_USER_FILTER' in os.environ and os.environ['LDAP_USER_FILTER']:
ldap_user_filter = os.environ['LDAP_USER_FILTER']
ldap_group_filter = "(cn=*)"
if 'LDAP_GROUP_FILTER' in os.environ and os.environ['LDAP_GROUP_FILTER']:
ldap_group_filter = os.environ['LDAP_GROUP_FILTER']
ldap_conf = {