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 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'}
