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 get_groups_names():
""" Get groups names
Returns
-------
dict
error, error message and list of groups names
"""
dataInstance = Data(ca, session)
result = dataInstance.get_groups_names()
return result
def set_validated():
"""
"""
data = request.get_json()
dataInstance = Data(ca, session)
gene = dataInstance.set_validated(data["gene"], data["newstatus"])
if gene["isValidated"] == data["newstatus"]:
result = {'error': False, 'errorMessage': ""}
else:
result = {'error': True, 'errorMessage': "No Update!"}
return result
def set_groups_amount():
"""Update the number of groups
Returns
-------
dict
error, error message and updated number of groups
"""
data = request.get_json()
dataInstance = Data(ca, session)
result = dataInstance.set_number_of_groups(data)
return result
def update_group_name():
"""Update the name of a group
Returns
-------
dict
error, error message and group name
"""
data = request.get_json()
dataInstance = Data(ca, session)
result = dataInstance.update_group_name(data)
return result
def get_groups_amount():
"""get the number of groups in the database
Returns
-------
int
Number of groups in the database
"""
dataInstance = Data(ca, session)
groupsAmount = dataInstance.get_number_of_groups()
result = {'error': False, 'errorMessage': "", 'groupsAmount': groupsAmount}
return result
def save_level():
"""
"""
data = request.get_json()
dataInstance = Data(current_app, session)
result = dataInstance.save_level(data) # TODO not implemented, code lost
return {
'truc': result,
'error': False,
'errorMessage': "",
}
def count_all_genes():
"""Get the quantity of genes to annotate
Returns
-------
dict
error, error message and quantity of genes to annotate
"""
error = False
errorMessage = []
dataInstance = Data(ca, session)
result = dataInstance.count_all_genes()
return {'error': error, 'errorMessage': errorMessage, 'genes': result}
def admin_get_genes():
""" Gets all the genes in the database to display them in the admin tab
Returns
-------
json
error : Boolean
errorMessage : str
genes : List
"""
dataInstance = Data(ca, session)
gene_list = dataInstance.get_all_positions()
result = {'error': False, 'errorMessage': "", 'genes': gene_list}
return result
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"]}
def get_answers_amount():
"""get the number of annotations in the database
Return
------
int
Number of annotations
"""
dataInstance = Data(ca, session)
answers_amount = dataInstance.get_number_of_answers()
result = {
'error': False,
'errorMessage': "",
'answersAmount': answers_amount
}
return result
def set_annotable():
""" set the received gene as Annotable in the database
Returns
-------
json
error : Boolean
errorMessage : str
"""
data = request.get_json()
dataInstance = Data(ca, session)
gene = dataInstance.set_annotable(data["gene"], data["newstatus"])
if gene["isAnnotable"] == data["newstatus"]:
result = {'error': False, 'errorMessage': ""}
else:
result = {'error': True, 'errorMessage': "No Update!"}
return result
def get_level():
"""Get information about levels
Returns
-------
json
"""
try:
data_instance = Data(current_app, session)
all_levels = data_instance.get_level(
) # TODO not implemented, code lost
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'levels': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({'levels': all_levels, 'error': False, 'errorMessage': ''})
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 get_groups():
"""Get all groups
Returns
-------
json
users: list of all groups info
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
data_instance = Data(current_app, session)
all_groups = data_instance.get_all_groups()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'groups': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({'groups': all_groups, 'error': False, 'errorMessage': ''})
def remove_all_genes_from_db():
"""Remove all genes from de db
Return
------
json
error : Boolean
errorMessage: str
"""
dataInstance = Data(ca, session)
gene_list = dataInstance.get_all_positions()
db = ca.mongo.db
fs = gridfs.GridFS(db, collection="genes")
for element in gene_list:
fs.delete(element['_id'])
result = {
'error': False,
'errorMessage': "",
}
return result
def get_top_annotation():
dataInstance = Data(ca, session)
result = dataInstance.get_top_annotation()
return result
def get_all_answers():
dataInstance = Data(ca, session)
answers = dataInstance.get_all_answers()
result = {'error': False, 'errorMessage': "", 'answer': answers}
return result
def create_app(config='config/genocrowd.ini',
app_name='genocrowd',
blueprints=None):
"""Create the Genocrowd app
Parameters
----------
config : str, optional
Path to the config file
app_name : str, optional
Application name
blueprints : None, optional
Flask blueprints
Returns
-------
Flask
Genocrowd Flask application
"""
conf = configparser.ConfigParser()
conf.read(config)
sentry_dsn = None
try:
sentry_dsn = conf['sentry']['server_dsn']
except Exception:
pass
if sentry_dsn:
version = get_distribution('genocrowd').version
name = get_distribution('genocrowd').project_name
sentry_sdk.init(dsn=sentry_dsn,
release="{}@{}".format(name, version),
integrations=[FlaskIntegration(),
CeleryIntegration()])
app = Flask(app_name, static_folder='static', template_folder='templates')
app.iniconfig = FlaskIni()
with app.app_context():
app.iniconfig.read(config)
proxy_path = None
try:
proxy_path = app.iniconfig.get('genocrowd', 'reverse_proxy_path')
app.config['REVERSE_PROXY_PATH'] = proxy_path
except Exception:
pass
mongo_dbname = app.iniconfig.get('flask', 'mongo_dbname')
app.config['MONGO_DBNAME'] = mongo_dbname
mongo_uri = app.iniconfig.get('flask', 'mongo_uri')
app.config['MONGO_URI'] = mongo_uri
if not mongo_uri:
raise Exception("Missing mongo_uri in config file")
if not mongo_dbname:
raise Exception("Missing mongo_dbname in config file")
app.mongo = PyMongo(app)
app.bcrypt = Bcrypt(app)
users = app.mongo.db.users
app.mongo.db.genes
app.mongo.db.answers
groups = app.mongo.db.groups
app.genocrowd_admin_email = app.iniconfig.get('genocrowd',
'genocrowd_admin_email')
app.genocrowd_admin_password = app.iniconfig.get(
'genocrowd', 'genocrowd_admin_password')
app.apollo_admin_email = app.iniconfig.get('genocrowd',
'apollo_admin_email')
app.apollo_admin_password = app.iniconfig.get('genocrowd',
'apollo_admin_password')
app.apollo_dataset_path = app.iniconfig.get('genocrowd',
'apollo_dataset_path')
app.apollo_org_id = app.iniconfig.get('genocrowd', 'apollo_org_id')
app.apollo_url = app.iniconfig.get('genocrowd', 'apollo_url')
# We don't want ending slash
if app.apollo_url.endswith("/"):
app.apollo_url = app.apollo_url[:-1]
app.apollo_url_ext = app.iniconfig.get('genocrowd', 'apollo_url_ext')
# We don't want ending slash
if app.apollo_url_ext.endswith("/"):
app.apollo_url_ext = app.apollo_url_ext[:-1]
configure_logging(app)
if users.find_one() is None:
# Create default admin user
local_auth = LocalAuth(app, None)
local_auth.add_user_to_database('admin', app.genocrowd_admin_email,
app.genocrowd_admin_password,
'admin', 'admin')
if blueprints is None:
blueprints = BLUEPRINTS
for blueprint in blueprints:
app.register_blueprint(blueprint)
if groups.find_one() is None:
# Initiate the groups database
data = Data(app, None)
data.initiate_groups()
if proxy_path:
ReverseProxyPrefixFix(app)
return app