def setUp(self):
test_config_file = StringIO('''
[flask]
; should be a string
secret_key : 12345678
debug : true
permanent_session_lifetime : 100
server_name = testserv
send_file_max_age_default : 3600
some_other_flask_var : something with multiple words
[wibble]
wobble : woo
warble = 123
[foo bar]
bar : http://baz/qux
interp : %(bar)s/hi
''')
app = flask.Flask(__name__)
with app.app_context():
app.iniconfig = FlaskIni()
# Tests the readfp() primarily - separate test case for read()
app.iniconfig.readfp(test_config_file)
@app.route('/hello')
def hello_world():
return 'Hello world!'
self.app = app
def create_app(config='config/askomics.ini',
app_name='askomics',
blueprints=None):
"""Create the AskOmics app
Parameters
----------
config : str, optional
Path to the config file
app_name : str, optional
Application name
blueprints : None, optional
Flask blueprints
Returns
-------
Flask
AskOmics 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('askomics').version
name = get_distribution('askomics').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('askomics', 'reverse_proxy_path')
app.config['REVERSE_PROXY_PATH'] = proxy_path
except Exception:
pass
if blueprints is None:
blueprints = BLUEPRINTS
for blueprint in blueprints:
app.register_blueprint(blueprint)
if proxy_path:
ReverseProxyPrefixFix(app)
return app
config_file = os.getenv('LAUNCHER_CONFIG', 'settings.ini')
assert config_file is not None and os.path.isfile(
config_file), "invalid LAUNCHER_CONFIG"
default_file = os.path.join(os.path.dirname(config_file), "default.json")
assert os.path.isfile(
default_file), "Cannot find default.json: %s" % default_file
with open(default_file) as default_fh:
default_config = default_fh.read()
base_config = json.loads(default_config)
assert 'storages' in base_config, "incomplete configuration - missing " \
"`storages` in %s" % default_file
app.iniconfig = FlaskIni()
with app.app_context():
app.iniconfig.read(config_file)
app.logger.setLevel(
logging.getLevelName(
app.iniconfig.get('default', 'log_level', fallback='ERROR')))
redis_db = RedisDatabase(app.iniconfig.get('redis', 'host'),
app.iniconfig.get('redis', 'port', fallback=6379),
app.iniconfig.get('redis', 'db', fallback=0),
app.iniconfig.get('redis', 'password', fallback=None))
redis_db_without_decode = RedisDatabase(
app.iniconfig.get('redis', 'host'),
app.iniconfig.get('redis', 'port', fallback=6379),
def setUp(self):
app = flask.Flask(__name__)
app.iniconfig = FlaskIni()
self.app = app
self.filename = 'test_config.ini'
from datetime import timedelta
from flask import make_response, request, current_app
from functools import update_wrapper
from flask_cors import CORS, cross_origin
from aggregations import plotA1, plotA2, plotA3, plotA4, plotA5, plotB1, plotB2, plotB3, plotB4, plotB5
UPLOAD_FOLDER = '/data'
ALLOWED_EXTENSIONS = ['csv']
# Flask init
application = Flask(__name__)
application.logger.info("application.py init")
application.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
with application.app_context():
application.iniconfig = FlaskIni()
application.iniconfig.read(os.environ['APP_SETTINGS'])
application.logger.info("Loading application settings")
CORS(application)
def allowed_file(filename):
return '.' in filename and \
filename.rsplit('.', 1)[1].lower() in ALLOWED_EXTENSIONS
@application.route('/upload', methods=['GET', 'POST'])
def upload():
if request.method == 'POST':
# check if the post request has the file part
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
