def create_app(debug=False, local=False, object_config=None):
# ----------------------------------
# Create App
marvin_base = os.environ.get('MARVIN_BASE', 'marvin2')
app = Flask(__name__, static_url_path='/{0}/static'.format(marvin_base))
api = Blueprint("api", __name__, url_prefix='/{0}/api'.format(marvin_base))
app.debug = debug
# Add Marvin Logger
app.logger.addHandler(log)
# Turn on debug stuff in config
if app.debug is True:
sentry = None
config.use_sentry = False
config.add_github_message = False
# Find which connection to make
connection = getDbMachine()
local = (connection == 'local') or local
# ----------------------------------
# Set some other variables
config._inapp = True
url_prefix = '/marvin2' if local else '/{0}'.format(marvin_base)
# ----------------------------------
# Load the appropriate Flask configuration object for debug or production
if not object_config:
if app.debug or local:
app.logger.info('Loading Development Config!')
object_config = type('Config', (DevConfig, CustomConfig), dict())
else:
app.logger.info('Loading Production Config!')
object_config = type('Config', (ProdConfig, CustomConfig), dict())
app.config.from_object(object_config)
# ------------------------------------------
# Add lib directory as a new static path
@app.route('/{0}/lib/<path:filename>'.format(marvin_base))
def lib(filename):
return send_from_directory(app.config["LIB_PATH"], filename)
# Register global session update before every request
@app.before_request
def global_update():
''' updates the global session / config '''
updateGlobalSession()
# ----------------------------------
# Registration
register_extensions(app, app_base=marvin_base)
register_api(app, api)
register_blueprints(app, url_prefix=url_prefix)
return app
def _setDbConfig(self):
''' Set the db configuration '''
self.db = getDbMachine()
def create_app(debug=False, local=False, use_profiler=True):
#from marvin.api import theapi as api
from marvin.api.cube import CubeView
from marvin.api.maps import MapsView
from marvin.api.modelcube import ModelCubeView
from marvin.api.plate import PlateView
from marvin.api.rss import RSSView
from marvin.api.spaxel import SpaxelView
from marvin.api.query import QueryView
from marvin.api.general import GeneralRequestsView
from marvin.web.controllers.index import index
from marvin.web.controllers.galaxy import galaxy
from marvin.web.controllers.search import search
from marvin.web.controllers.plate import plate
from marvin.web.controllers.images import images
from marvin.web.controllers.users import users
# ----------------------------------
# Create App
marvin_base = os.environ.get('MARVIN_BASE', 'marvin2')
app = Flask(__name__, static_url_path='/{0}/static'.format(marvin_base))
api = Blueprint("api", __name__, url_prefix='/{0}/api'.format(marvin_base))
app.debug = debug
jsg.JSGLUE_JS_PATH = '/{0}/jsglue.js'.format(marvin_base)
jsglue = jsg.JSGlue(app)
# Add Marvin Logger
app.logger.addHandler(log)
# Setup the profile configuration
app.config["flask_profiler"] = {
"enabled": True,
"storage": {
"engine": "sqlite",
"FILE": os.path.join(os.environ['MARVIN_DIR'],
'flask_profiler.sql')
},
'endpointRoot': '{0}/profiler'.format(marvin_base),
"basicAuth": {
"enabled": False
}
}
# ----------------------------------
# Initialize logging + Sentry + UWSGI config for Production Marvin
if app.debug is False:
# ----------------------------------------------------------
# Set up getsentry.com logging - only use when in production
dsn = os.environ.get('SENTRY_DSN', None)
app.config['SENTRY_DSN'] = dsn
sentry = Sentry(app, logging=True, level=logging.ERROR)
# --------------------------------------
# Configuration when running under uWSGI
try:
import uwsgi
app.use_x_sendfile = True
except ImportError:
pass
else:
sentry = None
config.use_sentry = False
config.add_github_message = False
# Change the implementation of "decimal" to a C-based version (much! faster)
#
# This is producing this error [ Illegal value: Decimal('3621.59598486') ]on some of the remote API tests with getSpectrum
# Turning this off for now
#
# try:
# import cdecimal
# sys.modules["decimal"] = cdecimal
# except ImportError:
# pass # no available
# Find which connection to make
connection = getDbMachine()
local = (connection == 'local') or local
# ----------------------------------
# Set some environment variables
config._inapp = True
os.environ['SAS_REDUX'] = 'sas/mangawork/manga/spectro/redux'
os.environ['SAS_ANALYSIS'] = 'sas/mangawork/manga/spectro/analysis'
os.environ['SAS_SANDBOX'] = 'sas/mangawork/manga/sandbox'
release = os.environ.get('MARVIN_RELEASE', 'mangawork')
os.environ[
'SAS_PREFIX'] = 'marvin2' if release == 'mangawork' else 'dr13/marvin'
url_prefix = '/marvin2' if local else '/{0}'.format(marvin_base)
# ----------------------------------
# Load the appropriate Flask configuration file for debug or production
if app.debug:
if local:
server_config_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'configuration',
'localhost.cfg')
elif connection == 'utah':
server_config_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'configuration',
'utah.cfg')
else:
server_config_file = None
app.logger.debug(
"Trying to run in debug mode, but not running on a development machine that has database access."
)
# sys.exit(1)
else:
try:
import uwsgi
server_config_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'configuration',
uwsgi.opt['flask-config-file'])
except ImportError:
app.logger.debug(
"Trying to run in production mode, but not running under uWSGI. You might try running again with the '--debug' flag."
)
sys.exit(1)
if server_config_file:
app.logger.info('Loading config file: {0}'.format(server_config_file))
app.config.from_pyfile(server_config_file)
# ----------------------------------
# Initialize feature flags
feature_flags = FeatureFlag(app)
# configFeatures(debug=app.debug)
# Update any config parameters
app.config["UPLOAD_FOLDER"] = os.environ.get("MARVIN_DATA_DIR", None)
app.config["LIB_PATH"] = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'lib')
# Add lib directory as a new static path
@app.route('/{0}/lib/<path:filename>'.format(marvin_base))
def lib(filename):
return send_from_directory(app.config["LIB_PATH"], filename)
# Register update global session
@app.before_request
def global_update():
''' updates the global session / config '''
updateGlobalSession()
# send_request()
# ----------------
# Error Handling
# ----------------
def _is_api(request):
''' Checks if the error comes from the api '''
return request.blueprint == 'api' or 'api' in request.url
@app.errorhandler(404)
def page_not_found(error):
name = 'Page Not Found'
if _is_api(request):
return make_error_json(error, name, 404)
else:
return make_error_page(app, name, 404, sentry=sentry)
@app.errorhandler(500)
def internal_server_error(error):
name = 'Internal Server Error'
if _is_api(request):
return make_error_json(error, name, 500)
else:
return make_error_page(app, name, 500, sentry=sentry)
@app.errorhandler(400)
def bad_request(error):
name = 'Bad Request'
if _is_api(request):
return make_error_json(error, name, 400)
else:
return make_error_page(app, name, 400, sentry=sentry)
@app.errorhandler(405)
def method_not_allowed(error):
name = 'Method Not Allowed'
if _is_api(request):
return make_error_json(error, name, 405)
else:
return make_error_page(app, name, 405, sentry=sentry)
@app.errorhandler(422)
def handle_unprocessable_entity(error):
name = 'Unprocessable Entity'
data = getattr(error, 'data')
if data:
# Get validations from the ValidationError object
messages = data['messages']
else:
messages = ['Invalid request']
if _is_api(request):
return make_error_json(error, name, 422)
else:
return make_error_page(app,
name,
422,
sentry=sentry,
data=messages)
# These should be moved into the api module but they need the api blueprint to be registered on
# I had these in the api.__init__ with the api blueprint defined there as theapi
# which was imported here, see line 39
# This should all be moved into the Brain and abstracted since it is
# general useful standardized stuff (what?)
@api.errorhandler(422)
def handle_unprocessable_entity(err):
# webargs attaches additional metadata to the `data` attribute
data = getattr(err, 'data')
if data:
# Get validations from the ValidationError object
messages = data['messages']
else:
messages = ['Invalid request']
return jsonify({
'validation_errors': messages,
}), 422
# ----------------------------------
# Registration
config.use_sentry = False
#
# API route registration
CubeView.register(api)
MapsView.register(api)
ModelCubeView.register(api)
PlateView.register(api)
RSSView.register(api)
SpaxelView.register(api)
GeneralRequestsView.register(api)
QueryView.register(api)
app.register_blueprint(api)
# Web route registration
app.register_blueprint(index, url_prefix=url_prefix)
app.register_blueprint(galaxy, url_prefix=url_prefix)
app.register_blueprint(search, url_prefix=url_prefix)
app.register_blueprint(plate, url_prefix=url_prefix)
app.register_blueprint(images, url_prefix=url_prefix)
app.register_blueprint(users, url_prefix=url_prefix)
# Register all custom Jinja filters in the file.
app.register_blueprint(jinjablue)
# Register error handlers
app.register_blueprint(web)
# Initialize the Flask-Profiler ; see results at localhost:portnumber/flask-profiler
if use_profiler:
try:
flask_profiler.init_app(app)
except Exception as e:
pass
return app