def create_app(config_file,
blueprints=[],
custom_error_endpoints=False,
custom_template_paths=[],
custom_before_handler=None,
custom_before_handler_args=[],
custom_before_handler_kargs={},
custom_after_handler=None,
custom_after_handler_args=[],
custom_after_handler_kargs={},
template_folder=None,
cors=True,
ssl_only=True,
db_enabled=True,
static_url_path=None,
static_folder=None):
if config_file is None:
raise (Exception("Hey, 'config_files' cannot be 'None'!"))
flask_init_options = {}
if template_folder:
flask_init_options['template_folder'] = template_folder
if static_url_path:
flask_init_options['static_url_path'] = static_url_path
if static_folder:
flask_init_options['static_folder'] = static_folder
app = Flask(__name__, **flask_init_options)
app = load_config(app, config_file)
if ssl_only is True and app.config.get("DEBUG") is False:
sslify = SSLify(app)
app = setup_templates(app, custom_template_paths)
app = setup_debug_log(app)
app = register_blue_prints(app, blueprints)
app = error_endpoints(app, custom_error_endpoints)
app = before_handler(app, custom_before_handler,
custom_before_handler_args,
custom_before_handler_kargs)
app = after_handler(app, custom_after_handler, custom_after_handler_args,
custom_after_handler_kargs, db_enabled)
if db_enabled:
app = init_db(app)
app = setup_routes(app)
if cors is True:
cors = CORS(app)
app.config['CORS_HEADERS'] = 'Content-Type'
if app.config.get('DEBUG') is False:
mail = Mail(app)
mail_on_500(app, app.config.get('ADMINS'))
return app
def setup_error_emails(app):
"""Sets up emails on errors if the SMTP server is specified in the settings.
"""
if 'OPBEAT' in app.config:
app.logger.info("setting up opbeat")
config = app.config['OPBEAT']
opbeat = Opbeat(app,
organization_id=config['ORGANIZATION_ID'],
app_id=config['APP_ID'],
secret_token=config['SECRET_TOKEN'])
if app.debug:
return
if 'ERROR_EMAIL_RECIPIENTS' not in app.config:
return
sender = app.config.get("MAIL_DEFAULT_SENDER")
recipients = app.config['ERROR_EMAIL_RECIPIENTS'].split(",")
mail_on_500(app, recipients, sender=sender)
def setup_error_emails(app):
"""Sets up emails on errors if the SMTP server is specified in the settings.
"""
if 'OPBEAT' in app.config:
app.logger.info("setting up opbeat")
config = app.config['OPBEAT']
opbeat = Opbeat(app,
organization_id=config['ORGANIZATION_ID'],
app_id=config['APP_ID'],
secret_token=config['SECRET_TOKEN'])
if app.debug:
return
if 'ERROR_EMAIL_RECIPIENTS' not in app.config:
return
sender = app.config.get("MAIL_DEFAULT_SENDER")
recipients = app.config['ERROR_EMAIL_RECIPIENTS'].split(",")
mail_on_500(app, recipients, sender=sender)
from multiprocessing import Process
import glob
import sqlite3
import traceback
import time
logging.getLogger().addHandler(logging.StreamHandler())
logging.getLogger().setLevel(logging.INFO)
ADMINISTRATORS = (
'*****@*****.**',
)
app = Flask(__name__)
mail_on_500(app, ADMINISTRATORS)
Compress(app)
app.config['COMPRESS_DEBUG'] = True
cache = SimpleCache()
EXAC_FILES_DIRECTORY = '../exac_data/'
REGION_LIMIT = 1E5
EXON_PADDING = 50
# Load default config and override config from an environment variable
app.config.update(dict(
DB_HOST='localhost',
DB_PORT=27017,
DB_NAME='exac',
DEBUG=True,
SECRET_KEY='development key',
LOAD_DB_PARALLEL_PROCESSES = 4, # contigs assigned to threads, so good to make this a factor of 24 (eg. 2,3,4,6,8)
def test_install_sanity():
mail_on_500(Flask('Fake Flask App'), ('*****@*****.**', ))
app.config["SECURITY_SEND_PASSWORD_CHANGE_EMAIL"] = False
app.config["SECURITY_SEND_PASSWORD_RESET_NOTICE_EMAIL"] = False
app.config["SECURITY_PASSWORD_HASH"] = 'sha512_crypt'
app.config["SECURITY_PASSWORD_SALT"] = '' # Set password salt
# Flask-Mail
app.config['MAIL_SERVER'] = 'smtp.gmail.com'
app.config['MAIL_PORT'] = 587
app.config['MAIL_USE_TLS'] = True
app.config['MAIL_USERNAME'] = '' # Place email address
app.config['MAIL_PASSWORD'] = '' # Place password
mail = Mail(app)
# Flask-ErrorMail
ADMINISTRATORS = [""] # Set administrators emails
mail_on_500(app, ADMINISTRATORS, sender='') # Add sender email
# Flask-DebugToolBar
app.config['DEBUG_TB_PANELS'] = ['flask.ext.mongoengine.panels.MongoDebugPanel']
app.config['DEBUG_TB_ENABLED'] = True
# Flask-MongoEngine
db = MongoEngine(app)
app.session_interface = MongoEngineSessionInterface(db)
login_manager = LoginManager()
login_manager.init_app(app)
login_manager.session_protection = "strong"
assets = Environment(app)
js = Bundle('js/jquery.min.js', 'js/bootstrap.js', 'js/tooltip.js', 'js/notify.min.js', 'js/moment.min.js', 'js/application.js', 'js/app.js', filters="jsmin", output="lib/application.js")
from collections import defaultdict, OrderedDict
from werkzeug.contrib.cache import SimpleCache
from multiprocessing import Process
import glob
import sqlite3
import traceback
import time
logging.getLogger().addHandler(logging.StreamHandler())
logging.getLogger().setLevel(logging.INFO)
ADMINISTRATORS = ('*****@*****.**', )
app = Flask(__name__)
mail_on_500(app, ADMINISTRATORS)
Compress(app)
app.config['COMPRESS_DEBUG'] = True
cache = SimpleCache()
EXAC_FILES_DIRECTORY = '../exac_data/'
REGION_LIMIT = 1E5
EXON_PADDING = 50
# Load default config and override config from an environment variable
app.config.update(
dict(
DB_HOST='localhost',
DB_PORT=27017,
DB_NAME='exac',
DEBUG=True,
SECRET_KEY='development key',
'[in %(pathname)s:%(lineno)d]'
))
app.logger.addHandler(file_handler)
if os.getenv("LOGFILE", None):
import logging.handlers, logging
file_handler = logging.handlers.RotatingFileHandler(os.getenv("LOGFILE"), 'a', 10000000, 1000)
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(logging.Formatter(
'%(asctime)s %(levelname)s: %(message)s '
'[in %(pathname)s:%(lineno)d]'
))
app.logger.addHandler(file_handler)
mail_on_500(app, ["*****@*****.**", ])
# Replace this.
DOC_KEY="xx"
def ldapsearch(uid):
cmd = 'ldapsearch -l 5 -LLL -x -h ldap-too -b "ou=users,ou=moira,dc=mit,dc=edu" ' + pipes.quote("uid=" + uid)
try:
output = subprocess.check_output(cmd, shell=True)
except subprocess.CalledProcessError, e:
app.logger.error(str(e))
return None
out = {}
lines = output.strip().splitlines()
for line in lines:
key, val = line.split(":", 1)
from flask_errormail import mail_on_500
from datetime import datetime
from os import listdir
from os.path import isfile, join
app = Flask(__name__)
app.wsgi_app = ProxyFix(app.wsgi_app)
# Load configs
app.config.from_object('app.settings.common')
app.config.from_envvar('GRAFFATHON_SETTINGS')
mail_on_500(app, app.config['ADMINISTRATORS'],
sender=app.config['MAIL_DEFAULT_SENDER'])
db = SQLAlchemy(app)
login_manager = LoginManager()
login_manager.init_app(app)
login_manager.login_view = '/login'
mail = Mail(app)
mail.init_app(app)
thumb = Thumbnail(app)
from models import SignUp, Admin
from forms import SignUpForm, LoginForm
from emails import send_email, send_all
def test_install_sanity():
mail_on_500(Flask("Fake Flask App"), ("*****@*****.**",))
# Load default config
app.config.from_object('config.default')
# Load instance configuration if exists
app.config.from_pyfile('config.py', silent=True)
# Load configuration file specified in BRAVO_CONFIG_FILE environment variable if exists
app.config.from_envvar('BRAVO_CONFIG_FILE', silent=True)
#app.config.from_object('flask_config.BravoFreeze5GRCh38Config')
if app.config['PROXY']: app.wsgi_app = ProxyFix(app.wsgi_app)
if 'GVS_URL_PREFIX' in os.environ:
app.config['URL_PREFIX'] = os.environ['GVS_URL_PREFIX']
if 'BRAVO_ADMIN_MODE' in os.environ:
app.config['ADMIN'] = True if os.environ['BRAVO_ADMIN_MODE'].lower(
) == 'true' else False
mail_on_500(app, app.config['ADMINS'])
app.config['COMPRESS_LEVEL'] = 2 # Since we don't cache, faster=better
Compress(app)
app.config['SEND_FILE_MAX_AGE_DEFAULT'] = 5 # 5 second browser cache timeout
app.config['TEMPLATES_AUTO_RELOAD'] = True
BASE_COVERAGE = []
BASE_COVERAGE.extend({
'bp-min-length': 0,
'path': path
} for path in glob.glob(app.config['BASE_COVERAGE_DIRECTORY'] +
'full/*.json.gz'))
BASE_COVERAGE.extend({
'bp-min-length': 300,
'binned': True,
'path': path
class MyFlask(Flask):
@cached_property
def connection(self):
return Connection(self.config['MONGODB_HOST'], self.config['MONGODB_PORT'])
@cached_property
def db(self):
return getattr(self.connection, self.config['MONGODB_DB'])
app = MyFlask(__name__)
app.root_path = '/'.join(app.root_path.split('/')[:-1])
app.config.from_object('project.settings')
if mail_on_500: mail_on_500(app, app.config['ADMINS'])
markdown = Markdown(app)
command_manager = Manager(app)
assets = Environment(app)
static = {}
static['js'] = map(lambda x: 'js/%s' % x, (
'jquery.min.js',
'underscore.js',
'backbone.js',
'backbone-forms.js',
'ejs.js',
'jquery.form.js',
'bootstrap-tooltip.js',
'jquery.reject.js',
