def configure(config="DefaultConfig", config_file=None):
configStr = 'ga4gh.serverconfig:{0}'.format(config)
app.config.from_object(configStr)
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
if config_file is not None:
app.config.from_pyfile(args.config_file)
cors.CORS(app, allow_headers='Content-Type')
def boot(application, config):
if config and config['origins']:
try:
from flask.ext import cors
for i in config.keys():
application.config['CORS_%s' % i.upper()] = config[i]
cors.CORS(application)
except Exception as e:
raise Exception('Failed to init cors support %s' % e)
def create():
app = flask.Flask(__name__, static_folder=None)
app.logger.setLevel(logging.DEBUG)
cors.CORS(app)
db_url = 'sqlite:///{}/buckit.sqlite'.format(os.getcwd())
app.config['SQLALCHEMY_DATABASE_URI'] = db_url
app.db = SQLAlchemy(app)
buckit.routes.initialize(app)
return app
def configure(configFile=None, baseConfig="ProductionConfig", extraConfig={}):
"""
TODO Document this critical function! What does it do? What does
it assume?
"""
configStr = 'ga4gh.serverconfig:{0}'.format(baseConfig)
app.config.from_object(configStr)
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
if configFile is not None:
app.config.from_pyfile(configFile)
app.config.update(extraConfig.items())
# Setup CORS
cors.CORS(app, allow_headers='Content-Type')
app.serverStatus = ServerStatus()
# Allocate the backend
# TODO is this a good way to determine what type of backend we should
# instantiate? We should think carefully about this. The approach of
# using the special strings __SIMULATED__ and __EMPTY__ seems OK for
# now, but is certainly not ideal.
dataSource = app.config["DATA_SOURCE"]
if dataSource == "__SIMULATED__":
randomSeed = app.config["SIMULATED_BACKEND_RANDOM_SEED"]
numCalls = app.config["SIMULATED_BACKEND_NUM_CALLS"]
variantDensity = app.config["SIMULATED_BACKEND_VARIANT_DENSITY"]
numVariantSets = app.config["SIMULATED_BACKEND_NUM_VARIANT_SETS"]
theBackend = backend.SimulatedBackend(randomSeed, numCalls,
variantDensity, numVariantSets)
elif dataSource == "__EMPTY__":
theBackend = backend.EmptyBackend()
else:
theBackend = backend.FileSystemBackend(dataSource)
theBackend.setRequestValidation(app.config["REQUEST_VALIDATION"])
theBackend.setResponseValidation(app.config["RESPONSE_VALIDATION"])
theBackend.setDefaultPageSize(app.config["DEFAULT_PAGE_SIZE"])
theBackend.setMaxResponseLength(app.config["MAX_RESPONSE_LENGTH"])
app.backend = theBackend
app = Flask(__name__)
app.debug = True
app.config['SQLALCHEMY_DATABASE_URI'] = sqla_conn_string()
app.config['APISPEC_FORMAT_RESPONSE'] = None
app.config['SQLALCHEMY_REPLICA_TASKS'] = [
'webservices.tasks.download.export_query',
]
app.config['SQLALCHEMY_FOLLOWERS'] = [
sa.create_engine(follower.strip())
for follower in env.get_credential('SQLA_FOLLOWERS', '').split(',')
if follower.strip()
]
# app.config['SQLALCHEMY_ECHO'] = True
db.init_app(app)
cors.CORS(app)
class FlaskRestParser(FlaskParser):
def handle_error(self, error):
message = error.messages
status_code = getattr(error, 'status_code', 422)
raise exceptions.ApiError(message, status_code)
parser = FlaskRestParser()
app.config['APISPEC_WEBARGS_PARSER'] = parser
v1 = Blueprint('v1', __name__, url_prefix='/v1')
api = restful.Api(v1)
def configure(configFile=None, baseConfig="ProductionConfig",
port=8000, extraConfig={}):
"""
TODO Document this critical function! What does it do? What does
it assume?
"""
file_handler = StreamHandler()
file_handler.setLevel(logging.WARNING)
app.logger.addHandler(file_handler)
configStr = 'ga4gh.server.serverconfig:{0}'.format(baseConfig)
app.config.from_object(configStr)
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
if configFile is not None:
app.config.from_pyfile(configFile)
app.config.update(extraConfig.items())
# Setup file handle cache max size
datamodel.fileHandleCache.setMaxCacheSize(
app.config["FILE_HANDLE_CACHE_MAX_SIZE"])
# Setup CORS
try:
cors.CORS(app, allow_headers='Content-Type')
except AssertionError:
pass
app.serverStatus = ServerStatus()
app.backend = _configure_backend(app)
if app.config.get('SECRET_KEY'):
app.secret_key = app.config['SECRET_KEY']
elif app.config.get('OIDC_PROVIDER'):
raise exceptions.ConfigurationException(
'OIDC configuration requires a secret key')
if app.config.get('CACHE_DIRECTORY'):
app.cache_dir = app.config['CACHE_DIRECTORY']
else:
app.cache_dir = '/tmp/ga4gh'
app.cache = FileSystemCache(
app.cache_dir, threshold=5000, default_timeout=600, mode=384)
app.oidcClient = None
app.myPort = port
if app.config.get('AUTH0_ENABLED'):
emails = app.config.get('AUTH0_AUTHORIZED_EMAILS', '').split(',')
[auth.authorize_email(e, app.cache) for e in emails]
if "OIDC_PROVIDER" in app.config:
# The oic client. If we're testing, we don't want to verify
# SSL certificates
app.oidcClient = oic.oic.Client(
verify_ssl=('TESTING' not in app.config))
try:
app.oidcClient.provider_config(app.config['OIDC_PROVIDER'])
except requests.exceptions.ConnectionError:
configResponse = message.ProviderConfigurationResponse(
issuer=app.config['OIDC_PROVIDER'],
authorization_endpoint=app.config['OIDC_AUTHZ_ENDPOINT'],
token_endpoint=app.config['OIDC_TOKEN_ENDPOINT'],
revocation_endpoint=app.config['OIDC_TOKEN_REV_ENDPOINT'])
app.oidcClient.handle_provider_config(configResponse,
app.config['OIDC_PROVIDER'])
# The redirect URI comes from the configuration.
# If we are testing, then we allow the automatic creation of a
# redirect uri if none is configured
redirectUri = app.config.get('OIDC_REDIRECT_URI')
if redirectUri is None and app.config.get('TESTING'):
redirectUri = 'https://{0}:{1}/oauth2callback'.format(
socket.gethostname(), app.myPort)
app.oidcClient.redirect_uris = [redirectUri]
if redirectUri is []:
raise exceptions.ConfigurationException(
'OIDC configuration requires a redirect uri')
# We only support dynamic registration while testing.
if ('registration_endpoint' in app.oidcClient.provider_info and
app.config.get('TESTING')):
app.oidcClient.register(
app.oidcClient.provider_info["registration_endpoint"],
redirect_uris=[redirectUri])
else:
response = message.RegistrationResponse(
client_id=app.config['OIDC_CLIENT_ID'],
client_secret=app.config['OIDC_CLIENT_SECRET'],
redirect_uris=[redirectUri],
verify_ssl=False)
app.oidcClient.store_registration_info(response)
def configure(configFile=None, baseConfig="ProductionConfig",
port=8000, extraConfig={}):
"""
TODO Document this critical function! What does it do? What does
it assume?
"""
configStr = 'ga4gh.serverconfig:{0}'.format(baseConfig)
app.config.from_object(configStr)
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
if configFile is not None:
app.config.from_pyfile(configFile)
app.config.update(extraConfig.items())
# Setup file handle cache max size
datamodel.fileHandleCache.setMaxCacheSize(
app.config["FILE_HANDLE_CACHE_MAX_SIZE"])
# Setup CORS
cors.CORS(app, allow_headers='Content-Type')
app.serverStatus = ServerStatus()
# Allocate the backend
# We use URLs to specify the backend. Currently we have file:// URLs (or
# URLs with no scheme) for the FileSystemBackend, and special empty:// and
# simulated:// URLs for empty or simulated data sources.
dataSource = urlparse.urlparse(app.config["DATA_SOURCE"], "file")
if dataSource.scheme == "simulated":
# Ignore the query string
randomSeed = app.config["SIMULATED_BACKEND_RANDOM_SEED"]
numCalls = app.config["SIMULATED_BACKEND_NUM_CALLS"]
variantDensity = app.config["SIMULATED_BACKEND_VARIANT_DENSITY"]
numVariantSets = app.config["SIMULATED_BACKEND_NUM_VARIANT_SETS"]
numReferenceSets = app.config[
"SIMULATED_BACKEND_NUM_REFERENCE_SETS"]
numReferencesPerReferenceSet = app.config[
"SIMULATED_BACKEND_NUM_REFERENCES_PER_REFERENCE_SET"]
numAlignmentsPerReadGroup = app.config[
"SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP"]
dataRepository = datarepo.SimulatedDataRepository(
randomSeed=randomSeed, numCalls=numCalls,
variantDensity=variantDensity, numVariantSets=numVariantSets,
numReferenceSets=numReferenceSets,
numReferencesPerReferenceSet=numReferencesPerReferenceSet,
numAlignments=numAlignmentsPerReadGroup)
elif dataSource.scheme == "empty":
dataRepository = datarepo.EmptyDataRepository()
elif dataSource.scheme == "file":
dataRepository = datarepo.FileSystemDataRepository(os.path.join(
dataSource.netloc, dataSource.path))
dataRepository.checkConsistency()
else:
raise exceptions.ConfigurationException(
"Unsupported data source scheme: " + dataSource.scheme)
theBackend = backend.Backend(dataRepository)
theBackend.setRequestValidation(app.config["REQUEST_VALIDATION"])
theBackend.setResponseValidation(app.config["RESPONSE_VALIDATION"])
theBackend.setDefaultPageSize(app.config["DEFAULT_PAGE_SIZE"])
theBackend.setMaxResponseLength(app.config["MAX_RESPONSE_LENGTH"])
app.backend = theBackend
app.secret_key = os.urandom(SECRET_KEY_LENGTH)
app.oidcClient = None
app.tokenMap = None
app.myPort = port
if "OIDC_PROVIDER" in app.config:
# The oic client. If we're testing, we don't want to verify
# SSL certificates
app.oidcClient = oic.oic.Client(
verify_ssl=('TESTING' not in app.config))
app.tokenMap = {}
try:
app.oidcClient.provider_config(app.config['OIDC_PROVIDER'])
except requests.exceptions.ConnectionError:
configResponse = message.ProviderConfigurationResponse(
issuer=app.config['OIDC_PROVIDER'],
authorization_endpoint=app.config['OIDC_AUTHZ_ENDPOINT'],
token_endpoint=app.config['OIDC_TOKEN_ENDPOINT'],
revocation_endpoint=app.config['OIDC_TOKEN_REV_ENDPOINT'])
app.oidcClient.handle_provider_config(configResponse,
app.config['OIDC_PROVIDER'])
# The redirect URI comes from the configuration.
# If we are testing, then we allow the automatic creation of a
# redirect uri if none is configured
redirectUri = app.config.get('OIDC_REDIRECT_URI')
if redirectUri is None and 'TESTING' in app.config:
redirectUri = 'https://{0}:{1}/oauth2callback'.format(
socket.gethostname(), app.myPort)
app.oidcClient.redirect_uris = [redirectUri]
if redirectUri is []:
raise exceptions.ConfigurationException(
'OIDC configuration requires a redirect uri')
# We only support dynamic registration while testing.
if ('registration_endpoint' in app.oidcClient.provider_info and
'TESTING' in app.config):
app.oidcClient.register(
app.oidcClient.provider_info["registration_endpoint"],
redirect_uris=[redirectUri])
else:
response = message.RegistrationResponse(
client_id=app.config['OIDC_CLIENT_ID'],
client_secret=app.config['OIDC_CLIENT_SECRET'],
redirect_uris=[redirectUri],
verify_ssl=False)
app.oidcClient.store_registration_info(response)
def configure(configFile=None,
baseConfig="ProductionConfig",
port=8000,
extraConfig={}):
"""
TODO Document this critical function! What does it do? What does
it assume?
"""
configStr = 'ga4gh.serverconfig:{0}'.format(baseConfig)
app.config.from_object(configStr)
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
if configFile is not None:
app.config.from_pyfile(configFile)
app.config.update(extraConfig.items())
# Setup file handle cache max size
datamodel.fileHandleCache.setMaxCacheSize(
app.config["FILE_HANDLE_CACHE_MAX_SIZE"])
# Setup CORS
cors.CORS(app, allow_headers='Content-Type')
app.serverStatus = ServerStatus()
# Allocate the backend
# TODO is this a good way to determine what type of backend we should
# instantiate? We should think carefully about this. The approach of
# using the special strings __SIMULATED__ and __EMPTY__ seems OK for
# now, but is certainly not ideal.
dataSource = app.config["DATA_SOURCE"]
if dataSource == "__SIMULATED__":
randomSeed = app.config["SIMULATED_BACKEND_RANDOM_SEED"]
numCalls = app.config["SIMULATED_BACKEND_NUM_CALLS"]
variantDensity = app.config["SIMULATED_BACKEND_VARIANT_DENSITY"]
numVariantSets = app.config["SIMULATED_BACKEND_NUM_VARIANT_SETS"]
numReferenceSets = app.config["SIMULATED_BACKEND_NUM_REFERENCE_SETS"]
numReferencesPerReferenceSet = app.config[
"SIMULATED_BACKEND_NUM_REFERENCES_PER_REFERENCE_SET"]
numAlignments = app.config[
"SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP"]
theBackend = backend.SimulatedBackend(randomSeed, numCalls,
variantDensity, numVariantSets,
numReferenceSets,
numReferencesPerReferenceSet,
numAlignments)
elif dataSource == "__EMPTY__":
theBackend = backend.EmptyBackend()
else:
theBackend = backend.FileSystemBackend(dataSource)
theBackend.setRequestValidation(app.config["REQUEST_VALIDATION"])
theBackend.setResponseValidation(app.config["RESPONSE_VALIDATION"])
theBackend.setDefaultPageSize(app.config["DEFAULT_PAGE_SIZE"])
theBackend.setMaxResponseLength(app.config["MAX_RESPONSE_LENGTH"])
app.backend = theBackend
app.secret_key = os.urandom(SECRET_KEY_LENGTH)
app.oidcClient = None
app.tokenMap = None
app.myPort = port
if "OIDC_PROVIDER" in app.config:
# The oic client. If we're testing, we don't want to verify
# SSL certificates
app.oidcClient = oic.oic.Client(
verify_ssl=('TESTING' not in app.config))
app.tokenMap = {}
try:
app.oidcClient.provider_config(app.config['OIDC_PROVIDER'])
except requests.exceptions.ConnectionError:
configResponse = message.ProviderConfigurationResponse(
issuer=app.config['OIDC_PROVIDER'],
authorization_endpoint=app.config['OIDC_AUTHZ_ENDPOINT'],
token_endpoint=app.config['OIDC_TOKEN_ENDPOINT'],
revocation_endpoint=app.config['OIDC_TOKEN_REV_ENDPOINT'])
app.oidcClient.handle_provider_config(configResponse,
app.config['OIDC_PROVIDER'])
# The redirect URI comes from the configuration.
# If we are testing, then we allow the automatic creation of a
# redirect uri if none is configured
redirectUri = app.config.get('OIDC_REDIRECT_URI')
if redirectUri is None and 'TESTING' in app.config:
redirectUri = 'https://{0}:{1}/oauth2callback'.format(
socket.gethostname(), app.myPort)
app.oidcClient.redirect_uris = [redirectUri]
if redirectUri is []:
raise exceptions.ConfigurationException(
'OIDC configuration requires a redirect uri')
# We only support dynamic registration while testing.
if ('registration_endpoint' in app.oidcClient.provider_info
and 'TESTING' in app.config):
app.oidcClient.register(
app.oidcClient.provider_info["registration_endpoint"],
redirect_uris=[redirectUri])
else:
response = message.RegistrationResponse(
client_id=app.config['OIDC_CLIENT_ID'],
client_secret=app.config['OIDC_CLIENT_SECRET'],
redirect_uris=[redirectUri],
verify_ssl=False)
app.oidcClient.store_registration_info(response)
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
import flask
import flask.ext.api as api
import flask.ext.cors as cors
app = api.FlaskAPI(__name__)
app.config.from_object('ga4gh.server.config:DefaultConfig')
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
cors.CORS(app, allow_headers='Content-Type')
def handleHTTPPost(request, endpoint):
"""
Handles the specified HTTP POST request, which maps to the specified
protocol handler handpoint and protocol request class.
"""
mimetype = "application/json"
if request.mimetype != mimetype:
raise api.exceptions.UnsupportedMediaType()
responseStr = endpoint(request.get_data())
return flask.Response(responseStr, status=200, mimetype=mimetype)
def handleHTTPOptions():
import flask_sqlalchemy
import datetime
import sqlalchemy
import flask_potion
import flask_potion.fields as fields
import flask
import flask.ext.cors as cors
import calendar
app = flask.Flask(__name__)
app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = True
db = flask_sqlalchemy.SQLAlchemy(app)
api = flask_potion.Api(app)
cors.CORS(app,
supports_credentials=True,
headers=['Content-Type'],
expose_headers=['Link', 'X-Total-Count'])
class Client(db.Model):
__table_args__ = (sqlalchemy.UniqueConstraint('name'), )
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String, nullable=False)
projects = sqlalchemy.orm.relationship(
"Project",
cascade="delete",
backref=sqlalchemy.orm.backref('client'),
)
workentries = sqlalchemy.orm.relationship(
"WorkEntry",
