def set_limits(self):
self._auth_key = AuthKey()
if self.auth_token_payload:
self._auth_key = AuthKey(
app_name=self.auth_token_payload['app_name'],
secret=self.auth_token_payload['secret'],
)
self._auth_key.get_loaded_data()
self.short_window_rate = int(self._auth_key.short_window_rate)
self.long_window_rate = int(self._auth_key.long_window_rate)
def setUpClass(cls):
auth_credentials = {
'domain': '',
'reference': '*****@*****.**',
'app_name': 'api-test',
'short_window_rate': '10000',
'secret': 'YNVukca767p49Czt7jOt42U3R6t1FscD',
'users_allowed': 'true',
'long_window_rate': '6000000'
}
cls.auth_key = AuthKey(**auth_credentials)
cls.app = create_app('testing')
cls.app.extensions['redis-user'].hmset(cls.auth_key.get_key(),
cls.auth_key.__dict__)
cls.app_context = cls.app.app_context()
cls.app_context.push()
cls.client = cls.app.test_client()
cls.host = 'http://' + cls.app_context.url_adapter.get_host('')
def create_app(config_name):
app = Flask(__name__, static_url_path='')
# This first loads the configuration from eg. config['development'] which corresponds to the DevelopmentConfig class in the config.py
app.config.from_object(config[config_name])
# Then you can override the values with the contents of the file the OPENTARGETS_API_LOCAL_SETTINGS environment variable points to.
# For eg:
# $ export OPENTARGETS_API_LOCAL_SETTINGS=/path/to/settings.cfg
#
# where settings.cfg looks like:
#
# DEBUG = False
# SECRET_KEY = 'foo'
#
app.config.from_envvar("OPENTARGETS_API_LOCAL_SETTINGS", silent=True)
config[config_name].init_app(app)
api_version = app.config['API_VERSION']
api_version_minor = app.config['API_VERSION_MINOR']
app.logger.info('looking for elasticsearch at: %s' % app.config['ELASTICSEARCH_URL'])
app.extensions['redis-core'] = Redis(app.config['REDIS_SERVER_PATH'], db=0) #served data
app.extensions['redis-service'] = Redis(app.config['REDIS_SERVER_PATH'], db=1) #cache, rate limit and internal things
app.extensions['redis-user'] = Redis(app.config['REDIS_SERVER_PATH'], db=2)# user info
'''setup cache'''
app.extensions['redis-service'].config_set('save','')
app.extensions['redis-service'].config_set('appendonly', 'no')
icache = InternalCache(app.extensions['redis-service'],
str(api_version_minor))
ip2org = IP2Org(icache)
if app.config['ELASTICSEARCH_URL']:
es = Elasticsearch(app.config['ELASTICSEARCH_URL'],
# # sniff before doing anything
# sniff_on_start=True,
# # refresh nodes after a node fails to respond
# sniff_on_connection_fail=True,
# # and also every 60 seconds
# sniffer_timeout=60
timeout=60 * 20,
maxsize=32,
)
else:
es = None
'''elasticsearch handlers'''
app.extensions['esquery'] = esQuery(es,
DataTypes(app),
DataSourceScoring(app),
index_data=app.config['ELASTICSEARCH_DATA_INDEX_NAME'],
index_efo=app.config['ELASTICSEARCH_EFO_LABEL_INDEX_NAME'],
index_eco=app.config['ELASTICSEARCH_ECO_INDEX_NAME'],
index_genename=app.config['ELASTICSEARCH_GENE_NAME_INDEX_NAME'],
index_expression=app.config['ELASTICSEARCH_EXPRESSION_INDEX_NAME'],
index_reactome=app.config['ELASTICSEARCH_REACTOME_INDEX_NAME'],
index_association=app.config['ELASTICSEARCH_DATA_ASSOCIATION_INDEX_NAME'],
index_search=app.config['ELASTICSEARCH_DATA_SEARCH_INDEX_NAME'],
index_relation=app.config['ELASTICSEARCH_DATA_RELATION_INDEX_NAME'],
docname_data=app.config['ELASTICSEARCH_DATA_DOC_NAME'],
docname_efo=app.config['ELASTICSEARCH_EFO_LABEL_DOC_NAME'],
docname_eco=app.config['ELASTICSEARCH_ECO_DOC_NAME'],
docname_genename=app.config['ELASTICSEARCH_GENE_NAME_DOC_NAME'],
docname_expression=app.config['ELASTICSEARCH_EXPRESSION_DOC_NAME'],
docname_reactome=app.config['ELASTICSEARCH_REACTOME_REACTION_DOC_NAME'],
docname_association=app.config['ELASTICSEARCH_DATA_ASSOCIATION_DOC_NAME'],
docname_search=app.config['ELASTICSEARCH_DATA_SEARCH_DOC_NAME'],
# docname_search_target=app.config['ELASTICSEARCH_DATA_SEARCH_TARGET_DOC_NAME'],
# docname_search_disease=app.config['ELASTICSEARCH_DATA_SEARCH_DISEASE_DOC_NAME'],
docname_relation=app.config['ELASTICSEARCH_DATA_RELATION_DOC_NAME'],
log_level=app.logger.getEffectiveLevel(),
cache=icache
)
app.extensions['es_access_store'] = esStore(es,
eventlog_index=app.config['ELASTICSEARCH_LOG_EVENT_INDEX_NAME'],
ip2org=ip2org,
)
'''mixpanel handlers'''
if Config.MIXPANEL_TOKEN:
mp = Mixpanel(Config.MIXPANEL_TOKEN, consumer=AsyncBufferedConsumer())
app.extensions['mixpanel']= mp
app.extensions['mp_access_store'] = MixPanelStore(mp,
ip2org=ip2org,
)
app.extensions['proxy'] = ProxyHandler(allowed_targets=app.config['PROXY_SETTINGS']['allowed_targets'],
allowed_domains=app.config['PROXY_SETTINGS']['allowed_domains'],
allowed_request_domains=app.config['PROXY_SETTINGS']['allowed_request_domains'])
# basepath = app.config['PUBLIC_API_BASE_PATH']+api_version
# cors = CORS(app, resources=r'/api/*', allow_headers='Content-Type,Auth-Token')
''' define cache'''
# cache = Cache(config={'CACHE_TYPE': 'simple'})
# cache.init_app(latest_blueprint)
# latest_blueprint.cache = cache
# latest_blueprint.extensions['cache'] = cache
# app.cache = SimpleCache()
app.cache = FileSystemCache('/tmp/cttv-rest-api-cache', threshold=100000, default_timeout=60*60, mode=777)
'''Set usage limiter '''
# limiter = Limiter(global_limits=["2000 per hour", "20 per second"])
# limiter.init_app(app)# use redis to store limits
'''Load api keys in redis'''
rate_limit_file = app.config['USAGE_LIMIT_PATH']
if not os.path.exists(rate_limit_file):
rate_limit_file = '../'+rate_limit_file
csvfile = None
if Config.GITHUB_AUTH_TOKEN:
r = requests.get('https://api.github.com/repos/opentargets/rest_api_auth/contents/rate_limit.csv',
headers = {'Authorization': 'token %s'%Config.GITHUB_AUTH_TOKEN,
'Accept': 'application/vnd.github.v3.raw'})
if r.ok:
csvfile = r.text.split('\n')
app.logger.info('Retrieved rate limit file from github remote')
else:
app.logger.warning('Cannot retrieve rate limit file from remote, SKIPPED!')
elif os.path.exists(rate_limit_file):
csvfile = open(rate_limit_file)
app.logger.info('Using dummy rate limit file')
if csvfile is None:
app.logger.error('cannot find rate limit file: %s. RATE LIMIT QUOTA LOAD SKIPPED!'%rate_limit_file)
else:
reader = csv.DictReader(csvfile)
for row in reader:
auth_key = AuthKey(**row)
app.extensions['redis-user'].hmset(auth_key.get_key(), auth_key.__dict__)
try:
csvfile.close()
except:
pass
app.logger.info('succesfully loaded rate limit file')
'''load ip name resolution'''
ip_resolver = defaultdict(lambda: "PUBLIC")
ip_list_file = app.config['IP_RESOLVER_LIST_PATH']
if not os.path.exists(ip_list_file):
ip_list_file = '../' + ip_list_file
if os.path.exists(ip_list_file):
with open(ip_list_file) as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
net = IPNetwork(row['ip'])
ip_resolver[net] = row['org']
else:
app.logger.warning('cannot find IP list for IP resolver. All traffic will be logged as PUBLIC')
app.config['IP_RESOLVER'] = ip_resolver
'''compress http response'''
compress = Compress()
compress.init_app(app)
latest_blueprint = Blueprint('latest', __name__)
current_version_blueprint = Blueprint(str(api_version), __name__)
current_minor_version_blueprint = Blueprint(str(api_version_minor), __name__)
specpath = '/cttv'
if app.config['PROFILE'] == True:
from werkzeug.contrib.profiler import ProfilerMiddleware
app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[30])
'''set the right prefixes'''
create_api(latest_blueprint, api_version, specpath)
create_api(current_version_blueprint, api_version, specpath)
create_api(current_minor_version_blueprint, api_version_minor, specpath)
# app.register_blueprint(latest_blueprint, url_prefix='/latest/platform')
app.register_blueprint(current_version_blueprint, url_prefix='/v'+str(api_version) + '/platform')
app.register_blueprint(current_minor_version_blueprint, url_prefix='/v'+str(api_version_minor) + '/platform')
'''serve the static docs'''
try:
'''
NOTE: this file gets created only at deployment time
'''
openapi_def = yaml.load(file('app/static/openapi.yaml', 'r'))
app.logger.info('parsing swagger from static/openapi.yaml')
except IOError:
'''if we are not deployed, then simply use the template'''
openapi_def = yaml.load(file('openapi.template.yaml', 'r'))
app.logger.error('parsing swagger from openapi.template.yaml')
with open("api-description.md", "r") as f:
desc = f.read()
openapi_def['info']['description'] = desc
openapi_def['basePath'] = '/v%s' % str(api_version)
@app.route('/v%s/platform/swagger' % str(api_version))
def serve_swagger(apiversion=api_version):
return jsonify(openapi_def)
@app.route('/v%s/platform/docs' % str(api_version))
def render_redoc(apiversion=api_version):
return render_template('docs.html',api_version=apiversion)
'''pre and post-request'''
@app.before_request
def before_request():
g.request_start = datetime.now()
@app.after_request
def after(resp):
try:
rate_limiter = RateLimiter()
now = datetime.now()
took = (now - g.request_start).total_seconds()*1000
if took > 500:
cache_time = str(int(3600*took))# set cache to last one our for each second spent in the request
resp.headers.add('X-Accel-Expires', cache_time)
took = int(round(took))
LogApiCallWeight(took)
# if took < RateLimiter.DEFAULT_CALL_WEIGHT:
# took = RateLimiter.DEFAULT_CALL_WEIGHT
current_values = increment_call_rate(took,rate_limiter)
now = datetime.now()
ceil10s=round(ceil_dt_to_future_time(now, 10),2)
ceil1h=round(ceil_dt_to_future_time(now, 3600),2)
usage_left_10s = rate_limiter.short_window_rate-current_values['short']
usage_left_1h = rate_limiter.long_window_rate - current_values['long']
min_ceil = ceil10s
if usage_left_1h <0:
min_ceil = ceil1h
if (usage_left_10s < 0) or (usage_left_1h <0):
resp.headers.add('Retry-After', min_ceil)
resp.headers.add('X-API-Took', took)
resp.headers.add('X-Usage-Limit-10s', rate_limiter.short_window_rate)
resp.headers.add('X-Usage-Limit-1h', rate_limiter.long_window_rate)
resp.headers.add('X-Usage-Remaining-10s', usage_left_10s)
resp.headers.add('X-Usage-Remaining-1h', usage_left_1h)
# resp.headers.add('X-Usage-Limit-Reset-10s', ceil10s)
# resp.headers.add('X-Usage-Limit-Reset-1h', ceil1h)
resp.headers.add('Access-Control-Allow-Origin', '*')
resp.headers.add('Access-Control-Allow-Headers','Content-Type,Auth-Token')
resp.headers.add('Access-Control-Allow-Methods', 'GET,PUT,POST,DELETE,OPTIONS')
if do_not_cache(request):# do not cache in the browser
resp.headers.add('Cache-Control', "no-cache, must-revalidate, max-age=0")
else:
resp.headers.add('Cache-Control', "no-transform, public, max-age=%i, s-maxage=%i"%(took*1800/1000, took*9000/1000))
return resp
except Exception as e:
app.logger.exception('failed request teardown function', str(e))
return resp
# Override the HTTP exception handler.
app.handle_http_exception = get_http_exception_handler(app)
return app
def create_app(config_name):
app = Flask(__name__, static_url_path='')
app.config.from_object(config[config_name])
app.config.from_envvar("OPENTARGETS_API_LOCAL_SETTINGS", silent=True)
config[config_name].init_app(app)
api_version = app.config['API_VERSION']
api_version_minor = app.config['API_VERSION_MINOR']
# log_level = logging.INFO
# if app.config['DEBUG']:
# log_level = logging.DEBUG
# Flask has a default logger which works well and pushes to stderr
# if you want to add different handlers (to file, or logstash, or whatever)
# you can use code similar to the one below and set the error level accordingly.
# logHandler = logging.StreamHandler()
# formatter = jsonlogger.JsonFormatter()
# logHandler.setFormatter(formatter)
# loghandler.setLevel(logging.INFO)
# app.logger.addHandler(logHandler)
# or for LOGSTASH
# app.logger.addHandler(logstash.LogstashHandler(app.config['LOGSTASH_HOST'], app.config['LOGSTASH_PORT'], version=1))
app.logger.info('looking for elasticsearch at: %s' %
app.config['ELASTICSEARCH_URL'])
print('looking for elasticsearch at: %s' % app.config['ELASTICSEARCH_URL'])
app.extensions['redis-core'] = Redis(app.config['REDIS_SERVER_PATH'],
db=0) #served data
app.extensions['redis-service'] = Redis(
app.config['REDIS_SERVER_PATH'],
db=1) #cache, rate limit and internal things
app.extensions['redis-user'] = Redis(app.config['REDIS_SERVER_PATH'],
db=2) # user info
'''setup cache'''
app.extensions['redis-service'].config_set('save', '')
app.extensions['redis-service'].config_set('appendonly', 'no')
icache = InternalCache(app.extensions['redis-service'],
str(api_version_minor))
ip2org = IP2Org(icache)
es = Elasticsearch(
app.config['ELASTICSEARCH_URL'],
# # sniff before doing anything
# sniff_on_start=True,
# # refresh nodes after a node fails to respond
# sniff_on_connection_fail=True,
# # and also every 60 seconds
# sniffer_timeout=60
timeout=60 * 20,
maxsize=100,
)
'''elasticsearch handlers'''
app.extensions['esquery'] = esQuery(
es,
DataTypes(app),
DataSourceScoring(app),
index_data=app.config['ELASTICSEARCH_DATA_INDEX_NAME'],
index_efo=app.config['ELASTICSEARCH_EFO_LABEL_INDEX_NAME'],
index_eco=app.config['ELASTICSEARCH_ECO_INDEX_NAME'],
index_genename=app.config['ELASTICSEARCH_GENE_NAME_INDEX_NAME'],
index_expression=app.config['ELASTICSEARCH_EXPRESSION_INDEX_NAME'],
index_reactome=app.config['ELASTICSEARCH_REACTOME_INDEX_NAME'],
index_association=app.
config['ELASTICSEARCH_DATA_ASSOCIATION_INDEX_NAME'],
index_search=app.config['ELASTICSEARCH_DATA_SEARCH_INDEX_NAME'],
index_relation=app.config['ELASTICSEARCH_DATA_RELATION_INDEX_NAME'],
docname_data=app.config['ELASTICSEARCH_DATA_DOC_NAME'],
docname_efo=app.config['ELASTICSEARCH_EFO_LABEL_DOC_NAME'],
docname_eco=app.config['ELASTICSEARCH_ECO_DOC_NAME'],
docname_genename=app.config['ELASTICSEARCH_GENE_NAME_DOC_NAME'],
docname_expression=app.config['ELASTICSEARCH_EXPRESSION_DOC_NAME'],
docname_reactome=app.
config['ELASTICSEARCH_REACTOME_REACTION_DOC_NAME'],
docname_association=app.
config['ELASTICSEARCH_DATA_ASSOCIATION_DOC_NAME'],
docname_search=app.config['ELASTICSEARCH_DATA_SEARCH_DOC_NAME'],
# docname_search_target=app.config['ELASTICSEARCH_DATA_SEARCH_TARGET_DOC_NAME'],
# docname_search_disease=app.config['ELASTICSEARCH_DATA_SEARCH_DISEASE_DOC_NAME'],
docname_relation=app.config['ELASTICSEARCH_DATA_RELATION_DOC_NAME'],
log_level=app.logger.getEffectiveLevel(),
cache=icache)
app.extensions['es_access_store'] = esStore(
es,
eventlog_index=app.config['ELASTICSEARCH_LOG_EVENT_INDEX_NAME'],
ip2org=ip2org,
)
'''mixpanel handlers'''
if Config.MIXPANEL_TOKEN:
mp = Mixpanel(Config.MIXPANEL_TOKEN, consumer=AsyncBufferedConsumer())
app.extensions['mixpanel'] = mp
app.extensions['mp_access_store'] = MixPanelStore(
mp,
ip2org=ip2org,
)
app.extensions['proxy'] = ProxyHandler(
allowed_targets=app.config['PROXY_SETTINGS']['allowed_targets'],
allowed_domains=app.config['PROXY_SETTINGS']['allowed_domains'],
allowed_request_domains=app.config['PROXY_SETTINGS']
['allowed_request_domains'])
basepath = app.config['PUBLIC_API_BASE_PATH'] + api_version
# cors = CORS(app, resources=r'/api/*', allow_headers='Content-Type,Auth-Token')
''' define cache'''
# cache = Cache(config={'CACHE_TYPE': 'simple'})
# cache.init_app(latest_blueprint)
# latest_blueprint.cache = cache
# latest_blueprint.extensions['cache'] = cache
# app.cache = SimpleCache()
app.cache = FileSystemCache('/tmp/cttv-rest-api-cache',
threshold=100000,
default_timeout=60 * 60,
mode=777)
'''Set usage limiter '''
# limiter = Limiter(global_limits=["2000 per hour", "20 per second"])
# limiter.init_app(app)# use redis to store limits
'''Load api keys in redis'''
rate_limit_file = app.config['USAGE_LIMIT_PATH']
if not os.path.exists(rate_limit_file):
rate_limit_file = '../' + rate_limit_file
if os.path.exists(rate_limit_file):
with open(rate_limit_file) as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
auth_key = AuthKey(**row)
app.extensions['redis-user'].hmset(auth_key.get_key(),
auth_key.__dict__)
print('INFO - succesfully loaded rate limit file')
else:
print('ERROR - cannot find rate limit file')
app.logger.error(
'cannot find rate limit file: %s. RATE LIMIT QUOTA LOAD SKIPPED!' %
rate_limit_file)
'''load ip name resolution'''
ip_resolver = defaultdict(lambda: "PUBLIC")
ip_list_file = app.config['IP_RESOLVER_LIST_PATH']
if not os.path.exists(ip_list_file):
ip_list_file = '../' + ip_list_file
if os.path.exists(ip_list_file):
with open(ip_list_file) as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
net = IPNetwork(row['ip'])
ip_resolver[net] = row['org']
else:
app.logger.warning(
'cannot find IP list for IP resolver. All traffic will be logged as PUBLIC'
)
app.config['IP_RESOLVER'] = ip_resolver
'''compress http response'''
compress = Compress()
compress.init_app(app)
latest_blueprint = Blueprint('latest', __name__)
current_version_blueprint = Blueprint(str(api_version), __name__)
current_minor_version_blueprint = Blueprint(str(api_version_minor),
__name__)
specpath = '/cttv'
if app.config['PROFILE'] == True:
from werkzeug.contrib.profiler import ProfilerMiddleware
app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[30])
create_api(latest_blueprint, api_version, specpath)
create_api(current_version_blueprint, api_version, specpath)
create_api(current_minor_version_blueprint, api_version_minor, specpath)
app.register_blueprint(latest_blueprint, url_prefix='/api/latest')
app.register_blueprint(current_version_blueprint,
url_prefix='/api/' + str(api_version))
app.register_blueprint(current_minor_version_blueprint,
url_prefix='/api/' + str(api_version_minor))
@app.route('/api-docs/%s' % str(api_version_minor))
def docs_current_minor_version():
return redirect('/api/swagger/index.html')
@app.route('/api-docs/%s' % str(api_version))
def docs_current_version():
return redirect('/api/swagger/index.html')
@app.route('/api-docs')
def docs():
return redirect('/api/swagger/index.html')
def serve_swagger():
return app.send_static_file('docs/swagger/swagger.yaml')
@app.route('/api/docs/swagger.yaml')
def send_swagger():
return serve_swagger()
@app.route('/api/latest/docs/swagger.yaml')
def send_swagger_latest():
return serve_swagger()
@app.route('/api/' + str(api_version) + '/docs/swagger.yaml')
def send_swagger_current_cersion():
return serve_swagger()
@app.before_request
def before_request():
g.request_start = datetime.now()
@app.after_request
def after(resp):
rate_limiter = RateLimiter()
now = datetime.now()
took = (now - g.request_start).total_seconds() * 1000
if took > 500:
cache_time = str(
int(3600 * took)
) # set cache to last one our for each second spent in the request
resp.headers.add('X-Accel-Expires', cache_time)
took = int(round(took))
LogApiCallWeight(took)
# if took < RateLimiter.DEFAULT_CALL_WEIGHT:
# took = RateLimiter.DEFAULT_CALL_WEIGHT
current_values = increment_call_rate(took, rate_limiter)
now = datetime.now()
ceil10s = round(ceil_dt_to_future_time(now, 10), 2)
ceil1h = round(ceil_dt_to_future_time(now, 3600), 2)
usage_left_10s = rate_limiter.short_window_rate - current_values[
'short']
usage_left_1h = rate_limiter.long_window_rate - current_values['long']
min_ceil = ceil10s
if usage_left_1h < 0:
min_ceil = ceil1h
if (usage_left_10s < 0) or (usage_left_1h < 0):
resp.headers.add('Retry-After', min_ceil)
resp.headers.add('X-API-Took', took)
resp.headers.add('X-Usage-Limit-10s', rate_limiter.short_window_rate)
resp.headers.add('X-Usage-Limit-1h', rate_limiter.long_window_rate)
resp.headers.add('X-Usage-Remaining-10s', usage_left_10s)
resp.headers.add('X-Usage-Remaining-1h', usage_left_1h)
# resp.headers.add('X-Usage-Limit-Reset-10s', ceil10s)
# resp.headers.add('X-Usage-Limit-Reset-1h', ceil1h)
resp.headers.add('Access-Control-Allow-Origin', '*')
resp.headers.add('Access-Control-Allow-Headers',
'Content-Type,Auth-Token')
if do_not_cache(request): # do not cache in the browser
resp.headers.add('Cache-Control',
"no-cache, must-revalidate, max-age=0")
else:
resp.headers.add(
'Cache-Control',
"no-transform, public, max-age=%i, s-maxage=%i" %
(took * 1800 / 1000, took * 9000 / 1000))
return resp
return app