def isMatchingIP(self, ip):
for permitted in PERMITTED_IPS:
match = fnmatch.filter([ip], permitted)
if match:
logging.info("WebHook: isMatchingIP() [%s, %s, %s]" % (ip, permitted, match))
return True
return False
def get(self, identity):
logging.info("uri=%s [%s] [%s]" % (self.request.uri, identity, self.request.arguments))
args = self.request.arguments
query = {}
for key in args.keys():
if key != "cancer":
continue
iargs = args[key]
if len(iargs) == 1:
query[key] = args[key][0].lower()
else:
query[key] = {"$in": map(lambda x: x.lower(), args[key])}
if "max_rank" not in args:
query["rank"] = {"$lt": 21}
else:
query["rank"] = {"$lt": int(args["max_rank"][0]) + 1}
collection = self.open_collection("qed_lookups", "mutsig_rankings")
items = []
if "cancer" in query:
items = collection.find(query)
json_items = map(self.jsonable_item, items)
if self.get_argument("output", "json") == "tsv":
WriteTsv(self, json_items)
self.set_status(200)
return
self.write(json.dumps({ "items": json_items }))
self.set_status(200)
def get(self, identity):
logging.info("uri=%s [%s] [%s]" % (self.request.uri, identity, self.request.arguments))
args = self.request.arguments
ids = identity.split("/")
query = {
"chr": str(args["chr"][0]),
"start": {"$gt": int(args["start"][0])},
"end": {"$lt": int(args["end"][0])},
"cancer": {"$in": map(lambda x: x.lower(), args["cancer"])},
"source": {"$in": map(lambda x: x.lower(), args["source"])}
}
logging.info("query=%s" % str(query))
query_limit = options.mongo_lookup_query_limit
collection = self.open_collection(ids[1], ids[2])
items = []
for idx, item in enumerate(collection.find(query, {'values':0})):
if idx > query_limit: break
items.append(item)
self.write(json.dumps({ "items": map(self.jsonable_item, items) }))
self.set_status(200)
def get(self, vcf_id, chromosome, coordinate):
global VCF_MAP
if vcf_id not in DATA_MAP:
logging.info("Unknown VCF id \'" + vcf_id + "\'")
raise tornado.web.HTTPError(404)
file_info = DATA_MAP[vcf_id]
file_path = file_info['path']
lookup_fn = None
if file_info['type'] == 'vcf':
lookup_fn = vcf_lookup
elif file_info['type'] == 'trio':
lookup_fn = triotype_lookup
else:
logging.error("Unknown type for file " + file_path)
raise tornado.web.HTTPError(404)
try:
result = lookup_fn(options.tabix_executable, file_path, chromosome, coordinate, coordinate)
response = {
"chr": result.chromosome,
"coordinate": result.coordinate,
"values": result.values
}
self.write(json.dumps(response, sort_keys=True))
self.set_status(200)
except Exception as e:
logging.error("Running tabix failed:")
logging.error(e)
raise tornado.web.HTTPError(404)
def main():
define("port", default=8321, help="Server port", type=int)
define("verbose", default=False, help="Prints debugging statements")
define("tabix_executable", default=".", help="Path to tabix executable")
define("vcf_config", default=".", help="Path to VCF configuration JSON")
tornado.options.parse_command_line()
logging.info("Starting Tornado web server on http://localhost:%s" % options.port)
logging.info("--tabix_executable=%s" % options.tabix_executable)
logging.info("--vcf_config=%s" % options.vcf_config)
logging.info("--verbose=%s" % options.verbose)
# Try loading the VCF mapping
logging.info("Loading VCF configuration file \'" + options.vcf_config + "\'...")
try:
global DATA_MAP
DATA_MAP = parse_vcf_config(options.vcf_config)
except Exception as e:
logging.error("Failed to load VCF configuration file:")
logging.error(e)
sys.exit(1)
application = tornado.web.Application([
(r"/(\w+)/(X|Y|M|\d{1,2})/(\d+)", TabixLookup)
], **settings)
application.listen(options.port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def open_collection(db_name, collection_name):
#if options.verbose:
logging.info("open_collection(%s)" % collection_name)
connection = pymongo.Connection(options.mongo_lookup_uri)
database = connection[db_name]
return database[collection_name]
def get(self, identity):
logging.info("uri=%s [%s] [%s]" % (self.request.uri, identity, self.request.arguments))
# TODO : Improve this logic to correctly parse arguments and convert to a proper mongo DB query
args = self.request.arguments
query = {}
for key in args.keys():
query[key] = args[key][0]
ids = identity.split("/")
db_name = ids[1]
collection = open_collection(db_name, ids[2])
query_limit = options.mongo_lookup_query_limit
json_items = []
for idx, item in enumerate(collection.find(query)):
if idx > query_limit: break
json_item = self.jsonable_item(item)
json_item["uri"] = self.request.uri + "/" + json_item["id"]
json_items.append(json_item)
self.write({ "items": json_items })
self.set_status(200)
return
def open_collection(self, db_name, collection_name):
#if options.verbose:
logging.info("open_collection(%s)" % collection_name)
connection = pymongo.Connection(options.mongo_lookup_uri)
database = connection[db_name]
return database[collection_name]
def get(self, vcf_id, chromosome, start_coordinate, end_coordinate):
global VCF_MAP
if vcf_id not in DATA_MAP:
logging.info("Unknown VCF id \'" + vcf_id + "\'")
raise tornado.web.HTTPError(404)
file_info = DATA_MAP[vcf_id]
file_path = file_info['path']
lookup_fn = None
if file_info['type'] == 'tsv':
lookup_fn = tsv_region_lookup
else:
logging.error("Unknown type for file " + file_path)
raise tornado.web.HTTPError(404)
try:
# The result.values array contains dictiories, for which the keys are read from the header line
# of the TSV file. For the header line to be included in the output of the tabix command, the "-h"
# flag has to be included in the command line.
result = lookup_fn(options.tabix_executable + " -h", file_path, chromosome, start_coordinate, end_coordinate)
response = {
"chr": result.chromosome,
"start": result.start,
"end": result.end,
"values": result.values
}
self.write(json.dumps(response, sort_keys=True))
self.set_status(200)
except Exception as e:
logging.error("Running tabix failed:")
logging.error(e)
raise tornado.web.HTTPError(404)
def post(self, *args, **kwargs):
logging.info("WebHook: post()")
if not self.isPermittedIP():
self.set_status(401)
return
http_client = tornado.httpclient.HTTPClient()
response = http_client.fetch(options.github_repo_api_url)
repository = json.loads(response.body)
clone_url = repository["clone_url"].replace("https", "http")
self.pull(clone_url, options.github_project_root, "master")
branches_url = repository["branches_url"].replace("{/branch}", "")
response = http_client.fetch(branches_url)
branches = json.loads(response.body)
write_branches = []
for i, branch in enumerate(branches):
branch_name = branch["name"]
if not branch_name == "master":
deploy_path = os.path.join(options.github_branches_root, branch_name)
logging.info("WebHook: deploying branch [%s] to [%s]" % (branch_name, deploy_path))
self.pull(clone_url, deploy_path, branch_name)
write_branches.append({ "name": branch_name, "label": branch_name })
if not options.github_branches_json_path is None:
json.dump(write_branches, open(os.path.join(options.github_branches_json_path, "branches.json"), "w"))
def main():
tornado.options.parse_command_line()
logging.info("Starting Tornado web server on http://localhost:%s" % options.port)
application = tornado.web.Application([
(r"/", MainHandler),
], **settings)
application.listen(options.port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def main():
tornado.options.parse_command_line()
logging.info("Starting Tornado web server on http://localhost:%s" %
options.port)
application = tornado.web.Application([
(r"/", MainHandler),
], **settings)
application.listen(options.port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def get(self):
logging.info("AuthWhoAmiHandler.get")
whoami = {
"user": "******",
"label": "Hector Rovira"
}
self.write(whoami)
self.set_status(200)
def SaveUserinfo(whoami, userinfo):
logging.info("SaveUserinfo(%s)" % whoami)
existing_user = GetUserinfo(whoami)
userinfo["whoami"] = whoami
collection = open_collection("private_userinfo")
if existing_user is None:
collection.insert(userinfo)
else:
collection.update(existing_user, userinfo)
def on_message(self, message):
logging.info("New Note %s" % message)
newnote = message
newnote_json = json.loads(newnote)
newnote_json["timestamp"] = datetime.now()
notes = get_notes_collection()
notes.insert(newnote_json)
for connected_user in connected_users:
connected_user.write_message(json.dumps([newnote_json], default=json_util.default))
def SaveUserinfo(whoami, userinfo):
logging.info("SaveUserinfo(%s)" % whoami)
existing_user = GetUserinfo(whoami)
userinfo["whoami"] = whoami
collection = open_collection("private_userinfo")
if existing_user is None:
collection.insert(userinfo)
else:
collection.update(existing_user, userinfo)
def redis_listener():
try:
ps = r.pubsub()
ps.subscribe(settings.REDIS['channel'])
io_loop = tornado.ioloop.IOLoop.instance()
for message in ps.listen():
for socket in LISTENERS['ws']:
io_loop.add_callback(partial(socket.on_message,message))
# Note: Not sure if this block will be reached at all
except:
logging.info('redis_listener() aborted. Stop subscribing.')
ps.close()
def main():
tornado.options.parse_command_line()
tornado.web.RequestHandler.instanceNum = options.instn
port = 9900 + options.instn
logging.info("Starting Tornado web server on http://localhost:%s" % port)
application = tornado.web.Application([
(r"/",MainHandler),
(r"/greet", Greeter),
(r"/fingreet",MongoGreeter)
], **settings)
application.listen(port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def open(self):
logging.info("Connection opened")
notes = get_notes_collection()
most_recent_notes = list(
notes.find({"loc": {"$exists": "true"}, "timestamp": {"$exists": "true"}}, limit=25).sort(
"timestamp", DESCENDING
)
)
connected_users.append(self)
self.write_message(json.dumps(most_recent_notes, default=json_util.default))
def post(self, identity):
logging.info("MongoDbHandler.post(%s)" % identity)
ids = identity.split("/")
if len(ids) <= 0: raise HTTPError(401)
stored_item = json.loads(self.request.body)
# Figure out issue where label is getting set as an array
labels = stored_item["label"]
if not labels is None and type(labels) is list: stored_item["label"] = labels[0]
collection = open_collection(ids[0])
insert_id = str(collection.insert(stored_item))
self.write({ "id": insert_id, "uri": self.request.uri + "/" + insert_id })
self.set_status(200)
def plot(timeseries,fig_name):
matplotlib.rc('font', **settings.PLOT['font'])
plt.figure(figsize=(14,2.5), dpi=72)
ax = plt.subplot(1,1,1)
rts = pd.rolling_mean(timeseries, settings.PLOT['rolling_mean_min'])
plt.plot(rts.index, rts.values, settings.PLOT['fill'])
plt.ylabel('Tweets per minute (TPM)')
ax.fill_between(rts.index, rts.values, 0, color=settings.PLOT['fill'])
ax.xaxis.set_major_locator(md.HourLocator(interval=settings.PLOT['xaxis_interval_hr']))
ax.xaxis.set_major_formatter(md.DateFormatter(settings.PLOT['datetime_format']))
ax.autoscale_view()
plt.grid(True)
plt.xlabel('Time (SGT)')
fig = os.path.join(settings.SERVER['static_files_path'],'images',fig_name)
plt.savefig(fig,bbox_inches='tight')
logging.info('Saving %s' % fig)
def get(self, identity):
logging.info("MongoDbHandler.get(%s)" % identity)
ids = identity.split("/")
if len(ids) == 1:
args = self.request.arguments
query = {}
normalize_fn = lambda x: x.lower()
for key in args.keys():
iargs = args[key]
if len(iargs) == 1:
query[key] = normalize_fn(args[key][0])
else:
query[key] = {"$in": map(normalize_fn, args[key])}
collection = open_collection(ids[0])
json_items = []
for idx, item in enumerate(collection.find(query)):
json_item = jsonable_item(item)
json_item["uri"] = self.request.uri + "/" + json_item["id"]
json_items.append(json_item)
json_items.append({
"First Name": "Hector",
"Last Name": "Rovira",
"Birth Date": "03/14/13",
"status": "incomplete"
})
self.write({ "items": json_items })
self.set_status(200)
return
if len(ids) == 2:
collection = open_collection(ids[0])
item = collection.find_one({"_id": objectid.ObjectId(ids[1]) })
if not item is None:
json_item = jsonable_item(item)
json_item["uri"] = self.request.uri
self.write(json_item)
self.set_status(200)
return
self.set_status(404)
def get(self, tabix_id, chromosome, start_coordinate, end_coordinate=None):
if end_coordinate is None:
end_coordinate = start_coordinate
if tabix_id not in self._config_map.keys():
if options.verbose:
logging.info("Unknown tabix loookup ID [%s]" % tabix_id)
raise tornado.web.HTTPError(404)
file_info = self._config_map[tabix_id]
file_path = file_info['path']
lookup_fn = None
tabix_exe = None
if file_info['type'] == 'vcf':
lookup_fn = vcf_singleline_lookup
tabix_exe = options.tabix_executable
elif file_info['type'] == 'trio':
lookup_fn = triotype_singleline_lookup
tabix_exe = options.tabix_executable
elif file_info['type'] == 'tsv':
lookup_fn = tsv_region_lookup
# For parsing the tabix output for TSV files, the header has to be included. Therefore, the "-h"
# flag has to be included in the command line.
tabix_exe = options.tabix_executable + " -h"
else:
logging.error("Unknown type for file " + file_path)
raise tornado.web.HTTPError(404)
try:
result = lookup_fn(tabix_exe, file_path, chromosome, start_coordinate, end_coordinate)
response = {
"chr": result.chromosome,
"start": result.start,
"end": result.end,
"values": result.values,
"snpid": result.snpid,
"info": result.info
}
self.write(json.dumps(response, sort_keys=True))
self.set_status(200)
except Exception as e:
logging.error("Running tabix failed:")
logging.error(e)
raise tornado.web.HTTPError(404)
def get(self, identity):
logging.info("uri=%s [%s] [%s]" % (self.request.uri, identity, self.request.arguments))
args = self.request.arguments
ids = identity.split("/")
feature_matrix_name = ids[1]
gene_label_1 = args['gene1'][0]
gene_label_2 = args['gene2'][0]
cancer_label = args['cancer'][0].lower()
# Get feature IDs
fmx_collection = self.open_feature_matrix_collection("qed_lookups", "fmx_" + feature_matrix_name)
pairwise_collection = self.open_pairwise_collection("qed_lookups", "pw_" + feature_matrix_name + "_" + cancer_label)
features_1 = filter(self.feature_filter_fn, fmx_collection.find({"cancer": cancer_label, "gene": gene_label_1}))
features_2 = filter(self.feature_filter_fn, fmx_collection.find({"cancer": cancer_label, "gene": gene_label_2}))
feature_ids_1 = map(lambda f: f['id'], features_1)
feature_ids_2 = map(lambda f: f['id'], features_2)
# Get pairwise values
pairwise_results = []
for id1, id2 in product(feature_ids_1, feature_ids_2):
pw = self.get_pairwise_result(pairwise_collection, id1, id2)
if pw is not None:
pairwise_results.append(pw)
result = {
"features": {
gene_label_1: map(self.jsonable_item, features_1),
gene_label_2: map(self.jsonable_item, features_2)
},
"pairwise_results": map(self.jsonable_item, pairwise_results)
}
log_msg = "Features found: "
log_msg += gene_label_1 + ": " + str(len(feature_ids_1))
log_msg += "\t" + gene_label_2 + ": " + str(len(feature_ids_2))
log_msg += "\tPairwise results: " + str(len(pairwise_results))
logging.info(log_msg)
self.write(json.dumps(result))
self.set_status(200)
def get(self, identity):
logging.info("uri=%s [%s] [%s]" % (self.request.uri, identity, self.request.arguments))
ids = identity.split("/")
db_name = ids[1]
collection = self.open_collection(db_name, ids[2])
# TODO : Improve this logic to correctly parse arguments and convert to a proper mongo DB query
args = self.request.arguments
query = {}
case_sensitive_lookups = frozenset(options.case_sensitive_lookups)
normalize_fn = None
if db_name in case_sensitive_lookups:
normalize_fn = lambda x: x
else:
normalize_fn = lambda x: x.lower()
for key in args.keys():
if key != "output":
iargs = args[key]
if len(iargs) == 1:
query[key] = normalize_fn(args[key][0])
else:
query[key] = {"$in": map(normalize_fn, args[key])}
query_limit = options.mongo_lookup_query_limit
json_items = []
for idx, item in enumerate(collection.find(query)):
if idx > query_limit:
break
json_item = self.jsonable_item(item)
json_item["uri"] = self.request.uri + "/" + json_item["id"]
json_items.append(json_item)
if self.get_argument("output", "json") == "tsv":
WriteTsv(self, json_items)
self.set_status(200)
return
self.write({"items": json_items})
self.set_status(200)
return
def get(self, identity):
logging.info("uri=%s [%s] [%s]" % (self.request.uri, identity, self.request.arguments))
args = self.request.arguments
cancer_mappings= {
"brca": "brca_pw_manuscript"
}
gene = args["gene"][0]
source = args["source"][0]
dataset = cancer_mappings[args["cancer"][0]]
logging.info("query=[%s][%s][%s]" % (gene, source, dataset))
cli = HTTPClient()
response = cli.fetch("http://explorer.cancerregulome.org/data/distributed_select/?q=%2Bf1source%3A%22" + source + "%22%2Bf1label%3A(%22" + gene + "%22)%20%2Blogged_pvalue%3A%5B6%20TO%20*%5D&sort=logged_pvalue%20desc&rows=200&fl=alias1%2Calias2%2Cf1qtinfo%2Cf2qtinfo%2Clink_distance%2Clogged_pvalue%2Ccorrelation%2Cnum_nonna&wt=json&fq=%2Bdataset%3A" + dataset)
cli.close()
self.write(response.body)
self.set_status(200)
def main():
tornado.options.parse_command_line()
logging.info("Starting Tornado web server on http://localhost:%s" % options.port)
logging.info("--data_path=%s" % options.data_path)
logging.info("--executable=%s" % options.executable)
logging.info("--verbose=%s" % options.verbose)
application = tornado.web.Application([
(r"/", RealtimePairwise),
(r"/svc/rt_pairwise", RealtimePairwise),
], **settings)
application.listen(options.port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def main():
parse_command_line()
if not options.config_file is None:
parse_config_file(options.config_file)
parse_command_line()
if not options.client_secret is None:
settings["cookie_secret"] = options.client_secret
logging.info("Starting tornadoweb on http://localhost:%s" % options.port)
if not options.config_file is None:
logging.info("--config_file=%s" % options.config_file)
application = Application([
(r"/auth/whoami", AuthWhoAmiHandler),
(r"/auth/signout", AuthSignoutHandler),
(r"/dao/?(.*)", MongoDbHandler),
(r"/", RootHandler),
(r"/(.*)", StaticFileHandler, {"path": "_public"})
], **settings)
application.listen(options.port, **server_settings)
IOLoop.instance().start()
def GetUserinfo(whoami):
logging.info("GetUserinfo(%s)" % whoami)
collection = open_collection("private_userinfo")
return collection.find_one({ "whoami": whoami })
from tornado.options import logging
from tornado import httpserver, ioloop
def handle_request(request):
message = """
<!DOCTYPE html>
<html lang="en">
<head>
<title>Good to see it. - test designed By Richard, </title>
<meta charset="UTF-8" />
</head>
<body>
It's good to see it here. Server has been started in master branch.
</body>
</html>
"""
request.write("HTTP/1.1 200 OK\r\nContent-Length: %d\r\n\r\n%s" % (len(message), message))
request.finish()
if __name__ == "__main__":
logging.info("Now I am at master branch! In the first commit")
http_server = httpserver.HTTPServer(handle_request)
http_server.listen(8888)
ioloop.IOLoop.instance().start()
# master.py ended here
def main():
tornado.options.parse_command_line()
if not options.config_file is None:
tornado.options.parse_config_file(options.config_file)
tornado.options.parse_command_line()
settings["cookie_secret"] = options.client_secret
logging.info("Starting Tornado web server on http://localhost:%s" % options.port)
logging.info("--data_path=%s" % options.data_path)
logging.info("--client_host=%s" % options.client_host)
logging.info("--authorized_users=%s" % options.authorized_users)
logging.info("--mongo_uri=%s" % options.mongo_uri)
logging.info("--mongo_lookup_uri=%s" % options.mongo_lookup_uri)
logging.info("--mongo_lookup_query_limit=%s" % options.mongo_lookup_query_limit)
if not options.config_file is None:
logging.info("--config_file=%s" % options.config_file)
application = tornado.web.Application([
(r"/", MainHandler),
(r"/data?(.*)", LocalFileHandler),
(r"/auth/signin/google", GoogleOAuth2Handler),
(r"/auth/signin/google/oauth2_callback", GoogleOAuth2Handler),
(r"/auth/signout/google", GoogleSignoutHandler),
(r"/auth/whoami", WhoamiHandler),
(r"/auth/providers", AuthProvidersHandler),
(r"/storage/(.*)", MongoDbStorageHandler),
(r"/lookups?(.*)", MongoDbLookupHandler),
(r"/mutsig_rankings?(.*)", MongoDbMutSigHandler),
(r"/pw_lookups?(.*)", MongoDbMutSigHandler),
(r"/features_by_location?(.*)", MongoDbFeaturesByLocationHandler),
(r"/RE/query/?(.*)", RegulomeExplorerDbQueryHandler)
], **settings)
application.listen(options.port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def main():
tornado.options.parse_command_line()
if not options.config_file is None:
tornado.options.parse_config_file(options.config_file)
tornado.options.parse_command_line()
settings["cookie_secret"] = options.client_secret
logging.info("Starting Tornado web server on http://localhost:%s" %
options.port)
logging.info("--data_path=%s" % options.data_path)
logging.info("--client_host=%s" % options.client_host)
logging.info("--authorized_users=%s" % options.authorized_users)
logging.info("--mongo_uri=%s" % options.mongo_uri)
logging.info("--mongo_lookup_uri=%s" % options.mongo_lookup_uri)
logging.info("--mongo_lookup_query_limit=%s" %
options.mongo_lookup_query_limit)
if not options.config_file is None:
logging.info("--config_file=%s" % options.config_file)
application = tornado.web.Application(
[(r"/", MainHandler), (r"/data?(.*)", LocalFileHandler),
(r"/auth/signin/google", GoogleOAuth2Handler),
(r"/auth/signin/google/oauth2_callback", GoogleOAuth2Handler),
(r"/auth/signout/google", GoogleSignoutHandler),
(r"/auth/whoami", WhoamiHandler),
(r"/auth/providers", AuthProvidersHandler),
(r"/storage/(.*)", MongoDbStorageHandler),
(r"/lookups?(.*)", MongoDbLookupHandler)], **settings)
application.listen(options.port, **server_settings)
tornado.ioloop.IOLoop.instance().start()
def GetUserinfo(whoami):
logging.info("GetUserinfo(%s)" % whoami)
collection = open_collection("private_userinfo")
return collection.find_one({ "whoami": whoami })
import tornado.web
from tornado.options import define, options, logging
define('port', default=8888, help='run on the given port', type=int)
# Set up logging location
tornado.options.options['log_file_prefix'].set(settings.SERVER['log_file_prefix'])
# Register handlers for each application
handlers = [
(r'/stream', stream.WebHandler), # Register a handler for real-time TPM
(r'/ws_stream', stream.WSHandler), # Register a handler for real-time TPM Websocket
(r'/(.*)', tornado.web.StaticFileHandler, {'path': settings.SERVER['static_files_path']},), # Register a handler for a base directory for static files, e.g., images, scripts, etc.
]
settings = dict(
template_path=os.path.join(os.path.dirname(__file__),'static/templates'),
debug='True',
)
application = tornado.web.Application(handlers,**settings)
# Start HTTP server
if __name__ == '__main__':
threading.Thread(target=stream.redis_listener).start()
tornado.options.parse_command_line() # Enable pretty console logging
logging.info('Starting Tornado server on port %s' % options.port)
http_server = tornado.httpserver.HTTPServer(application)
http_server.listen(options.port)
tornado.ioloop.IOLoop.instance().start()
def open_collection(self, mongo_uri, db_name, collection_name):
logging.info("open_collection(%s)" % collection_name)
connection = pymongo.Connection(mongo_uri)
database = connection[db_name]
return database[collection_name]