def connect():
client = ArangoClient(
host=os.getenv('ARANGO_HOST'),
port=os.getenv('ARANGO_PORT'),
username=os.getenv('ARANGO_USER'),
password=os.getenv('ARANGO_ROOT_PASSWORD'),
)
client.databases()
def arangoConnect(getIp, getPort, getUser, getPass, getNewdb):
client = ArangoClient(protocol='http',
host=getIp,
port=getPort,
username=getUser,
password=getPass,
enable_logging=True)
print("connected?")
try:
client.create_database(getNewdb)
print('Created new db, ' + getNewdb)
return (client.databases())
except:
print('failed to create new DB, ' + getNewdb)
print(client.databases())
return (client.databases())
#/usr/bin/env python3
from arango import ArangoClient
from datetime import tzinfo
from db_credentials import db_credentials
# Configure your ArangoDB server connection here
conn = ArangoClient(protocol=db_credentials['protocol'],
host=db_credentials['host'],
port=db_credentials['port'],
username=db_credentials['username'],
password=db_credentials['password'])
dbName = 'polBotCheck'
if dbName not in conn.databases():
db = conn.create_database(dbName)
db = conn.db(dbName)
def getCollection(collectionName, edge=False):
collectionNames = map(lambda c: c['name'], db.collections())
if collectionName not in collectionNames:
db.create_collection(collectionName, edge=edge)
return db.collection(collectionName)
def getVertexCollection(graph, collectionName):
collectionNames = map(lambda c: c['name'], db.collections())
if collectionName not in collectionNames:
graph.create_vertex_collection(collectionName)
def test_empty_arango(app, arango: ArangoClient):
assert app.config.get('ARANGO_DB') not in arango.databases()
def test_migration(app, arango: ArangoClient):
assert app.config.get('ARANGO_DB') in arango.databases()
class ArangoHandler(object):
def __init__(self,
database,
protocol='http',
host='localhost',
port=8529,
username='******',
password=''):
self.BATCH_LIMIT = 10000
self.client = ArangoClient(protocol=protocol,
host=host,
port=port,
username=username,
password=password,
enable_logging=True)
self.db = self.retrieve_db(database)
def retrieve_db(self, database_name):
if self.has_db(database_name):
return self.client.database(database_name)
else:
return self.client.create_database(database_name)
def has_db(self, database_name):
database_list = self.client.databases()
if database_name in database_list:
return True
else:
return False
def insert_jsonl(self, collection_name, lines):
collection = self.retrieve_collection(collection_name)
commit = []
lines = lines.split(b"\n")
count = 0
for line in lines:
try:
dictionary = ujson.loads(line)
except Exception as error:
logging.error(u"Error loading jsonl: {}".format(line))
line = lines.pop()
continue
key_hash = hashlib.md5(line)
dictionary['_key'] = key_hash.hexdigest()
commit.append(dictionary)
if len(commit) == self.BATCH_LIMIT:
collection.import_bulk(commit,
sync=True,
on_duplicate="ignore")
commit[:] = []
count += 1
if len(commit) > 0:
collection.import_bulk(commit, sync=True, on_duplicate="ignore")
logging.info(u"Records Processed: {}".format(count))
def retrieve_collection(self, collection_name):
if self.has_collection(collection_name):
return self.db.collection(collection_name)
else:
return self.db.create_collection(collection_name)
def has_collection(self, collection_name):
collection_list = self.db.collections()
for collection_info in collection_list:
if collection_info['name'] == collection_name:
return True
return False
if len(header_line) > 1:
# each header line
for line in header_line:
val = line.split(r'=')
# add the id as the key
if val[0] == 'ID':
# set the
elm_ref = structure[val[1]] = {}
else:
# for this id, add the values
elm_ref[val[0].lower()] = re.sub('^\"|\"?$', '', val[1])
if len(sys.argv) > 2:
# Initialize the client for ArangoDB
client = ArangoClient(protocol='http',
host='localhost',
port=8529,
username='******',
password='******',
enable_logging=True)
if sys.argv[2] not in client.databases():
client.create_database(sys.argv[2])
# select the database
db = client.db(sys.argv[2])
# create our obj
loader = hapmap_load()
# start loading variants
loader.load_vcf(sys.argv[1], db)
else:
print "please specify a VCF and arango database"
