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def __init__(self, logger, hitlist, outputfile, settings):
''' The output file name will be used as prefix for contig names
'''
DefaultFormatter.__init__(self, logger, hitlist, outputfile)
self.outputfile = outputfile.split("/")[-1]
driver = GraphDatabase.driver("bolt://{}".format(settings.hostname), auth=basic_auth(settings.username, settings.password))
self.session = driver.session()
self.insert = []
self.sequence_node=settings.sequence_node
self.target_node=settings.target_node
if password is None:
password = 'neo4j'
try:
protocol, url = url.split('://')
if protocol.lower() != 'bolt':
warnings.warn('Switching protocols. Only Bolt is supported.')
except ValueError:
pass
try:
credentials, url = url.split('@')
except ValueError:
kw['auth'] = basic_auth(user, password)
else:
kw['auth'] = basic_auth(*credentials.split(':', 1))
self.driver = GraphDatabase.driver('bolt://%s' % url, **kw)
if user is None:
user = 'neo4j'
if password is None:
password = 'neo4j'
try:
protocol, url = url.split('://')
if protocol.lower() != 'bolt':
warnings.warn('Switching protocols. Only Bolt is supported.')
except ValueError:
pass
try:
credentials, url = url.split('@')
except ValueError:
kw['auth'] = basic_auth(user, password)
else:
kw['auth'] = basic_auth(*credentials.split(':', 1))
self.driver = GraphDatabase.driver('bolt://%s' % url, **kw)
from flask_cors import CORS
from flask_restful import Resource, reqparse
from flask_restful_swagger_2 import Api, swagger, Schema
from neo4j.v1 import GraphDatabase, basic_auth, ResultError
from . import config
app = Flask(__name__)
app.config['SECRET_KEY'] = 'super secret guy'
api = Api(app, title='Neo4j Movie Demo API', api_version='0.0.10')
CORS(app)
driver = GraphDatabase.driver('bolt://localhost', auth=basic_auth(config.DATABASE_USERNAME, str(config.DATABASE_PASSWORD)))
def get_db():
if not hasattr(g, 'neo4j_db'):
g.neo4j_db = driver.session()
return g.neo4j_db
@app.teardown_appcontext
def close_db(error):
if hasattr(g, 'neo4j_db'):
g.neo4j_db.close()
def set_user(sender, **extra):
auth_header = request.headers.get('Authorization')
# TODO: Store this relations in a redis-like cache
self.cache = Cache(cache_data)
self.cache.create_cache(self.DEST_RELS)
self.cache.create_cache(self.DOM_RELS)
self.cache.create_cache(self.SRC_RELS)
self.cache.create_cache(self.SRCDST_RELS)
self.cache.create_cache(self.SRCLOGIN_RELS)
self.cache.create_cache(self.SESSIONS_RELS)
self.cache.create_cache(self.FROM_SESSIONS)
self.cache.create_cache(self.USER_LIST)
self.cache.create_cache(self.DOM_LIST)
self.cache.create_cache(self.SRV_LIST)
self.cache.create_cache(self.SRVDOM_RELS)
# setup neo4j
self.drv = GraphDatabase.driver(data[0], auth=basic_auth(data[1], data[2]))
self.neo = self.drv.session()
self.neo.run("CREATE INDEX ON :User(sid)")
self.neo.run("CREATE INDEX ON :Computer(name)")
self.neo.run("CREATE INDEX ON :Domain(name)")
import QueryNCBIeUtils
except ImportError:
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '../kg-construction'))) # Go up one level and look for it
import QueryNCBIeUtils
import math
import MarkovLearning
import ReasoningUtilities as RU
requests_cache.install_cache('orangeboard')
sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/../../") # code directory
from RTXConfiguration import RTXConfiguration
RTXConfiguration = RTXConfiguration()
# Connection information for the neo4j server, populated with orangeboard
driver = GraphDatabase.driver(RTXConfiguration.bolt, auth=basic_auth("neo4j", "precisionmedicine"))
session = driver.session()
# Connection information for the ipython-cypher package
connection = "http://neo4j:precisionmedicine@" + RTXConfiguration.database
DEFAULT_CONFIGURABLE = {
"auto_limit": 0,
"style": 'DEFAULT',
"short_errors": True,
"data_contents": True,
"display_limit": 0,
"auto_pandas": False,
"auto_html": False,
"auto_networkx": False,
"rest": False,
"feedback": False, # turn off verbosity in ipython-cypher
"uri": connection,
def create_event_node():
# fetches the event nodes from neo4j
insert_query_guest = '''
MATCH (a:fb_event)
WITH collect({id:a.fb_event_id, name:a.event_name, group:0}) AS nodes RETURN nodes
'''
with GraphDatabase.driver("bolt://{}:7687".format(neo4j_dbip),
auth=basic_auth("neo4j", "{}".format(neo4j_password))) as driver:
with driver.session() as session:
result = session.run(insert_query_guest)
for record in result:
return json.dumps(record['nodes'])
def setup_neo4j_driver(host, port, password):
default_password = 'neo4j' # Travis will use a fresh Neo4j, with the default password.
local_password = password
uri = "bolt://"+host+":"+str(port)
# Try local_password.
try:
driver = GraphDatabase.driver(uri, auth=basic_auth("neo4j", local_password))
return driver
except:
pass
# Try default_password.
# Password handling from https://github.com/robinedwards/django-neomodel
driver = GraphDatabase.driver(uri, auth=basic_auth("neo4j", default_password))
with driver.session() as neo4j_session:
try:
result = neo4j_session.run("MATCH (a:Person) WHERE a.name = {name} RETURN a", {"name": "Crick"})
except CypherError as ce:
if 'The credentials you provided were valid, but must be changed before you can use this instance' in str(ce):
neo4j_session.run("CALL dbms.changePassword({password})", {'password': local_password})
print("New database with no password set, setting password to '", local_password, "'.")
neo4j_session.close()
np.warnings.filterwarnings('ignore')
import cypher
from collections import namedtuple
from neo4j.v1 import GraphDatabase, basic_auth
#import Q1Utils
import ReasoningUtilities as RU
import sys
import os
sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/../../") # code directory
from RTXConfiguration import RTXConfiguration
RTXConfiguration = RTXConfiguration()
# Connection information for the neo4j server, populated with orangeboard
driver = GraphDatabase.driver(RTXConfiguration.bolt, auth=basic_auth("neo4j", "precisionmedicine"))
session = driver.session()
# Connection information for the ipython-cypher package
connection = "http://neo4j:precisionmedicine@" + RTXConfiguration.database
DEFAULT_CONFIGURABLE = {
"auto_limit": 0,
"style": 'DEFAULT',
"short_errors": True,
"data_contents": True,
"display_limit": 0,
"auto_pandas": False,
"auto_html": False,
"auto_networkx": False,
"rest": False,
"feedback": False, # turn off verbosity in ipython-cypher
"uri": connection,