def recreate_game_of_graphql_graph(orientdb_location, username, password):
"""If the Game of GraphQL graph isn't present, construct it from the GamesOfThrones one."""
exising_config = Config.from_url(
'plocal://{}/GamesOfThrones'.format(orientdb_location), username,
password)
new_config = Config.from_url(
'plocal://{}/game_of_graphql'.format(orientdb_location), username,
password)
data = existing_dataset.load_all_data(exising_config)
new_dataset.create_game_of_graphql_graph(new_config, data)
def setUp(self):
g = self.g = Graph(Config.from_url('animals', 'root', 'root',
initial_drop=True))
g.create_all(AnimalsNode.registry)
g.create_all(AnimalsRelationship.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('animals', 'root', 'root',
initial_drop=True))
g.create_all(AnimalsNode.registry)
g.create_all(AnimalsRelationship.registry)
def testStrictness(self):
g = self.g
# Unknown properties get silently dropped by default
pentium = g.cpu.create(name='Pentium', version=6)
loaded_pentium = g.get_vertex(pentium._id)
# Version is not defined in cpu
assert not hasattr(pentium, 'version')
# But in strict mode they generate errors
g = self.g = Graph(Config.from_url('hardware',
'root',
'root',
initial_drop=False),
strict=True)
g.include(
g.build_mapping(declarative_node(),
declarative_relationship(),
auto_plural=True))
with self.assertRaises(AttributeError):
pentium = g.cpu.create(name='Pentium', version=6)
pentium = g.x86cpu.create(name='Pentium', version=6)
self.assertEquals('Pentium', pentium.name)
self.assertEquals(6, pentium.version)
def setUp(self):
g = self.g = Graph(
Config.from_url('abstract_classes',
'root',
'root',
initial_drop=True))
g.client.command('CREATE CLASS AbstractClass EXTENDS V ABSTRACT')
g.client.command('CREATE CLASS ConcreteClass EXTENDS V')
def setUp(self):
g = self.g = Graph(Config.from_url('custom_field', 'root', 'root'
, initial_drop=True))
g.create_all(ClassFieldNode.registry)
g.create_all(ClassFieldRelationship.registry)
g.client.command('ALTER CLASS classfieldvertex CUSTOM test_field_1=test_string_one')
g.client.command('ALTER CLASS classfieldvertex CUSTOM test_field_2="test string two"')
g.client.command('ALTER CLASS classfieldedge CUSTOM test_field_1="test string two"')
def setUp(self):
g = self.g = Graph(Config.from_url('custom_field', 'root', 'root'
, initial_drop=True))
g.create_all(ClassFieldNode.registry)
g.create_all(ClassFieldRelationship.registry)
g.client.command('ALTER CLASS classfieldvertex CUSTOM test_field_1=test_string_one')
g.client.command('ALTER CLASS classfieldvertex CUSTOM test_field_2="test string two"')
g.client.command('ALTER CLASS classfieldedge CUSTOM test_field_1="test string two"')
def testConfigs(self):
configs = [
'localhost:2424/test_config1',
'localhost/test_config2',
'plocal://localhost/test_config3',
'plocal://localhost:2424/test_config4',
'memory://localhost/test_config5',
'memory://localhost:2424/test_config6',
]
for conf in configs:
# the following line should not raise errors
Graph(Config.from_url(conf, 'root', 'root', initial_drop=True))
def testConfigs(self):
configs = [
'localhost:2424/test_config1',
'localhost/test_config2',
'plocal://localhost/test_config3',
'plocal://localhost:2424/test_config4',
'memory://localhost/test_config5',
'memory://localhost:2424/test_config6',
]
for conf in configs:
# the following line should not raise errors
Graph(Config.from_url(conf, 'root', 'root', initial_drop=True))
def __init__(self,
database='/na_server',
username='******',
password='******',
user=None):
try:
self.graph = Graph(
Config.from_url(database,
username,
password,
initial_drop=False,
serialization_type=OrientSerialization.Binary))
except:
print "WARNING: Serialisation flag ignored"
self.graph = Graph(
Config.from_url(database,
username,
password,
initial_drop=False))
self.graph.include(Node.registry)
self.graph.include(Relationship.registry)
self.user = user
self.query_processor = query_processor(self.graph)
def get_test_graph(graph_name):
"""Generate the test database and return the pyorient client."""
url = get_orientdb_url(graph_name)
config = Config.from_url(url, ORIENTDB_USER, ORIENTDB_PASSWORD, initial_drop=True)
Graph(config, strict=True)
client = OrientDB('localhost', ORIENTDB_PORT)
client.connect(ORIENTDB_USER, ORIENTDB_PASSWORD)
client.db_open(graph_name, ORIENTDB_USER, ORIENTDB_PASSWORD, db_type=DB_TYPE_GRAPH)
load_schema(client)
generate_data(client)
return client
def get_pyorient_client():
db_url = ''.join([
'plocal://', server_config.ORIENTDB_HOST, ':2424', '/',
server_config.ORIENTDB_DB
])
graph = Graph(Config.from_url(db_url, server_config.ORIENTDB_USER,
server_config.ORIENTDB_PASSWORD),
strict=True)
graph.include(
graph.build_mapping(declarative_node(),
declarative_relationship(),
auto_plural=False))
return graph
def db_setup(HOST: str, USER: str, dbname: str, PASSW: str, PORT: str,
keep: bool):
"""sets up database
:param HOST: OGM Graph ref
:param USER: OGM Graph ref
:param dbname: OGM Graph ref
:param PASSW: OGM Graph ref
:param PORT: OGM Graph ref
:param keep: boolean value to keep or destroy database
"""
print('(connecting to db)')
clear_database = ''
if (not keep):
clear_database = input(
'Are you sure you want to delete the database? (Y/N)')
if clear_database in ['Y', 'y', 'Yes', 'yes', 'YES']:
print('(dropping database)')
g = Graph(Config.from_url(dbname, USER, PASSW, initial_drop=True))
g.create_all(Node.registry)
g.create_all(Relationships.registry)
else:
print('(keeping database)')
g = Graph(Config.from_url(dbname, USER, PASSW, initial_drop=False))
SchemaNode = declarative_node()
SchemaRelationship = declarative_relationship()
classes_from_schema = g.build_mapping(SchemaNode,
SchemaRelationship,
auto_plural=True)
g.include(classes_from_schema)
g.client.command(
"ALTER DATABASE DATETIMEFORMAT \"yyyy-MM-dd'T'HH:mm:ss.SSS'Z'\"")
print('our db g', g)
return g
def run(host, port, graph_location, graph_user, graph_password):
"""Run the app."""
# pylint: disable=global-statement
global graph_config
# pylint: enable=global-statement
graph_config = Config.from_url(
'plocal://{}/game_of_graphql'.format(graph_location), graph_user, graph_password)
app.logger.info(u'Waiting for OrientDB to come alive...')
tools.wait_for_orientdb_to_come_alive(graph_location, graph_user, graph_password)
app.logger.info(u'Recreating the Game of GraphQL graph...')
tools.recreate_game_of_graphql_graph(graph_location, graph_user, graph_password)
app.logger.info(u'Starting server...')
app.run(host=host, port=port, debug=False)
def wait_for_orientdb_to_come_alive(orientdb_location, username, password):
"""Block until OrientDB is ready to serve requests."""
config = Config.from_url(
'plocal://{}/GamesOfThrones'.format(orientdb_location), username,
password)
retries = 100
for _ in range(retries):
try:
# This line will raise a connection error if OrientDB isn't ready yet.
Graph(config, strict=True)
return
except PyOrientConnectionException:
sleep(1.0)
raise RuntimeError(u'Could not connect to OrientDB at {}. '
u'Giving up after {} retries.'.format(
orientdb_location, retries))
def testStrictness(self):
g = self.g
# Unknown properties get silently dropped by default
pentium = g.cpu.create(name='Pentium', version=6)
loaded_pentium = g.get_vertex(pentium._id)
# Version is not defined in cpu
assert not hasattr(pentium, 'version')
# But in strict mode they generate errors
g = self.g = Graph(Config.from_url('hardware', 'root', 'root'
, initial_drop=False), strict=True)
g.include(g.build_mapping(
declarative_node(), declarative_relationship(), auto_plural=True))
with self.assertRaises(AttributeError):
pentium = g.cpu.create(name='Pentium', version=6)
pentium = g.x86cpu.create(name='Pentium', version=6)
self.assertEquals('Pentium', pentium.name)
self.assertEquals(6, pentium.version)
def get_test_orientdb_graph(
graph_name: str,
load_schema_func: Callable[[OrientDB], None],
generate_data_func: Callable[[OrientDB], None],
) -> OrientDB:
"""Generate the test database and return the pyorient client."""
url = get_orientdb_url(graph_name)
config = Config.from_url(url,
ORIENTDB_USER,
ORIENTDB_PASSWORD,
initial_drop=True)
Graph(config, strict=True)
client = OrientDB(host="localhost", port=ORIENTDB_PORT)
client.connect(ORIENTDB_USER, ORIENTDB_PASSWORD)
client.db_open(graph_name,
ORIENTDB_USER,
ORIENTDB_PASSWORD,
db_type=DB_TYPE_GRAPH)
load_schema_func(client)
generate_data_func(client)
return client
# Add content to new node:
self.g_orient.client.command('update %s content %s' % \
(nm._id, json.dumps(content)))
self.logger.info('created node: {0}({1})'.format(nm.element_type, nm.name))
# Connect nodes
self.g_orient.Owns.create(npl, n)
self.g_orient.HasData.create(n, arb)
self.g_orient.HasData.create(n, nm)
if nt:
self.g_orient.HasData.create(n, nt)
self.g_orient.Owns.create(ds_fc, n)
self.g_orient.Owns.create(ds_fc, nm)
self.g_orient.Owns.create(ds_fc, arb)
if __name__ == '__main__':
logging.basicConfig(level=logging.DEBUG, stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
g_orient = Graph(Config.from_url('/na_server','root', 'root', initial_drop=False,
serialization_type=OrientSerialization.Binary))# set to True to erase the database
g_orient.create_all(Node.registry)
g_orient.create_all(Relationship.registry)
vl = NTHULoader(g_orient)
vl.load_neurons('all_female_neurons.txt','flycircuit1.1')
def setUp(self):
g = self.g = Graph(Config.from_url('test_unicode', 'root', 'root',
initial_drop=True))
g.create_all(UnicodeNode.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('test_datetime', 'root', 'root',
initial_drop=True))
g.create_all(DateTimeNode.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('classes', 'root', 'root'
, initial_drop=True))
def setUp(self):
g = self.g = Graph(Config.from_url('money', 'root', 'root'
, initial_drop=True))
g.create_all(MoneyNode.registry)
g.create_all(MoneyRelationship.registry)
util for drop specific class
"""
import os
import django
from django.conf import settings
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "ops_platform.settings")
django.setup()
from pyorient import PyOrientSQLParsingException
from ngpyorient.graph import NgGraph
from ngpyorient.utils import write_error
from pyorient.ogm import Config
config = Config.from_url(
settings.DATABASES_NG["default"]["URL"],
settings.DATABASES_NG["default"]["USER"],
settings.DATABASES_NG["default"]["PASSWORD"],
)
graph = NgGraph(config)
try:
graph.drop_class_simple_by_class_name(sys.argv[1], sys.argv[2])
except PyOrientSQLParsingException as e:
write_error(e)
except IndexError as e:
write_error("you should specify classname and type(vertex or edge)")
graph.client.close()
from pyorient.ogm import Graph, Config
from pyorient.ogm.property import String, Float, DateTime
from pyorient.ogm.declarative import declarative_node, declarative_relationship
# Initialize Graph Database
graph = Graph(
Config.from_url('plocal://localhost:2424//DeeBeeTee', 'deebeetee',
'deebeetee'))
Node = declarative_node()
Relationship = declarative_relationship()
class TransactionsRel(Relationship):
element_plural = 'tx'
element_type = 'tx'
since = DateTime()
tx = Float()
class Person(Node):
element_plural = 'person'
element_type = 'person'
uid = String(indexed=True)
name = String(indexed=True)
credit_balance = Float(default=0.0, indexed=True)
debit_balance = Float(default=0.0, indexed=True)
balance = Float(default=0.0, indexed=True)
def setUp(self):
g = self.g = Graph(Config.from_url('hardware', 'root', 'root'
, initial_drop=True))
g.create_all(HardwareNode.registry)
g.create_all(HardwareRelationship.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('test_embedded_defaults', 'root', 'root',
initial_drop=True))
def setUp(self):
g = self.g = Graph(Config.from_url('test_embedded', 'root', 'root',
initial_drop=True))
g.create_all(EmbeddedNode.registry)
# Connect nodes
self.g_orient.Owns.create(npl, n)
self.g_orient.HasData.create(n, arb)
# self.g_orient.HasData.create(n, nm)
if nt:
self.g_orient.HasData.create(n, nt)
self.g_orient.Owns.create(ds_fc, n)
# self.g_orient.Owns.create(ds_fc, nm)
self.g_orient.Owns.create(ds_fc, arb)
if __name__ == '__main__':
logging.basicConfig(
level=logging.DEBUG,
stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
g_orient = Graph(
Config.from_url('/na_server',
'root',
'root',
initial_drop=False,
serialization_type=OrientSerialization.Binary)
) # set to True to erase the database
g_orient.create_all(Node.registry)
g_orient.create_all(Relationship.registry)
vl = NTHULoader(g_orient)
vl.load_neurons('all_female_neurons.txt', 'flycircuit1.1')
import pyorient.ogm from pyorient.ogm import Graph, Config # Connect to Database a = Config.from_url( 'plocal://localhost:2424/test', 'root', 'c208lilje') print(a.user) print(a.cred) print(a.db_name) print(a.host) print(a.port) print(a.storage)
def setUp(self):
g = self.g = Graph(Config.from_url('abstract_classes', 'root', 'root'
, initial_drop=True))
g.client.command('CREATE CLASS AbstractClass EXTENDS V ABSTRACT')
g.client.command('CREATE CLASS ConcreteClass EXTENDS V')
def setUp(self):
g = self.g = Graph(Config.from_url('money', 'root', 'root'
, initial_drop=True))
g.create_all(MoneyNode.registry)
g.create_all(MoneyRelationship.registry)
'HOST': config.get('postgresdbConf', 'DB_HOST'),
'PORT': config.get('postgresdbConf', 'DB_PORT'),
},
'orientdb': {
'NAME': config.get('orientdbConf', 'DB_NAME'),
'USER': config.get('orientdbConf', 'DB_USER'),
'PASSWORD': config.get('orientdbConf', 'DB_PASS'),
'HOST': config.get('orientdbConf', 'DB_HOST'),
'PORT': config.get('orientdbConf', 'DB_PORT'),
}
}
Config.from_url('plocal://' + DATABASES['orientdb']['HOST'] + ':' +
str(DATABASES['orientdb']['PORT']) + '/' +
DATABASES['orientdb']['NAME'] + '',
'' + DATABASES['orientdb']['USER'] + '',
'' + DATABASES['orientdb']['PASSWORD'] + '',
initial_drop=False,
serialization_type=OrientSerialization.Binary)
graph = Graph(
Config.from_url('' + DATABASES['orientdb']['HOST'] + '/' +
DATABASES['orientdb']['NAME'] + '',
'' + DATABASES['orientdb']['USER'] + '',
'' + DATABASES['orientdb']['PASSWORD'] + '',
initial_drop=False))
Node = declarative.declarative_node()
Relationship = declarative.declarative_relationship()
# Password validation
# https://docs.djangoproject.com/en/2.2/ref/settings/#auth-password-validators
def get_new_connection(self, conn_params):
config = Config.from_url(*conn_params)
conn = NgGraph(config)
return conn
def setUp(self):
g = self.g = Graph(Config.from_url('test_embedded', 'root', 'root',
initial_drop=True))
g.create_all(EmbeddedNode.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('test_embedded_defaults', 'root', 'root',
initial_drop=True))
def setUp(self):
g = self.g = Graph(Config.from_url('hardware', 'root', 'root'
, initial_drop=True))
g.create_all(HardwareNode.registry)
g.create_all(HardwareRelationship.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('classes', 'root', 'root'
, initial_drop=True))
connect_lpu_pat(lpu0_ports_sels, lpu0_lpu_ports_data,
lpu0_pat_ports_data)
connect_lpu_pat(lpu1_ports_sels, lpu1_lpu_ports_data,
lpu1_pat_ports_data)
if __name__ == '__main__':
logging.basicConfig(
level=logging.DEBUG,
stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
#g_orient = Graph(Config.from_url('/vision_demo','admin', 'admin', initial_drop=True)) # set to True to erase the database
g_orient = Graph(
Config.from_url('/ampa/bionet/databases/development/na_server',
'admin',
'admin',
initial_drop=False,
serialization_type=OrientSerialization.Binary)
) # set to True to erase the database
g_orient.create_all(Node.registry)
g_orient.create_all(Relationship.registry)
#g_orient.include(Node.registry)
#g_orient.include(Relationship.registry)
vl = NetworkXLoader(g_orient)
# Load LPU data:
vl.logger.info('Loading sample Lamina circuit...')
vl.load_lpu('lamina.gexf.gz', 'LAM')
def convert_complicate_list(a):
tmp = []
for region in a['regions']:
tmp.append(list(region))
a['regions'] = tmp
return a
# init db
# initial_drop = True
# test
# cx_db = 'localhost:8889/cx'
graph = Graph(Config.from_url(cx_db, 'root', 'root',
initial_drop=initial_drop))
# models.create_efficiently(graph, models.Node.registry)
# models.create_efficiently(graph, models.Relationship.registry)
if initial_drop:
graph.create_all(models.Node.registry)
graph.create_all(models.Relationship.registry)
else:
graph.include(models.Node.registry)
graph.include(models.Relationship.registry)
logging.basicConfig(level=logging.DEBUG,
stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
logger = logging.getLogger('cx')
logger.info('Start to Load Biological Data')
def setUp(self):
g = self.g = Graph(Config.from_url('test_datetime', 'root', 'root',
initial_drop=True))
g.create_all(DateTimeNode.registry)
"""
Assign neuron and synapse model parameters.
"""
import logging
import sys
import numpy as np
from pyorient.ogm import Graph, Config
import neuroarch.models as models
import neuroarch.query as query
import neuroarch.nxtools as nxtools
from cx_config import cx_db
graph = Graph(Config.from_url(cx_db, 'admin', 'admin',
initial_drop=False))
graph.include(models.Node.registry)
graph.include(models.Relationship.registry)
logging.basicConfig(level=logging.DEBUG, stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
logger = logging.getLogger('cx')
def leaky_iaf_params(lpu, extern):
"""
Generate LeakyIAF params.
"""
k = 1000
assert isinstance(extern, bool)
if lpu == 'BU' or lpu == 'bu':
return {'extern': extern,
def setUp(self):
g = self.g = Graph(Config.from_url('test_unicode', 'root', 'root',
initial_drop=True))
g.create_all(UnicodeNode.registry)
