def test_init_with_neuron_objects(self):
n1 = Neuron(name="AVAL")
n2 = Neuron(name="PVCR")
try:
Connection(n1, n2)
except Exception:
self.fail("Shouldn't fail on Connection init")
def make_syn():
import struct
u = struct.pack("=2f", random.random(), random.random())
z = struct.pack("=2f", random.random(), random.random())
a = Neuron(u.encode('hex'))
b = Neuron(z.encode('hex'))
v.value(a.neighbor(b))
return (a, b)
def test_init(self):
"""Initialization with positional parameters"""
c = Connection(Neuron(name='AVAL'), Neuron(name='ADAR'), 3, 'send', 'Serotonin')
self.assertIsInstance(c.pre_cell(), Neuron)
self.assertIsInstance(c.post_cell(), Neuron)
self.assertEqual(c.number(), 3)
self.assertEqual(c.syntype(), 'send')
self.assertEqual(c.synclass(), 'Serotonin')
def make_syn():
import struct
u = struct.pack("=2f", random.random(), random.random())
z = struct.pack("=2f", random.random(), random.random())
a = Neuron(u.encode('hex'))
b = Neuron(z.encode('hex'))
v.value(a.neighbor(b))
return (a, b)
def test_same_name_same_id(self):
"""
Test that two Neuron objects with the same name have the same
identifier. Saves us from having too many inserts of the same object.
"""
c = Neuron(name="boots")
c1 = Neuron(name="boots")
self.assertEqual(c.identifier, c1.identifier)
def test_adal_connections():
"""
See github issue openworm/PyOpenWorm#90
"""
for x in range(10):
adal = Neuron("ADAL")
post = Neuron()
Connection(pre_cell=adal, post_cell=post)
tuple(post.load())
def test_1(self):
import bibtex
bt = bibtex.parse("my.bib")
n1 = Neuron("AVAL")
n2 = Neuron("DA3")
c = Connection(pre_cell=n1, post_cell=n2, synclass="synapse")
e = Evidence(bibtex=bt['white86'])
e.asserts(c)
print(list(e.load()))
def test_get_evidence(self):
# Reference two neurons
n1 = Neuron(name='AVAL')
n2 = Neuron(name='PVCR')
# Declare a connection between them
c = Connection(n1, n2, number=1)
e = Evidence()
# Create an Evidence search-object
e.asserts(c)
# look for all of the evidence for the connection 'c'
for x in e.load():
print(x.author())
def test_adal_connections_property():
"""
See github issue openworm/PyOpenWorm#90
"""
for x in range(10):
adal = Neuron("ADAL")
tuple(adal.connection.get('either'))
def test_2(self):
# Reference two neurons
n1 = Neuron(name='AVAL')
n2 = Neuron(name='PVCR')
# Declare a connection between them
c = Connection(n1, n2, number=1)
c_id = c.identifier
# Attach some evidence for the connection
e = Evidence(author="Danny Glover")
e.asserts(c)
# look at what else this evidence has stated
e.save()
e = Evidence(author="Danny Glover")
r = e.asserts()
ids = set(x.identifier for x in r)
self.assertIn(c_id, ids)
def test_load_with_filter(self):
# Put the appropriate triples in. Try to load them
g = R.Graph()
self.config['rdf.graph'] = g
for t in self.trips:
g.add(t)
c = Connection(pre_cell=Neuron(name="PVCR"), conf=self.config)
r = c.load()
for x in r:
self.assertIsInstance(x, Connection)
def test_neuron_load():
list(Neuron().load())
def test_neuron_receptors():
for x in range(30):
post = Neuron()
list(post.receptor())
import PyOpenWorm as POW
from PyOpenWorm.worm import Worm
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.network import Network
import OpenWormData as OWD
if __name__ == "__main__":
with POW.connect('default.conf') as conn:
ctx = POW.Context(ident=OWD.BIO_ENT_NS['worm0'], conf=conn.conf).stored
print("Neurons:")
print(", ".join(sorted(Neuron().name.get())))
with ctx.stored(Worm, Neuron, Network) as cctx:
w = cctx.Worm()
net = cctx.Network()
neur = cctx.Neuron()
print(net.count())
import PyOpenWorm
from time import time
from PyOpenWorm.neuron import Neuron
PyOpenWorm.connect(configFile='PyOpenWorm/default.conf')
t0 = time()
print("Neurons:")
print(", ".join(sorted(Neuron().name.get())))
print("Receptors:")
print(", ".join(sorted(Neuron().receptor.get())))
tot = time() - t0
print("Took {} seconds".format(tot))