def __init__(self, conf=False):
Configure.__init__(self)
Configureable.__init__(self,conf)
# We copy over all of the configuration that we were given
self.copy(self.conf)
self.namespace = Namespace("http://openworm.org/entities/")
self.molecule_namespace = Namespace("http://openworm.org/entities/molecules/")
self['nx'] = _B(self._init_networkX)
self['rdf.namespace'] = self.namespace
self['molecule_name'] = self._molecule_hash
self['new_graph_uri'] = self._molecule_hash
self._init_rdf_graph()
def __init__(self, conf=False):
Configure.__init__(self)
Configureable.__init__(self, conf)
# We copy over all of the configuration that we were given
self.copy(self.conf)
self.namespace = Namespace("http://openworm.org/entities/")
self.molecule_namespace = Namespace(
"http://openworm.org/entities/molecules/")
self['nx'] = _B(self._init_networkX)
self['rdf.namespace'] = self.namespace
self['molecule_name'] = self._molecule_hash
self['new_graph_uri'] = self._molecule_hash
self._init_rdf_graph()
def setUp(self):
PyOpenWorm.connect(conf=Configure(
**{
'rdf.store_conf': 'tests/test.db',
'rdf.source': 'ZODB'
}))
self.g = PyOpenWorm.config("rdf.graph")
def main():
c = Configure()
c['neuronscsv'] = 'https://raw.github.com/openworm/data-viz/master/HivePlots/neurons.csv'
c['connectomecsv'] = 'https://raw.github.com/openworm/data-viz/master/HivePlots/connectome.csv'
c['sqldb'] = '/home/markw/work/openworm/PyOpenWorm/db/celegans.db'
c = Data(c)
net = PyOpenWorm.Network(c)
nml_doc = NeuroMLDocument(id="IafNet")
ns = net.neurons()
nml_net = neuroml.Network(id="IafNet")
nml_doc.networks.append(nml_net)
for n in [net.aneuron_nocheck(n) for n in ns]:
s(nml_doc, nml_net, n)
syn0 = ExpOneSynapse(id="syn0", gbase="65nS", erev="0mV", tau_decay="3ms")
for k in net.synapses():
n1 = net.aneuron_nocheck(k[0])
n2 = net.aneuron_nocheck(k[1])
connect(nml_net, n1, n2, 'syn0')
f = "test.nml"
writers.NeuroMLWriter.write(nml_doc, f)
v(f)
def test_init_config_no_Data(self):
""" Should fail if given a non-Data configuration """
# XXX: This test touches some machinery in
# PyOpenWorm/__init__.py. Feel like it's a bad test
tmp = Configureable.conf
Configureable.conf = Configure()
with self.assertRaises(BadConf):
DataUser()
Configureable.conf = tmp
def setUp(self):
# Set do_logging to True if you like walls of text
self.TestConfig = Configure.open(TEST_CONFIG)
td = '__tempdir__'
z = self.TestConfig['rdf.store_conf']
if z.startswith(td):
x = z[len(td):]
h = tempfile.mkdtemp()
self.TestConfig['rdf.store_conf'] = h + x
self.delete_dir()
PyOpenWorm.connect(conf=self.TestConfig, do_logging=False)
def setUpClass(cls):
import csv
PyOpenWorm.connect(conf=Configure(
**{
'rdf.store_conf': 'tests/test.db',
'rdf.source': 'ZODB'
}))
PyOpenWorm.loadData(skipIfNewer=False)
PyOpenWorm.disconnect()
# grab the list of the names of the 302 neurons
csvfile = open('OpenWormData/aux_data/neurons.csv', 'r')
reader = csv.reader(csvfile, delimiter=';', quotechar='|')
# array that holds the names of the 302 neurons at class-level scope
cls.neurons = []
for row in reader:
if len(row[0]) > 0: # Only saves valid neuron names
cls.neurons.append(row[0])
def open(cls,file_name):
""" Open a file storing configuration in a JSON format """
Configureable.conf = Configure.open(file_name)
return cls()
def open(cls, file_name):
""" Open a file storing configuration in a JSON format """
Configureable.conf = Configure.open(file_name)
return cls()