Пример #1
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 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()
Пример #2
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 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()
Пример #3
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 def setUp(self):
     PyOpenWorm.connect(conf=Configure(
         **{
             'rdf.store_conf': 'tests/test.db',
             'rdf.source': 'ZODB'
         }))
     self.g = PyOpenWorm.config("rdf.graph")
Пример #4
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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)
Пример #5
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 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
Пример #6
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 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)
Пример #7
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    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])
Пример #8
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 def open(cls,file_name):
     """ Open a file storing configuration in a JSON format """
     Configureable.conf = Configure.open(file_name)
     return cls()
Пример #9
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 def open(cls, file_name):
     """ Open a file storing configuration in a JSON format """
     Configureable.conf = Configure.open(file_name)
     return cls()