def test_blast_space(self):
"""
Test that setting the lineage name gives the blast cell.
"""
c = Cell(name="carrots")
c.lineageName("a tahsuetoahusenoatu")
self.assertEqual(c.blast(), "a")
def test_blast_dot(self):
"""
Test that setting the lineage name gives the blast cell.
"""
c = Cell(name="peas")
c.lineageName("ab.tahsuetoahusenoatu")
self.assertEqual(c.blast(), "ab")
def __init__(self, name=False, **kwargs):
Cell.__init__(self, name=name, **kwargs)
self.innervatedBy = Muscle.ObjectProperty("neurons",
owner=self,
value_type=P.Neuron,
multiple=True)
Muscle.DatatypeProperty("receptors", owner=self, multiple=True)
def __init__(self, name=False, **kwargs):
Cell.__init__(self,name=name,**kwargs)
# Get neurons connected to this neuron
Neighbor(owner=self)
# Get connections from this neuron
Connection(owner=self)
Neuron.DatatypeProperty("type",self, multiple=True)
Neuron.DatatypeProperty("receptor", self, multiple=True)
Neuron.DatatypeProperty("innexin", self, multiple=True)
Neuron.DatatypeProperty("neurotransmitter", self, multiple=True)
Neuron.DatatypeProperty("neuropeptide", self, multiple=True)
### Aliases ###
self.get_neighbors = self.neighbor
self.receptors = self.receptor
def test_synonyms(self):
""" Test that we can add and retrieve synonyms. """
c = Cell(name="ADAL", conf=self.config)
c.synonym("lineage name: ABplapaaaapp")
c.save()
self.assertEqual(set(["lineage name: ABplapaaaapp"]),
Cell(name="ADAL").synonym())
def test_same_name_same_id(self):
"""
Test that two Cell objects with the same name have the same identifier()
Saves us from having too many inserts of the same object.
"""
c = Cell(name="boots")
c1 = Cell(name="boots")
self.assertEqual(c.identifier(), c1.identifier())
def test_loading_cells_retrieves_all_cells(self):
"""
Test that retrieving all Cells gives us the right number of Cell objects.
"""
num_cells = len(list(Cell().load()))
m = list(Muscle().load())
num_muscles = len(m)
n = list(Neuron().load())
num_neurons = len(n)
sum_cells = num_neurons + num_muscles
self.assertEqual(sum_cells, num_cells)
def test_parentOf(self):
"""
Test that we can get the children of a cell
Tests for anterior, posterior, left, right, ventral, dorsal divisions
"""
p = Cell(name="peas")
base = 'ab.tahsuetoahusenoat'
p.lineageName(base)
p.save()
c = ["carrots", "jam", "peanuts", "celery", "tuna", "chicken"]
division_directions = "alvpdr"
for x, l in zip(c, division_directions):
ln = base + l
Cell(name=x, lineageName=ln).save()
names = set(str(x.name()) for x in p.parentOf())
self.assertEqual(set(c), names)
def test_daughterOf(self):
"""
Test that we can get the parent of a cell
"""
base = "ab.tahsuetoahusenoat"
child = base + "u"
p = Cell(name="peas")
p.lineageName(base)
p.save()
c = Cell(name="carrots")
c.lineageName(child)
c.save()
parent_p = c.daughterOf().name()
self.assertEqual("peas", parent_p)
def test_wormbaseID(self):
""" Test that a Cell object has a wormbase ID """
c = Cell(name="ADAL", conf=self.config)
c.wormbaseID("WBbt:0004013")
c.save()
self.assertEqual("WBbt:0004013", Cell(name="ADAL").wormbaseID())
def test_lineageName(self):
""" Test that we can retrieve the lineage name """
c = Cell(name="ADAL", conf=self.config)
c.lineageName("AB plapaaaapp")
c.save()
self.assertEqual("AB plapaaaapp", Cell(name="ADAL").lineageName())
def test_DataUser(self):
do = Cell('', conf=self.config)
self.assertTrue(isinstance(do, DataUser))
def test_str(self):
self.assertEqual('cell_name', str(Cell('cell_name')))
def test_morphology_is_NeuroML_morphology(self):
""" Check that the morphology is the kind made by neuroml """
c = Cell(name="ADAR", conf=self.config)
# get the morph
m = c.morphology()
self.assertIsInstance(m, neuroml.Morphology)
def __init__(self, name=False, **kwargs):
Cell.__init__(self, name=name, **kwargs)
self.innervatedBy = Muscle.ObjectProperty("neurons",owner=self,value_type=P.Neuron, multiple=True)
Muscle.DatatypeProperty("receptors",owner=self,multiple=True)
