def upload_muscles():
""" Upload muscles and the neurons that connect to them
"""
try:
ev = P.Evidence(title="C. elegans sqlite database")
conn = sqlite3.connect(SQLITE_DB_LOC)
cur = conn.cursor()
w = P.Worm()
cur.execute("""
SELECT DISTINCT a.Entity, b.Entity
FROM tblrelationship innervatedBy, tblentity b, tblentity a, tblrelationship type_b
WHERE innervatedBy.EnID1=a.id and innervatedBy.Relation = '1516' and innervatedBy.EnID2=b.id
and type_b.EnID1 = b.id and type_b.Relation='1515' and type_b.EnID2='1519'
""") # 1519 is the
for r in cur.fetchall():
neuron_name = str(r[0])
muscle_name = str(r[1])
m = P.Muscle(muscle_name)
n = P.Neuron(neuron_name)
w.muscle(m)
m.innervatedBy(n)
ev.asserts(w)
ev.save()
#second step, get the relationships between them and add them to the graph
print("uploaded muscles")
except Exception:
traceback.print_exc()
finally:
conn.close()
def get(self, request, format=None):
Muscles = []
try:
for muscle in P.Muscle().load():
Muscles.append(Muscle(name=str(muscle.name())))
finally:
print "done"
serializer = MuscleSerializer(Muscles, many=True)
return Response(serializer.data)
def get(self, request, format=None):
Cells = []
try:
for neuron in P.Neuron().load():
Cells.append(Cell(name=str(neuron.name())))
for muscle in P.Muscle().load():
Cells.append(Cell(name=str(muscle.name())))
finally:
print "done"
serializer = CellSerializer(Cells, many=True)
return Response(serializer.data)
def get(self,request, format=None):
neurons=[]
muscles=[]
for neuron in P.Neuron().load():
neurons.append(str(neuron.name()))
for muscle in P.Muscle().load():
muscles.append(str(muscle.name()))
cellname = self.request.query_params.get('cellname', None)
if cellname==None:
Channels=[]
else:
if cellname in neurons:
net = P.Worm().get_neuron_network()
neuron = net.aneuron(cellname)
serializer = NeuronDetailSerializer(NeuronDetail(neuron))
elif cellname in muscles:
muscle = P.Muscle(cellname)
serializer = MuscleDetailSerializer(MuscleDetail(muscle))
print serializer.data
return Response(serializer.data)
def marshall(name):
ret = []
res = None
res2 = None
if name in neurons:
res = P.Neuron(name)
elif name in muscles:
res = P.Muscle(name)
elif name in to_expand_muscles:
name_l = name + 'L'
name_r = name + 'R'
res = P.Muscle(name_l)
res2 = P.Muscle(name_r)
elif name in other_cells:
res = P.Cell(name)
if res is not None:
ret.append(res)
if res2 is not None:
ret.append(res2)
return ret
def scoring_muscles(self):
print 'calculating muscle completion scores'
score = 0
for m in P.Muscle().load():
score = 0
if len(m.neurons()) > 0:
score += 1
if len(m.receptors()) > 0:
score += 1
for ch in m.channel():
score += IonChannel.objects.get(name=str(ch.name())).completion
score = int((float(score) / (2 + 5 * len(m.channel()))) * float(5))
muscle = Muscle(name=m.name(), completion=score)
muscle.save()
print 'done'
def get(self,request, format=None):
print "in cell channel get data set view"
serializer_class = ChannelSerializer
cellname = self.request.query_params.get('cellname', None)
if cellname==None:
Channels=[]
else:
neurons=[]
muscles=[]
for n in P.Neuron().load():
neurons.append(n.name())
for m in P.Muscle().load():
muscles.append(m.name())
if cellname in neurons:
Channels=[]
for ch in P.Neuron(name=str(cellname)).channel():
Channels.append(Channel(name=ch.name()))
if cellname in muscles:
Channels=[]
for ch in P.Muscle(name=str(cellname)).channel():
Channels.append(Channel(name=ch.name()))
serializer = ChannelSerializer(Channels, many=True)
print serializer.data
return Response(serializer.data)
def Muscles(request):
P.connect()
try:
MUSCLE_DICT = {}
for muscle in P.Muscle().load():
MUSCLE_DICT[str(muscle)] = {
'name': str(muscle),
'completeness': '#2B7558'
}
finally:
P.disconnect()
return render_to_response('pyopenworm/muscles.html',
{'muscles': MUSCLE_DICT})
def Muscle(request, muscle_id):
P.connect()
try:
muscle_dict = {}
for muscle in P.Muscle(muscle_id).load():
'''
'neurons': list(muscle.neurons.get()),
'receptors': list(muscle.receptors.get()),
'''
muscle_dict[str(muscle)] = {
'name': str(muscle),
'completeness': '#2B7558'
}
finally:
P.disconnect()
return render_to_response('pyopenworm/muscle.html',
{'muscle': muscle_dict[muscle_id]})
def upload_muscles():
""" Upload muscles and the neurons that connect to them
"""
try:
with open(CELL_NAMES_SOURCE) as csvfile:
csvreader = csv.reader(csvfile)
ev = P.Evidence(title="C. elegans Cell List - WormBase.csv")
w = WORM
for num, line in enumerate(csvreader):
if num < 4: # skip rows with no data
continue
if line[7] or line[8] or line[
9] == '1': # muscle's marked in these columns
muscle_name = normalize(line[0]).upper()
m = P.Muscle(name=muscle_name)
w.muscle(m)
ev.asserts(w)
#second step, get the relationships between them and add them to the graph
print("uploaded muscles")
except Exception:
traceback.print_exc()
def test_muscle(self):
self.assertTrue(
isinstance(PyOpenWorm.Muscle('MDL08'), PyOpenWorm.Muscle))
def __init__(self):
self.Allcells = []
for neuron in P.Neuron().load():
self.Allcells.append(str(neuron.name()))
for muscle in P.Muscle().load():
self.Allcells.append(str(muscle.name()))
def expand_muscle(name):
return P.Muscle(name + 'L'), P.Muscle(name + 'R')
