class POW:
def __init__(self):
self.ctx: Context = None
self.worm: Worm = None
self.net: Network = None
def __enter__(self):
# if P.connected:
# raise RuntimeError("Already connected")
P.connect(POW_CONF_PATH)
self.ctx = Context(ident=WORM_IDENT)
self.worm = self.ctx.stored(Worm)()
self.net = self.worm.neuron_network()
return self
def __exit__(self, exc_type, exc_val, exc_tb):
self.ctx = None
self.worm = None
self.net = None
P.disconnect()
ctx = Context(ident='http://example.org/data')
evctx = Context(ident='http://example.org/meta')
# Create a new Neuron object to work with
n = ctx(Neuron)(name='AVAL')
# Create a new Evidence object with `doi` and `pmid` fields populated.
# See `PyOpenWorm/evidence.py` for other available fields.
d = evctx(Document)(key='Anonymous2011', doi='125.41.3/ploscompbiol', pmid='12345678')
e = evctx(Evidence)(key='Anonymous2011', reference=d)
# Evidence object asserts something about the enclosed dataObject.
# Here we add a receptor to the Neuron we made earlier, and "assert it".
# As the discussion (see top) reads, this might be asserting the existence of
# receptor UNC-8 on neuron AVAL.
n.receptor('UNC-8')
e.supports(ctx.rdf_object)
# Save the Neuron and Evidence objects to the database.
ctx.save_context()
evctx.save_context()
# What does my evidence object contain?
for e_i in evctx.stored(Evidence)().load():
print(e_i.reference())
print(e_i.supports())
# Disconnect from the database.
P.disconnect()
evctx = Context(ident='http://example.org/meta', conf=conn.conf)
# Create a new Neuron object to work with
n = ctx(Neuron)(name='AVAL')
# Create a new Evidence object with `doi` and `pmid` fields populated.
# See `PyOpenWorm/evidence.py` for other available fields.
d = evctx(Document)(key='Anonymous2011',
doi='125.41.3/ploscompbiol',
pmid='12345678')
e = evctx(Evidence)(key='Anonymous2011', reference=d)
# Evidence object asserts something about the enclosed dataObject.
# Here we add a receptor to the Neuron we made earlier, and "assert it".
# As the discussion (see top) reads, this might be asserting the existence of
# receptor UNC-8 on neuron AVAL.
n.receptor('UNC-8')
e.supports(ctx.rdf_object)
# Save the Neuron and Evidence objects to the database.
ctx.save_context()
evctx.save_context()
# What does my evidence object contain?
for e_i in evctx.stored(Evidence)().load():
print(e_i.reference(), e_i.supports())
# Disconnect from the database.
P.disconnect(conn)
if len(lctx) == 0:
return frozenset()
else:
lctx = frozenset(ctxs) & lctx
if len(lctx) == 0:
return lctx
return frozenset() if lctx is None else lctx
qctx = Context()
qctx(Neuron)('AVAL').innexin('UNC-7')
ctxs = query_context(conn.conf['rdf.graph'], qctx)
for c in ctxs:
mqctx = Context(conf=conn.conf)
print('CONTEXT', c.identifier)
ev = mqctx.stored(Evidence)()
ev.supports(Context(ident=c.identifier, conf=conn.conf).rdf_object)
for x in ev.load():
ref = x.reference()
if isinstance(ref, Document):
print(ref)
print('AUTHOR:', ref.author())
print('URI:', ref.uri())
print('DOI:', ref.doi())
print('PMID:', ref.pmid())
print('WBID:', ref.wbid())
print()
elif isinstance(ref, Website):
print(ref)
print('TITLE:', ref.title())
print('URL:', ref.url())
if len(lctx) == 0:
return frozenset()
else:
lctx = frozenset(ctxs) & lctx
if len(lctx) == 0:
return lctx
return frozenset() if lctx is None else lctx
qctx = Context()
qctx(Neuron)('AVAL').innexin('UNC-7')
ctxs = query_context(conn.conf['rdf.graph'], qctx)
for c in ctxs:
mqctx = Context(conf=conn.conf)
print('CONTEXT', c.identifier)
ev = mqctx.stored(Evidence)()
ev.supports(Context(ident=c.identifier, conf=conn.conf).rdf_object)
for x in ev.load():
ref = x.reference()
if isinstance(ref, Document):
print(ref)
print('AUTHOR:', ref.author())
print('URI:', ref.uri())
print('DOI:', ref.doi())
print('PMID:', ref.pmid())
print('WBID:', ref.wbid())
print()
elif isinstance(ref, Website):
print(ref)
print('TITLE:', ref.title())
print('URL:', ref.url())
from PyOpenWorm.evidence import Evidence
from PyOpenWorm.experiment import Experiment
#Connect to existing database.
P.connect('default.conf')
ctx = Context(ident="http://example.org/bio/ion_channel")
chan = ctx(Channel)(name='Ch0')
chan.subfamily("chanfam")
cm = ctx(PatchClampChannelModel)(key='patch-clamp-01')
cm.ion('K+')
cm.gating('voltage')
chan.model(cm)
pc = ctx(PatchClampExperiment)(
key='patch-clamp-01',
initial_voltage=Quantity(30, 'mV'),
pipette_solution='Ringer\'s solution',
start_time=datetime.datetime(2018, 5, 26, 15, 56, 41, 244489),
end_time=datetime.datetime(2018, 5, 26, 15, 57, 41, 244489),
type='current clamp')
cm.modeled_from(pc)
ctx.save_context()
print(cm.rdf.serialize(format='n3').decode('utf-8'))
chan1 = ctx.stored(Channel)()
print((set(chan1.load())))