def test_bound_condition():
bc = BoundCondition(Agent('RAF1'), True)
st = Phosphorylation(Agent('BRAF', bound_conditions=[bc]), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def call_biopax():
global stmts
sa = SBGNAssembler()
sa.add_statements(stmts)
sbgn_content = sa.make_model()
print 'BIOPAX CALLED'
socket.emit('BioPAXRequest', sbgn_content, 'partialBiopax')
def test_activeform():
erk = Agent('MAPK1', mods=[ModCondition('phosphorylation')])
st = ActiveForm(erk, 'kinase', True)
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 3, 2)
def test_activeform():
erkact = Agent('MAPK1', activity=ActivityCondition('kinase', True))
erkelk = Phosphorylation(erkact, Agent('ELK1'))
erkp = Agent('MAPK1', mods=[ModCondition('phosphorylation')])
st = ActiveForm(erkp, 'kinase', True)
sa = SBGNAssembler([st, erkelk])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def test_complex():
egfr1 = Agent('EGFR',
bound_conditions=[BoundCondition(Agent('EGF'), True)])
egfr2 = Agent('EGFR',
bound_conditions=[BoundCondition(Agent('EGF'), True)])
st = Complex([egfr1, egfr2])
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def update_layout():
sa = SBGNAssembler()
sa.add_statements(stmts)
sbgn_content = sa.make_model()
#params = {'room': room_id, 'userId': user_id,
# 'graph': sbgn_content, 'type': 'sbgn'}
#socket.emit('agentMergeGraphRequest', params)
params = {'room': room_id, 'userId': user_id}
socket.emit('agentNewFileRequest', params)
sbgn_params = {'graph': sbgn_content, 'type': 'sbgn'}
sbgn_params.update(params)
#socket.emit('agentLoadFileRequest', sbgn_params)
#socket.emit('agentRunLayoutRequest', sbgn_params)
socket.emit('agentMergeGraphRequest', sbgn_params)
def test_increaseamount():
st = IncreaseAmount(Agent(''), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def test_inhibition():
st = Inhibition(Agent('BRAF'), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)
def test_remove_modification():
st = Deacetylation(Agent('BRAF'), Agent('MAP2K1'))
sa = SBGNAssembler([st])
sbgn_xml = sa.make_model()
et = _parse_sbgn(sbgn_xml)
_test_numelements(et, 4, 3)