def test_association():
st = [Association([Event(Concept('a')), Event(Concept('b'))])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_inactivation():
st = [Inhibition(Agent('DUSP4'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_influence():
st = [Influence(Event(Concept('a')), Event(Concept('b')))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_complex():
st = [Complex([Agent('BRAF'), Agent('RAF1'), Agent('YWAH')])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 3
assert len(ga.graph.edges()) == 3
def test_phosphorylation():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_dephosphorylation_noenz():
st = [Dephosphorylation(None, Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 0
assert len(ga.graph.edges()) == 0
def test_influence():
st = [Influence(Concept('a'), Concept('b'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_get_string():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
graph_str = ga.get_string()
assert graph_str
def test_association():
st = [Association([Event(Concept('a')), Event(Concept('b'))])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_complex():
st = [Complex([Agent('BRAF'), Agent('RAF1'), Agent('YWAH')])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 3
assert len(ga.graph.edges()) == 3
def test_get_string():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
graph_str = ga.get_string()
assert graph_str
def test_inactivation():
st = [Inhibition(Agent('DUSP4'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_dephosphorylation_noenz():
st = [Dephosphorylation(None, Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 0
assert len(ga.graph.edges()) == 0
def test_dephosphorylation():
st = [Dephosphorylation(Agent('DUSP4'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_phosphorylation():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
model = ga.make_model()
assert 'MAP2K1' in model
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_influence():
# Add an extra standalone event just to make sure it doesn't error
st = [Influence(Event(Concept('a')), Event(Concept('b'))),
Event(Concept('a'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_save_pdf():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
ga.save_pdf('/dev/null')
def test_save_pdf():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
ga.save_pdf('/dev/null')