def test_export_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([st])
pa.make_model()
exp_str = pa.export_model('kappa')
assert exp_str
exp_str = pa.export_model('bngl')
assert exp_str
exp_str = pa.export_model('sbml', file_name='/dev/null')
assert exp_str
def test_export_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([st])
pa.make_model()
exp_str = pa.export_model('kappa')
assert exp_str
exp_str = pa.export_model('bngl')
assert exp_str
exp_str = pa.export_model('sbml', file_name='/dev/null')
assert exp_str
def test_kappa_cm_export():
stmts = [Complex([Agent('a'), Agent('b')])]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_cm', '/dev/null')
assert len(graph.nodes()) == 2
assert len(graph.edges()) == 1
def test_kappa_cm_export():
stmts = [Complex([Agent('a'), Agent('b')])]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_cm', '/dev/null')
assert len(graph.nodes()) == 2
assert len(graph.edges()) == 1
def test_kappa_im_export():
stmts = [Activation(Agent('a'), Agent('b')),
Activation(Agent('b',
activity=ActivityCondition('activity', True)),
Agent('c'))]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_im', '/dev/null')
assert len(graph.nodes) == 2
assert len(graph.edges) == 1
def test_kappa_im_export():
stmts = [Activation(Agent('a'), Agent('b')),
Activation(Agent('b',
activity=ActivityCondition('activity', True)),
Agent('c'))]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_im', '/dev/null')
assert len(graph.nodes) == 2
assert len(graph.edges) == 1
def test_assemble_export_sbgn():
# Add various statements to test their assembly
st = Phosphorylation(Agent('BRAF'), Agent('MAP2K1'))
mc = ModCondition('phosphorylation', None, None, True)
st2 = Activation(Agent('MAP2K1', mods=[mc]), Agent('MAPK1'))
st3 = Complex([Agent('MAPK1'), Agent('DUSP6')])
st4 = DecreaseAmount(None, Agent('DUSP6'))
pa = PysbAssembler([st, st2, st3, st4])
pa.make_model()
# Export to SBGN
model = pa.export_model('sbgn')
assert model is not None
# Test that the right elements are there in the result
et = ET.fromstring(model)
sbgn_ns = {'s': 'http://sbgn.org/libsbgn/pd/0.1'}
glyphs = et.findall('s:map/s:glyph', namespaces=sbgn_ns)
glyph_classes = [g.attrib.get('class') for g in glyphs]
assert glyph_classes.count('macromolecule') == 6
assert glyph_classes.count('complex') == 2
assert glyph_classes.count('process') == 10
return pa
def test_assemble_export_sbgn():
# Add various statements to test their assembly
st = Phosphorylation(Agent('BRAF'), Agent('MAP2K1'))
mc = ModCondition('phosphorylation', None, None, True)
st2 = Activation(Agent('MAP2K1', mods=[mc]), Agent('MAPK1'))
st3 = Complex([Agent('MAPK1'), Agent('DUSP6')])
st4 = DecreaseAmount(None, Agent('DUSP6'))
pa = PysbAssembler([st, st2, st3, st4])
pa.make_model()
# Export to SBGN
model = pa.export_model('sbgn')
assert model is not None
# Test that the right elements are there in the result
et = ET.fromstring(model)
from indra.assemblers.sbgn.assembler import sbgn_ns
sbgn_nss = {'s': sbgn_ns}
glyphs = et.findall('s:map/s:glyph', namespaces=sbgn_nss)
glyph_classes = [g.attrib.get('class') for g in glyphs]
assert glyph_classes.count('macromolecule') == 6
assert glyph_classes.count('complex') == 2
assert glyph_classes.count('process') == 10
return pa