def test_make_cm():
m = MRA()
ekb = ekb_from_text('MEK binds MAPK1. MEK binds MAPK3.')
res = m.build_model_from_ekb(ekb)
pysb_model = res['model_exec']
cm = make_contact_map(pysb_model)
assert len(list(cm.nodes())) == 3
assert len(list(cm.edges())) == 2
def test_make_im():
m = MRA()
ekb = ekb_from_text('KRAS activates BRAF. Active BRAF binds MEK.')
res = m.build_model_from_ekb(ekb)
pysb_model = res['model_exec']
im = make_influence_map(pysb_model)
assert len(list(im.nodes())) == 3
assert len(list(im.edges())) == 3
def test_build_model_from_ekb():
m = MRA()
ekb = ekb_from_text('MAP2K1 phosphorylates MAPK1.')
res = m.build_model_from_ekb(ekb)
assert(res.get('model'))
assert(res.get('model_id') == 1)
assert(res.get('model_exec'))
assert(len(m.models[1]) == 1)
assert(isinstance(m.models[1][0], sts.Phosphorylation))
assert(m.models[1][0].enz.name == 'MAP2K1')
def test_make_diagrams():
m = MRA()
ekb = ekb_from_text('KRAS activates BRAF. Active BRAF binds MEK.')
res = m.build_model_from_ekb(ekb)
diagrams = res['diagrams']
assert diagrams['reactionnetwork']
assert diagrams['reactionnetwork'].endswith('.png')
assert diagrams['contactmap']
assert diagrams['contactmap'].endswith('.png')
assert diagrams['influencemap']
assert diagrams['influencemap'].endswith('.png')
def test_expand_model_from_ekb():
m = MRA()
ekb = ekb_from_text('MAP2K1 phosphorylates MAPK1.')
res = m.build_model_from_ekb(ekb)
model_id = res.get('model_id')
assert(res.get('model'))
assert(res.get('model_id') == 1)
assert(len(m.models[1]) == 1)
ekb = ekb_from_text('MAP2K2 phosphorylates MAPK1.')
res = m.expand_model_from_ekb(ekb, model_id)
assert(res.get('model'))
assert(res.get('model_id') == 2)
assert(len(m.models[2]) == 2)
def test_sbgn():
m = MRA()
ekb = ekb_from_text('KRAS activates BRAF.')
res = m.build_model_from_ekb(ekb)
ekb = ekb_from_text('NRAS activates BRAF.')
res = m.expand_model_from_ekb(ekb, 1)
sbgn = res['diagrams']['sbgn']
tree = ET.fromstring(sbgn)
glyphs = tree.findall('s:map/s:glyph',
namespaces={'s': 'http://sbgn.org/libsbgn/0.3'})
assert len(glyphs) == 6
res = m.model_undo()
sbgn = res['diagrams']['sbgn']
tree = ET.fromstring(sbgn)
glyphs = tree.findall('s:map/s:glyph',
namespaces={'s': 'http://sbgn.org/libsbgn/0.3'})
assert len(glyphs) == 4
def test_has_mechanism():
m = MRA()
ekb = ekb_from_text('BRAF binds MEK')
m.build_model_from_ekb(ekb)
has_mechanism = m.has_mechanism(ekb, 1)
assert (has_mechanism)
