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_model_undo():
m = MRA()
stmts1 = [sts.Phosphorylation(sts.Agent('A'), sts.Agent('B'))]
m.new_model(stmts1)
res = m.model_undo()
action = res.get('action')
assert action is not None
assert action.get('action') == 'remove_stmts'
assert action.get('statements') == stmts1
def test_get_upstream():
m = MRA()
egfr = sts.Agent('EGFR', db_refs={'HGNC': '3236', 'TEXT': 'EGFR'})
kras = sts.Agent('KRAS', db_refs={'HGNC': '6407', 'TEXT': 'KRAS'})
stmts = [sts.Activation(egfr, kras)]
model_id = m.new_model(stmts)
upstream = m.get_upstream(kras, model_id)
assert(len(upstream) == 1)
assert(upstream[0].name == 'EGFR')
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_transformations():
m = MRA()
stmts1 = [sts.Phosphorylation(sts.Agent('A'), sts.Agent('B'))]
m.new_model(stmts1)
assert(len(m.transformations) == 1)
tr = m.transformations[0]
assert(tr[0] == 'add_stmts')
assert(tr[1] == stmts1)
assert(tr[2] is None)
assert(tr[3] == 1)
stmts2 = [sts.Phosphorylation(sts.Agent('C'), sts.Agent('D'))]
m.extend_model(stmts2, 1)
assert(len(m.transformations) == 2)
tr = m.transformations[1]
assert(tr[0] == 'add_stmts')
assert(tr[1] == stmts2)
assert(tr[2] == 1)
assert(tr[3] == 2)
def test_has_mechanism():
m = MRA()
stmtsj = json.dumps(stmts_json_from_text('BRAF binds MEK'))
m.build_model_from_json(stmtsj)
has_mechanism = m.has_mechanism(stmtsj, 1)
assert has_mechanism
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)