def test_get_matching_statements():
braf = sts.Agent('BRAF', db_refs={'HGNC': '1097'})
matching = {}
for fplx in ['BE', 'FPLX']:
raf = sts.Agent('RAF', db_refs={fplx: 'RAF'})
map2k1 = sts.Agent('MAP2K1', db_refs={'HGNC': '6840'})
mek = sts.Agent('MEK', db_refs={fplx: 'MEK'})
stmts = [
sts.Phosphorylation(braf, mek),
sts.Phosphorylation(raf, map2k1)
]
stmt_ref = sts.Phosphorylation(braf, map2k1)
matching[fplx] = _get_matching_stmts(stmts, stmt_ref)
assert any([len(matching[fplx]) == 2 for fplx in ['BE', 'FPLX']]),\
"Expected 2 matching for at least one name, got matching: %s" % (matching)
def test_respond_expand_model_from_json():
mm = MRA_Module(testing=True)
st = sts.Phosphorylation(sts.Agent('MEK'), sts.Agent('ERK'))
msg = KQMLList('BUILD-MODEL')
msg.sets('description', json.dumps(sts.stmts_to_json([st])))
msg.sets('format', 'indra_json')
reply = mm.respond_build_model(msg)
assert (reply.get('model'))
assert (reply.get('model-id') == '1')
st = sts.Phosphorylation(sts.Agent('RAF'), sts.Agent('MEK'))
msg = KQMLList('EXPAND-MODEL')
msg.sets('description', json.dumps(sts.stmts_to_json([st])))
msg.sets('format', 'indra_json')
msg.set('model-id', '1')
reply = mm.respond_expand_model(msg)
assert (reply.get('model'))
assert (reply.get('model-id') == '2')
def test_get_matching_statements():
braf = sts.Agent('BRAF', db_refs={'HGNC': '1097'})
map2k1 = sts.Agent('MAP2K1', db_refs={'HGNC': '6840'})
stmt_ref = sts.Phosphorylation(braf, map2k1)
idp = _get_matching_stmts(stmt_ref)
matching = idp.statements
assert len(matching) > 1, \
"Expected > 1 matching, got matching: %s" % matching
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_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_get_matching_statements():
if not CAN_CHECK_STATEMENTS:
raise SkipTest("Database api not accessible.")
braf = sts.Agent('BRAF', db_refs={'HGNC': '1097'})
map2k1 = sts.Agent('MAP2K1', db_refs={'HGNC': '6840'})
stmt_ref = sts.Phosphorylation(braf, map2k1)
idp = _get_matching_stmts(stmt_ref)
matching = idp.statements
assert len(matching) > 1, \
"Expected > 1 matching, got matching: %s" % matching
