def test_complex():
cja = CyJSAssembler()
cja.add_statements([st_complex])
cja.make_model()
assert(len(cja._nodes) == 3)
assert(len(cja._edges) == 3)
polarities = [edge['data']['polarity'] for edge in cja._edges]
assert(len(set(polarities))==1)
assert('none' in polarities)
def test_no_grouping():
st1 = Phosphorylation(Agent('A'), Agent('B'))
st2 = Phosphorylation(Agent('A'), Agent('C'))
st3 = Phosphorylation(Agent('C'), Agent('B'))
cja = CyJSAssembler()
cja.add_statements([st1, st2, st3])
cja.make_model(grouping=True)
parents = [node['data']['parent'] for node in cja._nodes]
for parent in parents:
assert parent == ''
def test_print_cyjs_graph():
cja = CyJSAssembler()
cja.add_statements([st_act, st_act2])
cja.make_model()
cyjs_str = cja.print_cyjs_graph()
# assert output is not empty
assert (len(cyjs_str) > len('{\n "edges": [],\n "nodes": []\n}'))
def test_act():
cja = CyJSAssembler()
cja.add_statements([st_act, st_act2])
cja.make_model()
assert(len(cja._nodes) == 3)
assert(len(cja._edges) == 2)
polarities = [edge['data']['polarity'] for edge in cja._edges]
assert(len(set(polarities))==2)
assert('positive' in polarities)
assert('negative' in polarities)
db_refs = [node['data']['db_refs'] for node in cja._nodes]
for node in cja._nodes:
if node['data']['name'] == 'MAP2K1':
assert(node['data']['db_refs'].get('HGNC'))
if node['data']['name'] == 'MAPK1':
assert(node['data']['db_refs'].get('UniProt'))
if node['data']['name'] == 'DUSP4':
assert(not node['data']['db_refs'])
def test_grouping_block_targeting_block():
st1 = Phosphorylation(Agent('A'), Agent('B'))
st2 = Phosphorylation(Agent('A'), Agent('C'))
st3 = Phosphorylation(Agent('D'), Agent('B'))
st4 = Phosphorylation(Agent('D'), Agent('C'))
cja = CyJSAssembler()
cja.add_statements([st1, st2, st3, st4])
cja.make_model(grouping=True)
for node in cja._nodes:
if node['data']['name'] == 'A':
parent_a = node['data']['parent']
if node['data']['name'] == 'B':
parent_b = node['data']['parent']
if node['data']['name'] == 'C':
parent_c = node['data']['parent']
if node['data']['name'] == 'D':
parent_d = node['data']['parent']
assert_element_properties(cja)
assert (parent_b == parent_c)
assert (parent_a == parent_d)
parent_b_name = [
x['data']['name'] for x in cja._nodes if x['data']['id'] == parent_b
][0]
parent_a_name = [
x['data']['name'] for x in cja._nodes if x['data']['id'] == parent_a
][0]
assert (parent_b_name.startswith('Group'))
assert (parent_a_name.startswith('Group'))
assert (len(cja._edges) == 5)
virtual_edges = [x for x in cja._edges if x['data']['i'] == 'Virtual']
assert (len(virtual_edges) == 4)
real_edges = [x for x in cja._edges if x['data']['i'] != 'Virtual']
assert (len(real_edges) == 1)
def test_grouping_node_targeting_block():
st1 = Phosphorylation(Agent('A'), Agent('B'))
st2 = Phosphorylation(Agent('A'), Agent('C'))
cja = CyJSAssembler()
cja.add_statements([st1, st2])
cja.make_model(grouping=True)
for node in cja._nodes:
if node['data']['name'] == 'A':
parent_a = node['data']['parent']
assert(parent_a == '')
if node['data']['name'] == 'B':
parent_b = node['data']['parent']
if node['data']['name'] == 'C':
parent_c = node['data']['parent']
assert_has_id(node)
for edge in cja._edges:
assert_has_id(edge)
assert(parent_b == parent_c)
parent_b_name = [x['data']['name'] for x in cja._nodes if
x['data']['id']==parent_b][0]
assert(parent_b_name.startswith('Group'))
assert(len(cja._edges) == 3)
virtual_edges = [x for x in cja._edges if
x['data']['i'] == 'Virtual']
assert(len(virtual_edges) == 2)
real_edges = [x for x in cja._edges if
x['data']['i'] != 'Virtual']
assert(len(real_edges) == 1)
def assemble_cyjs():
"""Assemble INDRA Statements and return Cytoscape JS network."""
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
stmts = stmts_from_json(stmts_json)
cja = CyJSAssembler()
cja.add_statements(stmts)
cja.make_model(grouping=True)
model_str = cja.print_cyjs_graph()
return model_str
def test_complex():
cja = CyJSAssembler()
cja.add_statements([st_complex])
cja.make_model()
assert (len(cja._nodes) == 3)
assert (len(cja._edges) == 3)
polarities = [edge['data']['polarity'] for edge in cja._edges]
assert (len(set(polarities)) == 1)
assert ('none' in polarities)
def test_selfmod():
cja = CyJSAssembler()
cja.add_statements([st_selfmod])
cja.make_model()
assert (len(cja._nodes) == 1)
assert (len(cja._edges) == 1)
polarities = [edge['data']['polarity'] for edge in cja._edges]
assert (len(polarities) == 1)
assert (polarities[0] == 'positive')
def test_ras():
cja = CyJSAssembler()
cja.add_statements([st_gef, st_gap])
cja.make_model()
assert (len(cja._nodes) == 3)
assert (len(cja._edges) == 2)
polarities = [edge['data']['polarity'] for edge in cja._edges]
assert (len(set(polarities)) == 2)
assert ('positive' in polarities)
assert ('negative' in polarities)
def test_no_grouping():
st1 = Phosphorylation(Agent('A'), Agent('B'))
st2 = Phosphorylation(Agent('A'), Agent('C'))
st3 = Phosphorylation(Agent('C'), Agent('B'))
cja = CyJSAssembler()
cja.add_statements([st1, st2, st3])
cja.make_model(grouping=True)
parents = [node['data']['parent'] for node in cja._nodes]
for parent in parents:
assert parent == ''
def test_edge_grouping_between_nongroup_nodes():
cja = CyJSAssembler()
cja.add_statements([st_phos_Y, st_phos_T])
cja.make_model(grouping=True)
assert(len(cja._nodes) == 2)
assert(len(cja._edges) == 1)
for edge in cja._edges:
assert(len(edge['data']['uuid_list']) == 2)
for node in cja._nodes:
assert(len(node['data']['uuid_list']) == 2)
def make_cyjs_network(results, model, stmts):
path_stmts = get_path_stmts(results, model, stmts)
path_genes = get_path_genes(path_stmts)
path_uuids = [list(path.keys()) for path in path_stmts]
all_path_uuids = []
for p in path_uuids:
all_path_uuids += p
print(json.dumps(path_uuids, indent=1))
#filtered_stmts = ac.filter_gene_list(stmts, path_genes, 'one')
filtered_stmts = ac.filter_uuid_list(stmts, all_path_uuids)
ca = CyJSAssembler(filtered_stmts)
cm = ca.make_model()
ca.set_CCLE_context(['SKMEL28_SKIN'])
ca.save_json('output/korkut_model')
def make_cyjs_network(results, model, stmts):
path_stmts = get_path_stmts(results, model, stmts)
path_genes = get_path_genes(path_stmts)
# Get UUIDs to use as filter
path_uuids = [list(path.keys()) for path in path_stmts]
all_path_uuids = []
for p in path_uuids:
all_path_uuids += p
#filtered_stmts = ac.filter_gene_list(stmts, path_genes, 'one')
filtered_stmts = ac.filter_uuid_list(stmts, all_path_uuids)
ac.dump_statements(filtered_stmts, 'output/korkut_cyjs_model.pkl')
ca = CyJSAssembler(filtered_stmts)
cm = ca.make_model()
ca.set_CCLE_context(['SKMEL28_SKIN'])
ca.save_json('output/korkut_model')
def test_act():
cja = CyJSAssembler()
cja.add_statements([st_act, st_act2])
cja.make_model()
assert (len(cja._nodes) == 3)
assert (len(cja._edges) == 2)
polarities = [edge['data']['polarity'] for edge in cja._edges]
assert (len(set(polarities)) == 2)
assert ('positive' in polarities)
assert ('negative' in polarities)
db_refs = [node['data']['db_refs'] for node in cja._nodes]
for node in cja._nodes:
if node['data']['name'] == 'MAP2K1':
assert (node['data']['db_refs'].get('HGNC'))
if node['data']['name'] == 'MAPK1':
assert (node['data']['db_refs'].get('UniProt'))
if node['data']['name'] == 'DUSP4':
assert (not node['data']['db_refs'])
def test_print_cyjs():
cja = CyJSAssembler()
cja.add_statements([st_act, st_act2])
cja.make_model()
cyjs_str = cja.print_cyjs()
print(cyjs_str)
