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_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_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_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_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_edge_aggregation_between_nongroup_nodes():
cja = CyJSAssembler()
cja.add_statements([st_phos_Y, st_phos_T])
cja.make_model(grouping=False)
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
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 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, refs in zip(cja._nodes, db_refs):
if node['data']['name'] == 'MAP2K1':
assert refs.get('HGNC') == \
'http://identifiers.org/hgnc/HGNC:6840', refs
assert refs.get('TEXT') == 'mek1', refs
if node['data']['name'] == 'MAPK1':
assert refs.get('UniProt')
if node['data']['name'] == 'DUSP4':
assert not refs
def post(self):
"""Assemble INDRA Statements and return Cytoscape JS network.
Parameters
----------
statements : list[indra.statements.Statement.to_json()]
A list of INDRA Statements to assemble.
Returns
-------
json_model : dict
Json dictionary containing graph information.
"""
args = request.json
stmts_json = args.get('statements')
stmts = stmts_from_json(stmts_json)
cja = CyJSAssembler(stmts)
cja.make_model(grouping=True)
model_str = cja.print_cyjs_graph()
return json.loads(model_str)
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_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_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_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 assemble_cyjs():
"""Assemble INDRA Statements and return Cytoscape JS network."""
if request.method == 'OPTIONS':
return {}
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_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_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 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 assemble_cyjs():
"""Assemble INDRA Statements and return Cytoscape JS network."""
if request.method == 'OPTIONS':
return {}
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_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_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, refs in zip(cja._nodes, db_refs):
if node['data']['name'] == 'MAP2K1':
assert refs.get('HGNC') == \
'http://identifiers.org/hgnc/HGNC:6840', refs
assert refs.get('TEXT') == 'mek1', refs
if node['data']['name'] == 'MAPK1':
assert refs.get('UniProt')
if node['data']['name'] == 'DUSP4':
assert not refs
def test_edge_aggregation_between_nongroup_nodes():
cja = CyJSAssembler()
cja.add_statements([st_phos_Y, st_phos_T])
cja.make_model(grouping=False)
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
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