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_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_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_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_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_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_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_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 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 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_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_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 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