def test_get_string(): st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))] ga = GraphAssembler() ga.add_statements(st) ga.make_model() graph_str = ga.get_string() assert (graph_str)
def test_phosphorylation(): st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))] ga = GraphAssembler() ga.add_statements(st) ga.make_model() assert (len(ga.graph.nodes()) == 2) assert (len(ga.graph.edges()) == 1)
def test_complex(): st = [Complex([Agent('BRAF'), Agent('RAF1'), Agent('YWAH')])] ga = GraphAssembler() ga.add_statements(st) ga.make_model() assert (len(ga.graph.nodes()) == 3) assert (len(ga.graph.edges()) == 3)
def test_inactivation(): st = [Inhibition(Agent('DUSP4'), Agent('MAPK1'))] ga = GraphAssembler() ga.add_statements(st) ga.make_model() assert (len(ga.graph.nodes()) == 2) assert (len(ga.graph.edges()) == 1)
def test_dephosphorylation_noenz(): st = [Dephosphorylation(None, Agent('MAPK1'))] ga = GraphAssembler() ga.add_statements(st) ga.make_model() assert (len(ga.graph.nodes()) == 0) assert (len(ga.graph.edges()) == 0)
def format_stmts(stmts, output_format): if output_format == 'tsv': msg = '' for stmt in stmts: if not stmt.evidence: logger.warning('Statement %s without evidence' % stmt.uuid) txt = '' pmid = '' else: txt = stmt.evidence[0].text if stmt.evidence[0].text else '' pmid = stmt.evidence[0].pmid if stmt.evidence[0].pmid else '' line = '%s\t%s\t%s\n' % (stmt, txt, pmid) msg += line return msg elif output_format == 'pkl': fname = 'indrabot.pkl' with open(fname, 'wb') as fh: pickle.dump(stmts, fh) return fname elif output_format == 'pdf': fname = 'indrabot.pdf' ga = GraphAssembler(stmts) ga.make_model() ga.save_pdf(fname) return fname elif output_format == 'json': msg = json.dumps(stmts_to_json(stmts), indent=1) return msg return None
def draw_graph(stmts, fname): graphpr = {'rankdir': 'TD'} nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0} ga = GraphAssembler(stmts, graph_properties=graphpr, node_properties=nodepr) ga.make_model() ga.save_dot('%s.dot' % fname) ga.save_pdf('%s.pdf' % fname)
def assemble_graph(): """Assemble INDRA Statements and return Graphviz graph dot string.""" response = request.body.read().decode('utf-8') body = json.loads(response) stmts_json = body.get('statements') stmts = stmts_from_json(stmts_json) ga = GraphAssembler(stmts) model_str = ga.make_model() res = {'model': model_str} return res
def test_save_pdf(): st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))] ga = GraphAssembler() ga.add_statements(st) ga.make_model() ga.save_pdf('/dev/null')
import sys import pickle from indra import reach from indra.assemblers import GraphAssembler txt = open('extension.txt', 'rt').read() rp = reach.process_text(txt, offline=True) st = rp.statements for s in st: print '%s\t%s' % (s, s.evidence[0].text) with open('extension.pkl', 'wb') as fh: pickle.dump(st, fh) graphpr = {'rankdir': 'TD'} nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0} ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr) ga.make_model() ga.save_dot('jnk_extension.dot') ga.save_pdf('jnk_extension.pdf')