def create_message(self): txt = 'Selumetinib decreases FOS in BT20 cells' explain = stmts_clj_from_text(txt) explain_stmt = self.bioagent.get_statement(explain)[0] assert explain_stmt.evidence[0].context, explain_stmt.evidence[0] content = KQMLList('USER-GOAL') content.set('explain', explain) msg = get_request(content) return msg, content
def _get_build_model_request(text, format=None): content = KQMLList('BUILD-MODEL') if format == 'ekb': descr = ekb_kstring_from_text(text) content.sets('description', descr) content.sets('format', 'ekb') else: descr = stmts_clj_from_text(text) content.set('description', descr) return get_request(content), content
def test_respond_model_get_upstream(): mm = MRA_Module(testing=True) egfr = sts.Agent('EGFR', db_refs={'HGNC': '3236', 'TEXT': 'EGFR'}) kras = sts.Agent('KRAS', db_refs={'HGNC': '6407', 'TEXT': 'KRAS'}) stmts = [sts.Activation(egfr, kras)] model_id = mm.mra.new_model(stmts) kras_term = ekb_from_agent(kras) msg = KQMLList('MODEL-GET-UPSTREAM') msg.sets('target', kras_term) msg.set('model-id', str(model_id)) reply = mm.respond_model_get_upstream(msg) ups = reply.get('upstream') assert(len(ups) == 1)
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_respond_expand_model_from_json(): mm = MRA_Module(testing=True) st = stmts_json_from_text('MEK phosphorylates ERK') msg = KQMLList('BUILD-MODEL') msg.sets('description', json.dumps(st)) msg.sets('format', 'indra_json') reply = mm.respond_build_model(msg) assert(reply.get('model')) assert(reply.get('model-id') == '1') st = stmts_json_from_text('Active BRAF inhibits MEK.') msg = KQMLList('EXPAND-MODEL') msg.sets('description', json.dumps(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 create_hasmech2(self): content = KQMLList('MODEL-HAS-MECHANISM') content.set('model-id', '1') content.sets('description', stmts_clj_from_text('NRAS activates BRAF')) msg = get_request(content) return msg, content
def create_remove(self): content = KQMLList('MODEL-REMOVE-MECHANISM') content.set('model-id', '1') content.set('description', stmts_clj_from_text('Unphosphorylated ERK')) msg = get_request(content) return msg, content
def create_remove2(self): content = KQMLList('MODEL-REMOVE-MECHANISM') content.set('model-id', '3') content.set('description', stmts_clj_from_text('NRAS activates BRAF')) msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('DESCRIBE-MODEL') content.set('model-id', str(self.bioagent.mra.id_counter)) msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('DESCRIBE-MODEL') content.set('model-id', '1') msg = get_request(content) return msg, content
def _get_build_model_request(text): content = KQMLList('BUILD-MODEL') descr = ekb_kstring_from_text(text) content.set('description', descr) return get_request(content), content
def _get_content(self, task, **contents): content = KQMLList(task) for key, value in contents.items(): content.set(key, value) msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('GET-COMMON') content.set('genes', KQMLList([mek])) content.sets('up-down', 'ONT::SUCCESSOR') msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('GET-COMMON') content.set('genes', KQMLList(self.inp_genes)) content.sets('up-down', self.param_dict[self.updown]) msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('GET-PAPER-MODEL') content.set('pmid', 'PMID-27906130') return get_request(content), content
def _get_expand_model_request(text, model_id): content = KQMLList('EXPAND-MODEL') descr = stmts_clj_from_text(text) content.set('description', descr) content.set('model-id', model_id) return get_request(content), content