def create_message(self): content = KQMLList('GET-COMMON') ekb = ekb_from_text('MEK') content.sets('genes', ekb) content.sets('up-down', 'ONT::SUCCESSOR') msg = get_request(content) return msg, content
def test_msa_paper_retrieval_failure(): content = KQMLList('GET-PAPER-MODEL') content.sets('pmid', 'PMID-00000123') msa = msa_module.MSA_Module(testing=True) resp = msa.respond_get_paper_model(content) assert resp.head() == 'SUCCESS', str(resp) assert resp.get('relations-found') == 0, resp
def _get_message(heading, target=None, residue=None, position=None): msa = msa_module.MSA_Module(testing=True) content = KQMLList(heading) if target is not None: content.sets('target', target) if residue and position: content.sets('site', '%s-%s' % (residue, position)) return msa.respond_phosphorylation_activating(content)
def test_msa_paper_retrieval_failure(): raise SkipTest("This feature is currently not available.") content = KQMLList('GET-PAPER-MODEL') content.sets('pmid', 'PMID-00000123') msa = msa_module.MSA_Module(testing=True) resp = msa.respond_get_paper_model(content) assert resp.head() == 'FAILURE', str(resp) assert resp.get('reason') == 'MISSING_MECHANISM'
def create_message(self): content = KQMLList('PHOSPHORYLATION-ACTIVATING') content.sets('target', ekb_from_text('MAPK1')) for name, value in [('residue', 'T'), ('position', '185')]: if value is not None: content.sets(name, value) msg = get_request(content) return (msg, content)
def create_message(self): content = KQMLList('PHOSPHORYLATION-ACTIVATING') content.sets('target', ekb_from_text('MAPK1')) for name, value in [('residue', 'T'), ('position', '185')]: if value is not None: content.sets(name, value) msg = get_request(content) return msg, content
def _get_message(heading, target=None, residue=None, position=None): msa = msa_module.MSA_Module(testing=True) content = KQMLList(heading) if target is not None: content.sets('target', ekb_from_text(target)) if residue and position: content.sets('site', '%s-%s' % (residue, position)) return msa.respond_phosphorylation_activating(content)
def _get_message(heading, target=None, residue=None, position=None): msa = msa_module.MSA_Module(testing=True) content = KQMLList(heading) if target is not None: content.sets('target', ekb_from_text(target)) for name, value in [('residue', residue), ('position', position)]: if value is not None: content.sets(name, value) return msa.respond_phosphorylation_activating(content)
def test_respond_build_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')
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 = 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_message(self): content = KQMLList('PHOSPHORYLATION-ACTIVATING') content.sets('target', mapk1) content.sets('site', 'T-185') msg = get_request(content) return msg, content
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_undo(self): content = KQMLList('MODEL-UNDO') content.sets('model-id', '4') msg = get_request(content) return msg, content
def create_get_json(self): content = KQMLList('MODEL-GET-JSON') content.sets('model-id', '1') msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('BUILD-MODEL') content.sets('description', '') content.sets('format', 'ekb') 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-COMMON') content.set('genes', KQMLList([mek])) content.sets('up-down', 'ONT::SUCCESSOR') msg = get_request(content) return msg, content