def create_message2(self): drug = agent_clj_from_text('Vemurafenib') content = KQMLList('FIND-DRUG-TARGETS') content.set('drug', drug) kagents = KQMLList([agent_clj_from_text('RAF1')]) content.set('filter_agents', kagents) return get_request(content), content
def create_message_failure(self): content = KQMLList('FIND-MUTATION-SIGNIFICANCE') gene = agent_clj_from_text('ACTN4') disease = agent_clj_from_text('abc cancer') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def create_message_PAAD(self): content = KQMLList('FIND-MUTATION-SIGNIFICANCE') gene = agent_clj_from_text('ACTN4') disease = agent_clj_from_text('pancreatic adenocarcinoma') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('FIND-MUTEX') gene = agent_clj_from_text('TP53') disease = agent_clj_from_text('breast cancer') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def create_message_failure(self): content = KQMLList('FIND-COMMON-UPSTREAMS') genes = KQMLList( [agent_clj_from_text('UGT2B10'), agent_clj_from_text('PTEN')]) content.set('genes', genes) msg = get_request(content) return msg, content
def create_message_OV(self): content = KQMLList('FIND-MUTATION-FREQUENCY') gene = agent_clj_from_text('TP53') disease = agent_clj_from_text('Ovarian serous cystadenocarcinoma') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def create_message_failure(self): source = agent_clj_from_text('MAPK1') target = agent_clj_from_text('RAS') content = KQMLList('FIND-CAUSAL-PATH') content.set('source', source) content.set('target', target) content.sets('direction', 'both') msg = get_request(content) return msg, content
def create_message_3(self): content = KQMLList('FIND-CELLULAR-LOCATION') genes = KQMLList( [agent_clj_from_text('AKT1'), agent_clj_from_text('MAPK1')]) content.set('genes', genes) msg = get_request(content) return msg, content
def create_message(self): content = KQMLList('FIND-COMMON-UPSTREAMS') genes = KQMLList([ agent_clj_from_text('AKT1'), agent_clj_from_text('BRAF'), agent_clj_from_text('MAPK1') ]) content.set('genes', genes) msg = get_request(content) return msg, content
def create_message(self): target = agent_clj_from_text(self.target) content = KQMLList('FIND-TARGET-DRUG') content.set('target', target) st = agent_clj_from_text('Staurosporine') st.sets('NAME', 'Staurosporine') print(st) filter_agents = KQMLList([st]) content.set('filter_agents', filter_agents) return get_request(content), content
def create_message_1(self): content = KQMLList('FIND-VARIANTS-FOR-GENES') genes = KQMLList( [agent_clj_from_text('EGFR'), agent_clj_from_text('PTEN')]) content.set('genes', genes) disease = agent_clj_from_text('glioblastoma') content.set('disease', disease) content.sets('dataset', "tcga") msg = get_request(content) return msg, content
def create_message(self): target = agent_clj_from_text('BRAF') content = KQMLList('FIND-CAUSALITY-SOURCE') content.set('target', target) content.sets('type', 'phosphorylation') msg = get_request(content) return msg, content
def create_message_AKT1(self): content = KQMLList('FIND-GENE-SUMMARY') genes = agent_clj_from_text('AKT1') content.set('gene', genes) msg = get_request(content) return msg, content
def create_message_05_explainable_again(self): time.sleep(2) source = agent_clj_from_text('AKT1') content = KQMLList('DATASET-CORRELATED-ENTITY') content.set('source', source) msg = get_request(content) return msg, content
def create_message_failure(self): target = agent_clj_from_text('BRAF') content = KQMLList('FIND-CAUSALITY-SOURCE') content.set('target', target) content.sets('type', 'activates') msg = get_request(content) return msg, content
def create_message_failure(self): source = agent_clj_from_text('MAPK1') content = KQMLList('FIND-CAUSALITY-TARGET') content.set('source', source) content.sets('type', 'activation') msg = get_request(content) return msg, content
def test_get_synonyms_chemical(): """raises InvalidAgentError when the agent is not recognized or if the input submitted is not valid XML or is not in the correct format """ synonyms = bs.get_synonyms( Bioagent.get_agent(agent_clj_from_text('vemurafenib'))) assert synonyms
def create_message_1(self): content = KQMLList('FIND-DRUGS-FOR-MUTATION-DATASET') genes = agent_clj_from_text('TP53') content.set('genes', genes) content.set('dataset', "CTRP") msg = get_request(content) return msg, content
def _get_qca_content(task, source, target): """Get the KQMLList content to be sent to the QCA for given task. Paramters --------- source, target : str The strings representing the proteins for source and target, respectively, for example 'BRAF'. Returns ------- content : KQMLList The KQML content to be sent to the QCA module as part of the request. """ content = KQMLList(task) content.set('source', agent_clj_from_text(source)) content.set('target', agent_clj_from_text(target)) return content
def create_message_1(self): content = KQMLList('GET-VARIANT-INFO') gene = agent_clj_from_text('TP53') content.set('gene', gene) mutation = 'p.S241F' content.sets('mutation', mutation) msg = get_request(content) return msg, content
def test_respond_choose_nonsense(): bs = BioSense_Module(testing=True) msg_content = KQMLList('CHOOSE-SENSE') msg_content.set('agent', agent_clj_from_text('bagel')) res = bs.respond_choose_sense(msg_content) print(res) assert res.head() == 'SUCCESS' agents_clj = res.get('agent') agent = Bioagent.get_agent(agents_clj) assert agent.name == 'BAGEL' assert len(agent.db_refs) == 1
def create_message(self): content = KQMLList('CHOOSE-SENSE') agent = agent_clj_from_text('BRAF') content.set('agent', agent) print(content) return get_request(content), content
class TestGetIndraRepInactiveRAFActivatesMEK(_GetIndraRepTemplate): kqml_file = 'Inactive_RAF_activates_MEK.kqml' def check_result(self, res): stmts = self.bioagent.get_statement(res) assert len(stmts) == 1, stmts stmt = stmts[0] assert isinstance(stmt, Activation), type(stmt) assert stmt.subj.name == 'RAF', stmt assert stmt.subj.activity, stmt assert not stmt.subj.activity.is_active, stmt assert stmt.obj.name == 'MEK', stmt mek1 = agent_clj_from_text('MEK1') mek1a = Bioagent.get_agent(mek1) mek = agent_clj_from_text('MEK') meka = Bioagent.get_agent(mek) dusp6 = agent_clj_from_text('DUSP6') dusp6a = Bioagent.get_agent(dusp6) braf = agent_clj_from_text('BRAF') brafa = Bioagent.get_agent(braf) bs = BioSense() def test_choose_sense_category(): cases = [(mek1a, [('kinase activity', 'TRUE'), ('enzyme', 'TRUE'), ('kinase', 'TRUE'), ('transcription-factor', 'FALSE'), ('W::KINASE', 'TRUE'), ('phosphatase', 'FALSE')]),
def create_message_failure(self): content = KQMLList('FIND-MUTEX') gene = agent_clj_from_text('BRAF') content.set('gene', gene) msg = get_request(content) return msg, content
def create_message(self): target = agent_clj_from_text(self.target) content = KQMLList('FIND-TARGET-DRUG') content.set('target', target) return get_request(content), content
def create_message(self): disease = agent_clj_from_text('common cold') content = KQMLList('FIND-TREATMENT') content.set('disease', disease) return get_request(content), content
def create_message(self): disease = agent_clj_from_text('prostate cancer') content = KQMLList('FIND-DISEASE-TARGETS') content.set('disease', disease) return get_request(content), content
def create_message(self): drug = agent_clj_from_text('SB525334') content = KQMLList('FIND-DRUG-TARGETS') content.set('drug', drug) return get_request(content), content