def phenotypes(): """Add phenotype(s) to the case model.""" ind_id = request.form['ind_id'] phenotype_id = request.form['phenotype_id'] if not phenotype_id: return abort(500, 'no phenotype_id submitted') ind_obj = app.db.individual(ind_id) terms_added = app.db.add_phenotype(ind_obj, phenotype_id) if len(terms_added) > 0: # update the HPO gene list for the case hpo_list = app.db.case_genelist(ind_obj.case) hpo_results = hpo_genes(ind_obj.case.phenotype_ids()) if hpo_results is None: return abort(500, "couldn't link to genes, try again" .format(phenotype_id)) gene_ids = [result['gene_id'] for result in hpo_results if result['gene_id']] hpo_list.gene_ids = gene_ids app.db.save() return redirect(request.referrer)
def update_hpolist(self, case_obj): """Update the HPO gene list for a case based on current terms.""" hpo_list = self.case_genelist(case_obj) hpo_results = hpo_genes(case_obj.phenotype_ids(), *self.phenomizer_auth) if hpo_results is None: pass # Why raise here? # raise RuntimeError("couldn't link to genes, try again") else: gene_ids = [result['gene_id'] for result in hpo_results if result['gene_id']] hpo_list.gene_ids = gene_ids self.save()
def update_hpolist(self, ind_id): """Update the HPO gene list for a case based on current terms.""" ind_obj = self.individual(ind_id) # update the HPO gene list for the case hpo_list = self.case_genelist(ind_obj.case) hpo_results = hpo_genes(ind_obj.case.phenotype_ids()) if hpo_results is None: pass #Why raise here? # raise RuntimeError("couldn't link to genes, try again") else: gene_ids = [result['gene_id'] for result in hpo_results if result['gene_id']] hpo_list.gene_ids = gene_ids self.save()
def update_hpolist(self, case_obj): """Update the HPO gene list for a case based on current terms.""" hpo_list = self.case_genelist(case_obj) hpo_results = hpo_genes(case_obj.phenotype_ids(), *self.phenomizer_auth) if hpo_results is None: pass # Why raise here? # raise RuntimeError("couldn't link to genes, try again") else: gene_ids = [ result['gene_id'] for result in hpo_results if result['gene_id'] ] hpo_list.gene_ids = gene_ids self.save()