def case_diagnosis(institute_id, case_name): """Add or remove a diagnosis for a case.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) user_obj = store.user(current_user.email) link = url_for(".case", institute_id=institute_id, case_name=case_name) level = "phenotype" if "phenotype" in request.form else "gene" omim_id = request.form["omim_term"].split("|")[0] if not "OMIM:" in omim_id: # Could be an omim number provided by user omim_id = ":".join(["OMIM", omim_id]) # Make sure omim term exists in database: omim_obj = store.disease_term(omim_id.strip()) if not omim_obj: flash("Couldn't find any disease term with id: {}".format(omim_id), "warning") remove = True if request.args.get("remove") == "yes" else False store.diagnose( institute_obj, case_obj, user_obj, link, level=level, omim_id=omim_id, remove=remove, ) return redirect(request.referrer)
def case_diagnosis(institute_id, case_name): """Add or remove a diagnosis for a case.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) user_obj = store.user(current_user.email) link = url_for(".case", institute_id=institute_id, case_name=case_name) omim_id = request.form["omim_term"].split("|")[0] omim_inds = request.form.getlist( "omim_inds") # Individual-level phenotypes if not "OMIM:" in omim_id: # Could be an omim number provided by user omim_id = ":".join(["OMIM", omim_id]) # Make sure omim term exists in database: omim_obj = store.disease_term(omim_id.strip()) if omim_obj is None: flash("Couldn't find any disease term with id: {}".format(omim_id), "warning") return redirect(request.referrer) remove = True if request.args.get("remove") == "yes" else False store.diagnose(institute_obj, case_obj, user_obj, link, omim_obj, omim_inds, remove) return redirect("#".join([link, "omim_assign"]))
def case_diagnosis(institute_id, case_name): """Add or remove a diagnosis for a case.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) user_obj = store.user(current_user.email) link = url_for('.case', institute_id=institute_id, case_name=case_name) level = 'phenotype' if 'phenotype' in request.form else 'gene' omim_id = request.form['omim_id'] remove = True if request.args.get('remove') == 'yes' else False store.diagnose(institute_obj, case_obj, user_obj, link, level=level, omim_id=omim_id, remove=remove) return redirect(request.referrer)
def case_diagnosis(institute_id, case_name): """Add or remove a diagnosis for a case.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) user_obj = store.user(current_user.email) link = url_for('.case', institute_id=institute_id, case_name=case_name) level = 'phenotype' if 'phenotype' in request.form else 'gene' omim_id = request.form['omim_id'] remove = True if request.args.get('remove') == 'yes' else False store.diagnose(institute_obj, case_obj, user_obj, link, level=level, omim_id=omim_id, remove=remove) return redirect(request.referrer)
def case_diagnosis(institute_id, case_name): """Add or remove a diagnosis for a case.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) user_obj = store.user(current_user.email) link = url_for(".case", institute_id=institute_id, case_name=case_name) level = "phenotype" if "phenotype" in request.form else "gene" omim_id = request.form["omim_id"] remove = True if request.args.get("remove") == "yes" else False store.diagnose( institute_obj, case_obj, user_obj, link, level=level, omim_id=omim_id, remove=remove, ) return redirect(request.referrer)