def clinvar(institute_id, case_name, variant_id): """Build a clinVar submission form for a variant.""" data = clinvar_export(store, institute_id, case_name, variant_id) if request.method == "GET": return data # POST form_dict = {} # flatten up HPO and OMIM terms lists into string of keys separated by semicolon for key, value in request.form.items(): if key.startswith("conditions@") or key.startswith("clin_features@"): conditions = request.form.getlist( key) # can be HPO or OMIM conditions if conditions: variant_id = key.split("@")[1] cond_types = [] cond_values = [] for condition in conditions: cond_types.append( condition.split("_")[0]) # 'HPO' or 'OMIM' cond_values.append( condition.split("_")[1]) # HPO id or OMIM ID if key.startswith( "conditions@" ): # Filling in 'condition_id_type' and 'condition_id_value' in variant data form_dict["@".join(["condition_id_type", variant_id])] = ";".join( cond_types) # Flattened list form_dict["@".join(["condition_id_value", variant_id])] = ";".join( cond_values) # Flattened list elif key.startswith( "clin_features@" ): # Filling in 'clin_features' in casedata form_dict["@".join(["clin_features", variant_id])] = ";".join( cond_values) # Flattened list else: form_dict[key] = value # A tuple of submission objects (variants and casedata objects): submission_objects = set_submission_objects(form_dict) # Add submission data to an open clinvar submission object, # or create a new if no open submission is found in database open_submission = store.get_open_clinvar_submission(institute_id) updated_submission = store.add_to_submission(open_submission["_id"], submission_objects) # Redirect to clinvar submissions handling page, and pass it the updated_submission_object return redirect( url_for("cases.clinvar_submissions", institute_id=institute_id))
def test_parse_clinvar_form(): """Test create list of submission objects (variants and casedata) from clinvar page form""" # Given a filled in form form_fields_dict = get_submission_dict() # Retrieve the IDs of variants in the form variant_ids = get_submission_variants(form_fields_dict) assert len(variant_ids) == 2 # obtain variant and casedata objects to include in submission subm_objs = set_submission_objects(form_fields_dict) assert len(subm_objs[0]) == 2 # one snv and one sv variant assert len(subm_objs[1]) ==1 # one case data object
def clinvar(institute_id, case_name, variant_id): """Build a clinVar submission form for a variant.""" data = controllers.clinvar_export(store, institute_id, case_name, variant_id) if request.method == 'GET': return data else: #POST form_dict = request.form.to_dict() submission_objects = set_submission_objects(form_dict) # A tuple of submission objects (variants and casedata objects) # Add submission data to an open clinvar submission object, # or create a new if no open submission is found in database open_submission = store.get_open_clinvar_submission(current_user.email, institute_id) updated_submission = store.add_to_submission(open_submission['_id'], submission_objects) # Redirect to clinvar submissions handling page, and pass it the updated_submission_object return redirect(url_for('cases.clinvar_submissions', institute_id=institute_id))
def clinvar(institute_id, case_name, variant_id): """Build a clinVar submission form for a variant.""" data = controllers.clinvar_export(store, institute_id, case_name, variant_id) if request.method == 'GET': return data else: #POST form_dict = request.form.to_dict() submission_objects = set_submission_objects(form_dict) # A tuple of submission objects (variants and casedata objects) # Add submission data to an open clinvar submission object, # or create a new if no open submission is found in database open_submission = store.get_open_clinvar_submission(current_user.email, institute_id) updated_submission = store.add_to_submission(open_submission['_id'], submission_objects) # Redirect to clinvar submissions handling page, and pass it the updated_submission_object return redirect(url_for('cases.clinvar_submissions', institute_id=institute_id))
def build_clinvar_submission(store, request, institute_id, case_name, variant_id): """Add some variants to a ClinVar submission object or create a new ClinVar submission Args: store(scout.adapter.MongoAdapter) request(flask.Request) institute_id(str): institute_obj['_id'] case_name(str): case_obj['display_name'] variant_id(str): variant_obj['document_id'] """ form_dict = {} # flatten up HPO and OMIM terms lists into string of keys separated by semicolon for key, value in request.form.items(): if "@" in key: variant_id = key.split("@")[1] if key.startswith("hpo_terms") and f"omim_terms@{variant_id}" not in request.form: form_dict["@".join(["condition_id_type", variant_id])] = "HPO" form_dict["@".join(["condition_id_value", variant_id])] = ";".join( request.form.getlist(key) ) elif key.startswith("omim_terms"): form_dict["@".join(["condition_id_type", variant_id])] = "OMIM" form_dict["@".join(["condition_id_value", variant_id])] = ";".join( request.form.getlist(key) ) elif key.startswith("clin_features"): form_dict[key] = ";".join(request.form.getlist(key)) else: form_dict[key] = value # A tuple of submission objects (variants and casedata objects): submission_objects = set_submission_objects(form_dict) # Add submission data to an open clinvar submission object, # or create a new if no open submission is found in database open_submission = store.get_open_clinvar_submission(institute_id) updated_submission = store.add_to_submission(open_submission["_id"], submission_objects)