def variant_update(institute_id, case_name, variant_id): """Update user-defined information about a variant: manual rank & ACMG.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variant_obj = store.variant(variant_id) user_obj = store.user(current_user.email) link = request.referrer manual_rank = request.form.get('manual_rank') if manual_rank: new_manual_rank = int(manual_rank) if manual_rank != '-1' else None store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj, new_manual_rank) if new_manual_rank: flash("updated variant tag: {}".format(new_manual_rank), 'info') else: flash("reset variant tag: {}".format(variant_obj['manual_rank']), 'info') elif request.form.get('acmg_classification'): new_acmg = request.form['acmg_classification'] acmg_classification = variant_obj.get('acmg_classification') if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]): new_acmg = None store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg) flash("updated ACMG classification: {}".format(new_acmg), 'info') return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id): """Update user-defined information about a variant: manual rank & ACMG.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variant_obj = store.variant(variant_id) user_obj = store.user(current_user.email) link = request.referrer manual_rank = request.form.get('manual_rank') if manual_rank: new_manual_rank = int(manual_rank) if manual_rank != '-1' else None store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj, new_manual_rank) if new_manual_rank: flash("updated variant tag: {}".format(new_manual_rank), 'info') else: flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info') elif request.form.get('acmg_classification'): new_acmg = request.form['acmg_classification'] acmg_classification = variant_obj.get('acmg_classification') if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]): new_acmg = None store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg) flash("updated ACMG classification: {}".format(new_acmg), 'info') new_dismiss = request.form.getlist('dismiss_variant') if request.form.getlist('dismiss_variant'): store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj, new_dismiss) if new_dismiss: flash("Dismissed variant: {}".format(new_dismiss), 'info') if variant_obj.get('dismiss_variant') and not new_dismiss: if 'dismiss' in request.form: store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj, new_dismiss) flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info') else: log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info') mosaic_tags = request.form.getlist('mosaic_tags') if mosaic_tags: store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj, mosaic_tags) if new_dismiss: flash("Added mosaic tags: {}".format(mosaic_tags), 'info') if variant_obj.get('mosaic_tags') and not mosaic_tags: if 'mosaic' in request.form: store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj, mosaic_tags) flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info') return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id): """Update user-defined information about a variant: manual rank & ACMG.""" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variant_obj = store.variant(variant_id) user_obj = store.user(current_user.email) link = request.referrer manual_rank = request.form.get('manual_rank') if manual_rank: new_manual_rank = int(manual_rank) if manual_rank != '-1' else None store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj, new_manual_rank) if new_manual_rank: flash("updated variant tag: {}".format(new_manual_rank), 'info') else: flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info') elif request.form.get('acmg_classification'): new_acmg = request.form['acmg_classification'] acmg_classification = variant_obj.get('acmg_classification') if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]): new_acmg = None store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg) flash("updated ACMG classification: {}".format(new_acmg), 'info') new_dismiss = request.form.getlist('dismiss_variant') if request.form.getlist('dismiss_variant'): store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj, new_dismiss) if new_dismiss: flash("Dismissed variant: {}".format(new_dismiss), 'info') if variant_obj.get('dismiss_variant') and not new_dismiss: if 'dismiss' in request.form: store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj, new_dismiss) flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info') else: log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info') mosaic_tags = request.form.getlist('mosaic_tags') if mosaic_tags: store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj, mosaic_tags) if new_dismiss: flash("Added mosaic tags: {}".format(mosaic_tags), 'info') if variant_obj.get('mosaic_tags') and not mosaic_tags: if 'mosaic' in request.form: store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj, mosaic_tags) flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info') return redirect(request.referrer)