scout/server/blueprints/variants/views.py
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)
Update user-defined information about a variant: manual rank & ACMG.