scout/commands/delete/delete_command.py
def case(context, institute, case_id, display_name):
    """Delete a case and it's variants from the database"""
    adapter = context.obj['adapter']
    if not (case_id or display_name):
        click.echo("Please specify what case to delete")
        context.abort()

    if display_name:
        if not institute:
            click.echo("Please specify the owner of the case that should be "
                       "deleted with flag '-i/--institute'.")
            context.abort()
        case_id = "{0}-{1}".format(institute, display_name)

    LOG.info("Running deleting case {0}".format(case_id))
    case = adapter.delete_case(
        case_id=case_id,
        institute_id=institute,
        display_name=display_name
    )

    if case.deleted_count == 1:
        adapter.delete_variants(case_id=case_id, variant_type='clinical')
        adapter.delete_variants(case_id=case_id, variant_type='research')
    else:
        LOG.warning("Case does not exist in database")
        context.abort()
def case(context, institute, case_id, display_name):
    """Delete a case and it's variants from the database"""
    adapter = context.obj['adapter']
    if not (case_id or display_name):
        click.echo("Please specify what case to delete")
        context.abort()

    if display_name:
        if not institute:
            click.echo("Please specify the owner of the case that should be "
                       "deleted with flag '-i/--institute'.")
            context.abort()
        case_id = "{0}-{1}".format(institute, display_name)

    LOG.info("Running deleting case {0}".format(case_id))
    case = adapter.delete_case(
        case_id=case_id,
        institute_id=institute,
        display_name=display_name
    )

    if case.deleted_count == 1:
        adapter.delete_variants(case_id=case_id, variant_type='clinical')
        adapter.delete_variants(case_id=case_id, variant_type='research')
    else:
        LOG.warning("Case does not exist in database")
        context.abort()
def case ( context , institute , case_id , display_name ) : adapter = context . obj [ 'adapter' ] if not ( case_id or display_name ) : click . echo ( "Please specify what case to delete" ) context . abort ( ) if display_name : if not institute : click . echo ( "Please specify the owner of the case that should be " "deleted with flag '-i/--institute'." ) context . abort ( ) case_id = "{0}-{1}" . format ( institute , display_name ) LOG . info ( "Running deleting case {0}" . format ( case_id ) ) case = adapter . delete_case ( case_id = case_id , institute_id = institute , display_name = display_name ) if case . deleted_count == 1 : adapter . delete_variants ( case_id = case_id , variant_type = 'clinical' ) adapter . delete_variants ( case_id = case_id , variant_type = 'research' ) else : LOG . warning ( "Case does not exist in database" ) context . abort ( )
Delete a case and it's variants from the database
Delete a case and it s variants from the database