scout/commands/update/omim.py
def omim(context, api_key, institute):
    """
    Update the automate generated omim gene panel in the database.
    """
    LOG.info("Running scout update omim")
    adapter = context.obj['adapter']
    
    api_key = api_key or context.obj.get('omim_api_key')
    if not api_key:
        LOG.warning("Please provide a omim api key to load the omim gene panel")
        context.abort()
    
    institute_obj = adapter.institute(institute)
    if not institute_obj:
        LOG.info("Institute %s could not be found in database", institute)
        LOG.warning("Please specify an existing institute")
        context.abort()

    try:
        adapter.load_omim_panel(api_key, institute=institute)
    except Exception as err:
        LOG.error(err)
        context.abort()
def omim(context, api_key, institute):
    LOG.info("Running scout update omim")
    adapter = context.obj['adapter']
    
    api_key = api_key or context.obj.get('omim_api_key')
    if not api_key:
        LOG.warning("Please provide a omim api key to load the omim gene panel")
        context.abort()
    
    institute_obj = adapter.institute(institute)
    if not institute_obj:
        LOG.info("Institute %s could not be found in database", institute)
        LOG.warning("Please specify an existing institute")
        context.abort()

    try:
        adapter.load_omim_panel(api_key, institute=institute)
    except Exception as err:
        LOG.error(err)
        context.abort()
def omim ( context , api_key , institute ) : LOG . info ( "Running scout update omim" ) adapter = context . obj [ 'adapter' ] api_key = api_key or context . obj . get ( 'omim_api_key' ) if not api_key : LOG . warning ( "Please provide a omim api key to load the omim gene panel" ) context . abort ( ) institute_obj = adapter . institute ( institute ) if not institute_obj : LOG . info ( "Institute %s could not be found in database" , institute ) LOG . warning ( "Please specify an existing institute" ) context . abort ( ) try : adapter . load_omim_panel ( api_key , institute = institute ) except Exception as err : LOG . error ( err ) context . abort ( )
Update the automate generated omim gene panel in the database.
Update the automate generated omim gene panel in the database .