scout/commands/update/disease.py
def diseases(context, api_key):
    """
    Update disease terms in mongo database.
    """
    adapter = context.obj['adapter']
    
    # Fetch the omim information
    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()

    try:
        mim_files = fetch_mim_files(api_key, genemap2=True)
    except Exception as err:
        LOG.warning(err)
        context.abort()
    
    LOG.info("Dropping DiseaseTerms")
    adapter.disease_term_collection.drop()
    LOG.debug("DiseaseTerms dropped")

    load_disease_terms(
        adapter=adapter,
        genemap_lines=mim_files['genemap2'], 
    )

    LOG.info("Successfully loaded all disease terms")
def diseases(context, api_key):
    adapter = context.obj['adapter']
    
    # Fetch the omim information
    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()

    try:
        mim_files = fetch_mim_files(api_key, genemap2=True)
    except Exception as err:
        LOG.warning(err)
        context.abort()
    
    LOG.info("Dropping DiseaseTerms")
    adapter.disease_term_collection.drop()
    LOG.debug("DiseaseTerms dropped")

    load_disease_terms(
        adapter=adapter,
        genemap_lines=mim_files['genemap2'], 
    )

    LOG.info("Successfully loaded all disease terms")
def diseases ( context , api_key ) : adapter = context . obj [ 'adapter' ] # Fetch the omim information 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 ( ) try : mim_files = fetch_mim_files ( api_key , genemap2 = True ) except Exception as err : LOG . warning ( err ) context . abort ( ) LOG . info ( "Dropping DiseaseTerms" ) adapter . disease_term_collection . drop ( ) LOG . debug ( "DiseaseTerms dropped" ) load_disease_terms ( adapter = adapter , genemap_lines = mim_files [ 'genemap2' ] , ) LOG . info ( "Successfully loaded all disease terms" )
Update disease terms in mongo database.
Update disease terms in mongo database .