scout/load/setup.py
def setup_scout(adapter, institute_id='cust000', user_name='Clark Kent',
                user_mail='clark.kent@mail.com', api_key=None, demo=False):
    """docstring for setup_scout"""
    ########################## Delete previous information ##########################
    LOG.info("Deleting previous database")
    for collection_name in adapter.db.collection_names():
        if not collection_name.startswith('system'):
            LOG.info("Deleting collection %s", collection_name)
            adapter.db.drop_collection(collection_name)
    LOG.info("Database deleted")

    ########################## Add a institute ##########################
    #####################################################################
    # Build a institute with id institute_name
    institute_obj = build_institute(
        internal_id=institute_id,
        display_name=institute_id,
        sanger_recipients=[user_mail]
    )

    # Add the institute to database
    adapter.add_institute(institute_obj)

    ########################## Add a User ###############################
    #####################################################################
    # Build a user obj
    user_obj = dict(
                _id=user_mail,
                email=user_mail,
                name=user_name,
                roles=['admin'],
                institutes=[institute_id]
            )

    adapter.add_user(user_obj)

    ### Get the mim information ###

    if not demo:
        # Fetch the mim files
        try:
            mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
        except Exception as err:
            LOG.warning(err)
            raise err
        mim2gene_lines = mim_files['mim2genes']
        genemap_lines = mim_files['genemap2']

        # Fetch the genes to hpo information
        hpo_gene_lines = fetch_hpo_genes()
        # Fetch the latest version of the hgnc information
        hgnc_lines = fetch_hgnc()
        # Fetch the latest exac pli score information
        exac_lines = fetch_exac_constraint()


    else:
        mim2gene_lines = [line for line in get_file_handle(mim2gene_reduced_path)]
        genemap_lines = [line for line in get_file_handle(genemap2_reduced_path)]

        # Fetch the genes to hpo information
        hpo_gene_lines = [line for line in get_file_handle(hpogenes_reduced_path)]
        # Fetch the reduced hgnc information
        hgnc_lines = [line for line in get_file_handle(hgnc_reduced_path)]
        # Fetch the latest exac pli score information
        exac_lines = [line for line in get_file_handle(exac_reduced_path)]


    builds = ['37', '38']
    ################## Load Genes and transcripts #######################
    #####################################################################
    for build in builds:
        # Fetch the ensembl information
        if not demo:
            ensembl_genes = fetch_ensembl_genes(build=build)
        else:
            ensembl_genes = get_file_handle(genes37_reduced_path)
        # load the genes
        hgnc_genes = load_hgnc_genes(
            adapter=adapter,
            ensembl_lines=ensembl_genes,
            hgnc_lines=hgnc_lines,
            exac_lines=exac_lines,
            mim2gene_lines=mim2gene_lines,
            genemap_lines=genemap_lines,
            hpo_lines=hpo_gene_lines,
            build=build,
        )

        # Create a map from ensembl ids to gene objects
        ensembl_genes = {}
        for gene_obj in hgnc_genes:
            ensembl_id = gene_obj['ensembl_id']
            ensembl_genes[ensembl_id] = gene_obj

        # Fetch the transcripts from ensembl
        if not demo:
            ensembl_transcripts = fetch_ensembl_transcripts(build=build)
        else:
            ensembl_transcripts = get_file_handle(transcripts37_reduced_path)
        # Load the transcripts for a certain build
        transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)

    hpo_terms_handle = None
    hpo_to_genes_handle = None
    hpo_disease_handle = None
    if demo:
        hpo_terms_handle = get_file_handle(hpoterms_reduced_path)
        hpo_to_genes_handle = get_file_handle(hpo_to_genes_reduced_path)
        hpo_disease_handle = get_file_handle(hpo_phenotype_to_terms_reduced_path)

    load_hpo(
        adapter=adapter,
        hpo_lines=hpo_terms_handle,
        hpo_gene_lines=hpo_to_genes_handle,
        disease_lines=genemap_lines,
        hpo_disease_lines=hpo_disease_handle
    )

    # If demo we load a gene panel and some case information
    if demo:
        parsed_panel = parse_gene_panel(
            path=panel_path,
            institute='cust000',
            panel_id='panel1',
            version=1.0,
            display_name='Test panel'
        )
        adapter.load_panel(parsed_panel)

        case_handle = get_file_handle(load_path)
        case_data = yaml.load(case_handle)

        adapter.load_case(case_data)

    LOG.info("Creating indexes")
    adapter.load_indexes()
    LOG.info("Scout instance setup successful")
def setup_scout(adapter, institute_id='cust000', user_name='Clark Kent',
                user_mail='clark.kent@mail.com', api_key=None, demo=False):
    """docstring for setup_scout"""
    ########################## Delete previous information ##########################
    LOG.info("Deleting previous database")
    for collection_name in adapter.db.collection_names():
        if not collection_name.startswith('system'):
            LOG.info("Deleting collection %s", collection_name)
            adapter.db.drop_collection(collection_name)
    LOG.info("Database deleted")

    ########################## Add a institute ##########################
    #####################################################################
    # Build a institute with id institute_name
    institute_obj = build_institute(
        internal_id=institute_id,
        display_name=institute_id,
        sanger_recipients=[user_mail]
    )

    # Add the institute to database
    adapter.add_institute(institute_obj)

    ########################## Add a User ###############################
    #####################################################################
    # Build a user obj
    user_obj = dict(
                _id=user_mail,
                email=user_mail,
                name=user_name,
                roles=['admin'],
                institutes=[institute_id]
            )

    adapter.add_user(user_obj)

    ### Get the mim information ###

    if not demo:
        # Fetch the mim files
        try:
            mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
        except Exception as err:
            LOG.warning(err)
            raise err
        mim2gene_lines = mim_files['mim2genes']
        genemap_lines = mim_files['genemap2']

        # Fetch the genes to hpo information
        hpo_gene_lines = fetch_hpo_genes()
        # Fetch the latest version of the hgnc information
        hgnc_lines = fetch_hgnc()
        # Fetch the latest exac pli score information
        exac_lines = fetch_exac_constraint()


    else:
        mim2gene_lines = [line for line in get_file_handle(mim2gene_reduced_path)]
        genemap_lines = [line for line in get_file_handle(genemap2_reduced_path)]

        # Fetch the genes to hpo information
        hpo_gene_lines = [line for line in get_file_handle(hpogenes_reduced_path)]
        # Fetch the reduced hgnc information
        hgnc_lines = [line for line in get_file_handle(hgnc_reduced_path)]
        # Fetch the latest exac pli score information
        exac_lines = [line for line in get_file_handle(exac_reduced_path)]


    builds = ['37', '38']
    ################## Load Genes and transcripts #######################
    #####################################################################
    for build in builds:
        # Fetch the ensembl information
        if not demo:
            ensembl_genes = fetch_ensembl_genes(build=build)
        else:
            ensembl_genes = get_file_handle(genes37_reduced_path)
        # load the genes
        hgnc_genes = load_hgnc_genes(
            adapter=adapter,
            ensembl_lines=ensembl_genes,
            hgnc_lines=hgnc_lines,
            exac_lines=exac_lines,
            mim2gene_lines=mim2gene_lines,
            genemap_lines=genemap_lines,
            hpo_lines=hpo_gene_lines,
            build=build,
        )

        # Create a map from ensembl ids to gene objects
        ensembl_genes = {}
        for gene_obj in hgnc_genes:
            ensembl_id = gene_obj['ensembl_id']
            ensembl_genes[ensembl_id] = gene_obj

        # Fetch the transcripts from ensembl
        if not demo:
            ensembl_transcripts = fetch_ensembl_transcripts(build=build)
        else:
            ensembl_transcripts = get_file_handle(transcripts37_reduced_path)
        # Load the transcripts for a certain build
        transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)

    hpo_terms_handle = None
    hpo_to_genes_handle = None
    hpo_disease_handle = None
    if demo:
        hpo_terms_handle = get_file_handle(hpoterms_reduced_path)
        hpo_to_genes_handle = get_file_handle(hpo_to_genes_reduced_path)
        hpo_disease_handle = get_file_handle(hpo_phenotype_to_terms_reduced_path)

    load_hpo(
        adapter=adapter,
        hpo_lines=hpo_terms_handle,
        hpo_gene_lines=hpo_to_genes_handle,
        disease_lines=genemap_lines,
        hpo_disease_lines=hpo_disease_handle
    )

    # If demo we load a gene panel and some case information
    if demo:
        parsed_panel = parse_gene_panel(
            path=panel_path,
            institute='cust000',
            panel_id='panel1',
            version=1.0,
            display_name='Test panel'
        )
        adapter.load_panel(parsed_panel)

        case_handle = get_file_handle(load_path)
        case_data = yaml.load(case_handle)

        adapter.load_case(case_data)

    LOG.info("Creating indexes")
    adapter.load_indexes()
    LOG.info("Scout instance setup successful")
docstring for setup_scout