scout/server/blueprints/variants/controllers.py
def verified_excel_file(store, institute_list, temp_excel_dir):
    """Collect all verified variants in a list on institutes and save them to file

    Args:
        store(adapter.MongoAdapter)
        institute_list(list): a list of institute ids
        temp_excel_dir(os.Path): folder where the temp excel files are written to

    Returns:
        written_files(int): the number of files written to temp_excel_dir
    """
    document_lines = []
    written_files = 0
    today = datetime.datetime.now().strftime('%Y-%m-%d')
    LOG.info('Creating verified variant document..')

    for cust in institute_list:
        verif_vars = store.verified(institute_id=cust)
        LOG.info('Found {} verified variants for customer {}'.format(len(verif_vars), cust))

        if not verif_vars:
            continue
        unique_callers = set()
        for var_type, var_callers in CALLERS.items():
            for caller in var_callers:
                unique_callers.add(caller.get('id'))
        cust_verified = export_verified_variants(verif_vars, unique_callers)

        document_name = '.'.join([cust, '_verified_variants', today]) + '.xlsx'
        workbook = Workbook(os.path.join(temp_excel_dir,document_name))
        Report_Sheet = workbook.add_worksheet()

        # Write the column header
        row = 0
        for col,field in enumerate(VERIFIED_VARIANTS_HEADER + list(unique_callers)):
            Report_Sheet.write(row,col,field)

        # Write variant lines, after header (start at line 1)
        for row, line in enumerate(cust_verified,1): # each line becomes a row in the document
            for col, field in enumerate(line): # each field in line becomes a cell
                Report_Sheet.write(row,col,field)
        workbook.close()

        if os.path.exists(os.path.join(temp_excel_dir,document_name)):
            written_files += 1

    return written_files
def verified_excel_file(store, institute_list, temp_excel_dir):
    """Collect all verified variants in a list on institutes and save them to file

    Args:
        store(adapter.MongoAdapter)
        institute_list(list): a list of institute ids
        temp_excel_dir(os.Path): folder where the temp excel files are written to

    Returns:
        written_files(int): the number of files written to temp_excel_dir
    """
    document_lines = []
    written_files = 0
    today = datetime.datetime.now().strftime('%Y-%m-%d')
    LOG.info('Creating verified variant document..')

    for cust in institute_list:
        verif_vars = store.verified(institute_id=cust)
        LOG.info('Found {} verified variants for customer {}'.format(len(verif_vars), cust))

        if not verif_vars:
            continue
        unique_callers = set()
        for var_type, var_callers in CALLERS.items():
            for caller in var_callers:
                unique_callers.add(caller.get('id'))
        cust_verified = export_verified_variants(verif_vars, unique_callers)

        document_name = '.'.join([cust, '_verified_variants', today]) + '.xlsx'
        workbook = Workbook(os.path.join(temp_excel_dir,document_name))
        Report_Sheet = workbook.add_worksheet()

        # Write the column header
        row = 0
        for col,field in enumerate(VERIFIED_VARIANTS_HEADER + list(unique_callers)):
            Report_Sheet.write(row,col,field)

        # Write variant lines, after header (start at line 1)
        for row, line in enumerate(cust_verified,1): # each line becomes a row in the document
            for col, field in enumerate(line): # each field in line becomes a cell
                Report_Sheet.write(row,col,field)
        workbook.close()

        if os.path.exists(os.path.join(temp_excel_dir,document_name)):
            written_files += 1

    return written_files
Collect all verified variants in a list on institutes and save them to file

    Args:
        store(adapter.MongoAdapter)
        institute_list(list): a list of institute ids
        temp_excel_dir(os.Path): folder where the temp excel files are written to

    Returns:
        written_files(int): the number of files written to temp_excel_dir