Source code for datacatalog.formats.sample_attributes.convert

import sys
import json
from ..converter import Converter, ConversionError, ValidationError
class SampleAttributes(Converter):
    """Convert generic samples attributes file to sample-set schema"""
    VERSION = '0.0.1'
    FILENAME = 'sample_attributes'

    def convert(self, input_fp, output_fp=None, verbose=True, config={}, enforce_validation=True):
        """Do the conversion by running a method in runner.py"""
        from .runner import convert_sample_attributes
        passed_config = config if config != {} else self.options
        tx_email = passed_config['tx']['email']
        tx_token = passed_config['tx']['token']
        return convert_sample_attributes(self.targetschema, self.encoding, input_fp, tx_email, tx_token, verbose=verbose, config=passed_config, output_file=output_fp, enforce_validation=enforce_validation)