Python schema_workflow_options_to_xml Examples

Example #1

    def test_load_preset(self):
        xml = IO.schema_workflow_options_to_xml(self._to_opts())
        preset_xml = get_temp_file(suffix="_preset.xml")
        log.debug(preset_xml)
        with open(preset_xml, 'w') as w:
            w.write(str(xml))

        preset_record = IO.parse_pipeline_preset_xml(preset_xml)
        workflow_level_opts = preset_record.to_workflow_level_opt()
        self.assertTrue(len(workflow_level_opts), len(self._to_opts()))

Example #2

File: test_pb_io.py Project: pb-cdunn/pbsmrtpipe

    def test_load_preset(self):
        xml = IO.schema_workflow_options_to_xml(self._to_opts())
        preset_xml = get_temp_file(suffix="_preset.xml")
        log.debug(preset_xml)
        with open(preset_xml, 'w') as w:
            w.write(str(xml))

        preset_record = IO.parse_pipeline_preset_xml(preset_xml)
        workflow_level_opts = preset_record.to_workflow_level_opt()
        self.assertTrue(len(workflow_level_opts), len(self._to_opts()))

Example #3

File: cli.py Project: mpkocher/pbsmrtpipe

def _args_run_show_workflow_level_options(args):

    from pbsmrtpipe.pb_io import REGISTERED_WORKFLOW_OPTIONS

    _print_option_schemas(REGISTERED_WORKFLOW_OPTIONS)

    output_file = args.output_preset_xml

    if output_file is not None:
        xml = IO.schema_workflow_options_to_xml(REGISTERED_WORKFLOW_OPTIONS)
        with open(output_file, 'w') as w:
            w.write(str(xml))
        log.info("wrote options to {x}".format(x=output_file))

    return 0

Example #4

def _args_run_show_workflow_level_options(args):

    from pbsmrtpipe.pb_io import REGISTERED_WORKFLOW_OPTIONS

    _print_option_schemas(REGISTERED_WORKFLOW_OPTIONS)

    output_file = args.output_preset_xml

    if output_file is not None:
        xml = IO.schema_workflow_options_to_xml(REGISTERED_WORKFLOW_OPTIONS)
        with open(output_file, 'w') as w:
            w.write(str(xml))
        log.info("wrote options to {x}".format(x=output_file))

    return 0

Example #5

 def test_to_xml(self):
     wopts = self._to_opts()
     xml = IO.schema_workflow_options_to_xml(wopts)
     log.debug(xml)
     self.assertIsNotNone(xml)

Example #6

File: test_pb_io.py Project: pb-cdunn/pbsmrtpipe

 def test_to_xml(self):
     wopts = self._to_opts()
     xml = IO.schema_workflow_options_to_xml(wopts)
     log.debug(xml)
     self.assertIsNotNone(xml)