main.py

#!/usr/bin/env python3

"""
.. See the NOTICE file distributed with this work for additional information
   regarding copyright ownership.

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
"""
import os
import sys
import json
import logging
import argparse

# from .eval import run
from basic_modules.workflow import Workflow
from utils import logger

from apps.jsonapp import JSONApp
from tool.VRE_SEG import SEG_RUNNER


class process_WF_RUNNER(Workflow):
    """
    Functions for demonstrating the pipeline set up.
    """

    configuration = {}

    def __init__(self, configuration=None):
        """
        Initialise the tool with its configuration.

        :param configuration: a dictionary containing parameters that define how the operation should be carried out,
        which are specific to each Tool.
        :type configuration: dict
        """
        logger.debug("Processing CWL Test")
        if configuration is None:
            configuration = {}

        self.configuration.update(configuration)

    def run(self, input_files, metadata, output_files):
        """
        Main run function for processing a test file.

        :param input_files: Dictionary of file locations.
        :param metadata: Required meta data.
        :param output_files: Locations of the output files to be returned by the pipeline.
        :type input_files: dict
        :type metadata: dict
        :type output_files: dict
        :return: Locations for the output txt (output_files), Matching metadata for each of the files (output_metadata).
        :rtype: dict, dict
        """
        try:
            logger.info("Initialise the CWL Test Tool")
            tt_handle = SEG_RUNNER(self.configuration)
            tt_files, tt_meta = tt_handle.run(input_files, metadata, output_files)
            return tt_files, tt_meta

        except Exception as error:
            errstr = "CAWL Test Tool wasn't processed successfully. ERROR: {}".format(error)
            logger.error(errstr)
            raise Exception(errstr)


def main_json(config, in_metadata, out_metadata):
    """
    Main function.

    This function launches the app using configuration written in two json files: config.json and input_metadata.json.

    :param config:
    :param in_metadata:
    :param out_metadata:
    :type config:
    :type in_metadata:
    :type out_metadata:
    :return: If result is True, execution finished successfully. False, otherwise.
    :rtype: bool
    """
    try:
        logger.info("1. Instantiate and launch the App")
        app = JSONApp()

        result = app.launch(process_WF_RUNNER, config, in_metadata, out_metadata)  # launch the app
        logger.info("2. App successfully launched; see " + out_metadata)
        return result

    except Exception as error:
        errstr = "App wasn't successfully launched. ERROR: {}".format(error)
        logger.error(errstr)
        raise Exception(errstr)


if __name__ == "__main__":

    # Set up the command line parameters
    parser = argparse.ArgumentParser(description="VRE CWL workflow runner")
    parser.add_argument("--config", help="Configuration file", required=True)
    parser.add_argument("--in_metadata", help="Location of input metadata file", required=True)
    parser.add_argument("--out_metadata", help="Location of output metadata file", required=True)
    parser.add_argument("--log_file", help="Location of the log file", required=False)
    parser.add_argument("--local", action="store_const", const=True, default=False)

    # Get the matching parameters from the command line
    args = parser.parse_args()

    CONFIG = args.config
    IN_METADATA = args.in_metadata
    OUT_METADATA = args.out_metadata
    LOCAL = args.local

    if args.log_file:
        sys.stderr = sys.stdout = open(args.log_file, "a")

    if LOCAL:
        sys._run_from_cmdl = True  # pylint: disable=protected-access

    RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)