VRE_NF_RUNNER.py

#!/usr/bin/env python

"""
.. 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.
"""
from __future__ import print_function
from __future__ import absolute_import

# Required for ReadTheDocs
from functools import wraps # pylint: disable=unused-import

import argparse
import os

from basic_modules.workflow import Workflow
from utils import logger

import tool.vre_nf
from tool.vre_nf import WF_RUNNER

import json

# ------------------------------------------------------------------------------

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

    configuration = {}

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

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

        self.configuration.update(configuration)

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

        Parameters
        ----------
        input_files : dict
           Dictionary of file locations
        metadata : list
           Required meta data
        output_files : dict
           Locations of the output files to be returned by the pipeline

        Returns
        -------
        output_files : dict
           Locations for the output txt
        output_metadata : dict
           Matching metadata for each of the files
        """

        # Initialise the test tool
        tt_handle = WF_RUNNER(self.configuration)
        tt_files, tt_meta = tt_handle.run(input_files, metadata, output_files, output_metadata)

        return (tt_files, tt_meta)

# ------------------------------------------------------------------------------

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.
    """
    # 1. Instantiate and launch the App
    logger.info("I. Instantiate and launch the App")
    from apps.jsonapp import JSONApp
    app = JSONApp()
    
    # Fixing possible problems in the input metadata
    with open(in_metadata,"r") as in_metF:
        in_metaArr = json.load(in_metF)
    
    in_fixed = False
    for in_m in in_metaArr:
        if in_m.get('taxon_id',0)  == 0:
            in_m['taxon_id'] = -1
            in_fixed = True
    
    if in_fixed:
        with open(in_metadata,"w") as in_metF:
            json.dump(in_metaArr,in_metF)

    ### UGLY TRICK
    abs_config_dir = os.path.dirname(os.path.abspath(config))
    process_WF_RUNNER.configuration[WF_RUNNER.CONFIG_DIR_KEY] = abs_config_dir
    
    result = app.launch(process_WF_RUNNER,
                        config,
                        in_metadata,
                        out_metadata)

    # 2. The App has finished
    logger.info("II. Execution finished; see " + out_metadata)

    return result

# ------------------------------------------------------------------------------

if __name__ == "__main__":

    # Set up the command line parameters
    PARSER = argparse.ArgumentParser(description="VRE NextFlow workflow runner")
    PARSER.add_argument("--config", help="Configuration file")
    PARSER.add_argument("--in_metadata", help="Location of input metadata file")
    PARSER.add_argument("--out_metadata", help="Location of output metadata file")
    PARSER.add_argument("--log_file", help="Location of the log file")
    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
    
    import sys
    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)