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annotate CHAP/runner.py @ 9:cc597d6571bc draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 9b179e6d8333851ea75448356f72c2f03157db8f-dirty
author kls286
date Wed, 29 Mar 2023 17:40:12 +0000
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1 #!/usr/bin/env python
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2 #-*- coding: utf-8 -*-
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3 #pylint: disable=
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4 """
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5 File : runner.py
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6 Author : Valentin Kuznetsov <vkuznet AT gmail dot com>
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7 Description:
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8 """
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9
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10 # system modules
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11 import argparse
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12 import logging
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13 import os
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14 import sys
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15 import yaml
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16
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17 # local modules
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18 from CHAP.pipeline import Pipeline
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19
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21 class OptionParser():
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22 def __init__(self):
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23 "User based option parser"
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24 self.parser = argparse.ArgumentParser(prog='PROG')
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25 self.parser.add_argument("--config", action="store",
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26 dest="config", default="", help="Input configuration file")
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27 self.parser.add_argument('--log-level', choices=logging._nameToLevel.keys(),
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28 dest='log_level', default='INFO', help='logging level')
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29
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30 def main():
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31 "Main function"
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32 optmgr = OptionParser()
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33 opts = optmgr.parser.parse_args()
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34 runner(opts)
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35
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36 def runner(opts):
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37 """
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38 Main runner function
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39
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40 :param opts: opts is an instance of argparse.Namespace which contains all input parameters
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41 """
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42
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43 logger = logging.getLogger(__name__)
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44 log_level = getattr(logging, opts.log_level.upper())
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45 logger.setLevel(log_level)
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46 log_handler = logging.StreamHandler()
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47 log_handler.setFormatter(logging.Formatter('{name:20}: {message}', style='{'))
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48 logger.addHandler(log_handler)
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49
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50 config = {}
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51 with open(opts.config) as file:
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52 config = yaml.safe_load(file)
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53 logger.info(f'Input configuration: {config}\n')
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54 pipeline_config = config.get('pipeline', [])
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55 objects = []
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56 kwds = []
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57 for item in pipeline_config:
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58 # load individual object with given name from its module
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59 if isinstance(item, dict):
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60 name = list(item.keys())[0]
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61 kwargs = item[name]
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62 else:
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63 name = item
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64 kwargs = {}
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65 modName, clsName = name.split('.')
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66 module = __import__(f'CHAP.{modName}', fromlist=[clsName])
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67 obj = getattr(module, clsName)()
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68 obj.logger.setLevel(log_level)
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69 obj.logger.addHandler(log_handler)
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70 logger.info(f'Loaded {obj}')
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71 objects.append(obj)
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72 kwds.append(kwargs)
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73 pipeline = Pipeline(objects, kwds)
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74 pipeline.logger.setLevel(log_level)
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75 pipeline.logger.addHandler(log_handler)
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76 logger.info(f'Loaded {pipeline} with {len(objects)} items\n')
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77 logger.info(f'Calling "execute" on {pipeline}')
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78 pipeline.execute()
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79
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80
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81 if __name__ == '__main__':
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82 main()