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annotate CHAP/reader.py @ 10:7cc954f15149 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 2d65c72740d0439b8385378a890b3763d717f152-dirty
author kls286
date Wed, 29 Mar 2023 17:53:07 +0000
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1 #!/usr/bin/env python
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2 """
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3 File : reader.py
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4 Author : Valentin Kuznetsov <vkuznet AT gmail dot com>
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5 Description: generic Reader module
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6 """
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7
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8 # system modules
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9 import argparse
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10 import json
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11 import logging
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12 import sys
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13 from time import time
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14
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15 # local modules
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16 # from pipeline import PipelineObject
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18 class Reader():
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19 """
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20 Reader represent generic file writer
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21 """
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22
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23 def __init__(self):
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24 """
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25 Constructor of Reader class
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26 """
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27 self.__name__ = self.__class__.__name__
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28 self.logger = logging.getLogger(self.__name__)
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29 self.logger.propagate = False
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30
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31 def read(self, type_=None, schema=None, encoding=None, **_read_kwargs):
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32 '''Read API
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33
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34 Wrapper to read, format, and return the data requested.
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35
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36 :param type_: the expected type of data read from `filename`, defualts
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37 to `None`
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38 :type type_: type, optional
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39 :param schema: the expected schema of the data read from `filename`,
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40 defaults to `None`
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41 :type schema: str, otional
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42 :param _read_kwargs: keyword arguments to pass to `self._read`, defaults
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43 to `{}`
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44 :type _read_kwargs: dict, optional
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45 :return: list with one item: a dictionary containing the data read from
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46 `filename`, the name of this `Reader`, and the values of `type_` and
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47 `schema`.
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48 :rtype: list[dict[str,object]]
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49 '''
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50
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51 t0 = time()
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52 self.logger.info(f'Executing "read" with type={type_}, schema={schema}, kwargs={_read_kwargs}')
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53
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54 data = [{'name': self.__name__,
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55 'data': self._read(**_read_kwargs),
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56 'type': type_,
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57 'schema': schema,
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58 'encoding': encoding}]
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59
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60 self.logger.info(f'Finished "read" in {time()-t0:.3f} seconds\n')
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61 return(data)
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62
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63 def _read(self, filename):
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64 '''Read and return the data from requested from `filename`
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65
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66 :param filename: Name of file to read from
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67 :return: specific number of bytes from a file
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68 '''
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69
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70 if not filename:
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71 self.logger.warning('No file name is given, will skip read operation')
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72 return None
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73
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74 with open(filename) as file:
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75 data = file.read()
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76 return(data)
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77
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78 class MultipleReader(Reader):
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79 def read(self, readers):
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80 '''Return resuts from multiple `Reader`s.
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81
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82 :param readers: a dictionary where the keys are specific names that are
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83 used by the next item in the `Pipeline`, and the values are `Reader`
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84 configurations.
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85 :type readers: list[dict]
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86 :return: The results of calling `Reader.read(**kwargs)` for each item
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87 configured in `readers`.
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88 :rtype: list[dict[str,object]]
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89 '''
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90
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91 t0 = time()
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92 self.logger.info(f'Executing "read" with {len(readers)} Readers')
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93
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94 data = []
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95 for reader_config in readers:
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96 reader_name = list(reader_config.keys())[0]
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97 reader_class = getattr(sys.modules[__name__], reader_name)
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98 reader = reader_class()
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99 reader_kwargs = reader_config[reader_name]
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100
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101 data.extend(reader.read(**reader_kwargs))
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102
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103 self.logger.info(f'Finished "read" in {time()-t0:.3f} seconds\n')
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104
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105 return(data)
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106
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107 class YAMLReader(Reader):
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108 def _read(self, filename):
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109 '''Return a dictionary from the contents of a yaml file.
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110
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111 :param filename: name of the YAML file to read from
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112 :return: the contents of `filename`
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113 :rtype: dict
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114 '''
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115
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116 import yaml
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117
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118 with open(filename) as file:
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119 data = yaml.safe_load(file)
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120 return(data)
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121
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122 class BinaryFileReader(Reader):
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123 def _read(self, filename):
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124 '''Return a content of a given file name
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125
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126 :param filename: name of the binart file to read from
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127 :return: the content of `filename`
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128 :rtype: binary
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129 '''
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130 with open(filename, 'rb') as file:
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131 data = file.read()
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132 return(data)
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133
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134 class NexusReader(Reader):
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135 def _read(self, filename, nxpath='/'):
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136 '''Return the NeXus object stored at `nxpath` in the nexus file
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137 `filename`.
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138
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139 :param filename: name of the NeXus file to read from
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140 :type filename: str
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141 :param nxpath: path to a specific loaction in the NeXus file to read
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142 from, defaults to `'/'`
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143 :type nxpath: str, optional
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144 :raises nexusformat.nexus.NeXusError: if `filename` is not a NeXus
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145 file or `nxpath` is not in `filename`.
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146 :return: the NeXus structure indicated by `filename` and `nxpath`.
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147 :rtype: nexusformat.nexus.NXobject
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148 '''
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149
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150 from nexusformat.nexus import nxload
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151
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152 nxobject = nxload(filename)[nxpath]
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153 return(nxobject)
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154
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155 class URLReader(Reader):
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156 def _read(self, url, headers={}):
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157 '''Make an HTTPS request to the provided URL and return the results.
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158 Headers for the request are optional.
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159
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160 :param url: the URL to read
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161 :type url: str
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162 :param headers: headers to attach to the request, defaults to `{}`
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163 :type headers: dict, optional
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164 :return: the content of the response
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165 :rtype: object
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166 '''
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167
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168 import requests
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169
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170 resp = requests.get(url, headers=headers)
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171 data = resp.content
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172
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173 self.logger.debug(f'Response content: {data}')
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174
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175 return(data)
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176
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177 class OptionParser():
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178 '''User based option parser'''
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179 def __init__(self):
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180 self.parser = argparse.ArgumentParser(prog='PROG')
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181 self.parser.add_argument("--filename", action="store",
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182 dest="filename", default="", help="Input file")
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183 self.parser.add_argument("--reader", action="store",
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184 dest="reader", default="Reader", help="Reader class name")
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185 self.parser.add_argument('--log-level', choices=logging._nameToLevel.keys(),
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186 dest='log_level', default='INFO', help='logging level')
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187
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188 def main():
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189 '''Main function'''
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190 optmgr = OptionParser()
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191 opts = optmgr.parser.parse_args()
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192 clsName = opts.reader
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193 try:
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194 readerCls = getattr(sys.modules[__name__],clsName)
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195 except:
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196 print(f'Unsupported reader {clsName}')
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197 sys.exit(1)
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198
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199 reader = readerCls()
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200 reader.logger.setLevel(getattr(logging, opts.log_level))
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201 log_handler = logging.StreamHandler()
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202 log_handler.setFormatter(logging.Formatter('{name:20}: {message}', style='{'))
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203 reader.logger.addHandler(log_handler)
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204 data = reader.read(filename=opts.filename)
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205
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206 print(f"Reader {reader} reads from {opts.filename}, data {data}")
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207
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208 if __name__ == '__main__':
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209 main()