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annotate CHAP/writer.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
parents cbbe42422d56
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1 #!/usr/bin/env python
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2 """
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3 File : writer.py
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4 Author : Valentin Kuznetsov <vkuznet AT gmail dot com>
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5 Description: generic Writer 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 os
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13 import sys
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14 from time import time
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16 # local modules
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17 # from pipeline import PipelineObject
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18
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19 class Writer():
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20 """
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21 Writer represent generic file writer
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22 """
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24 def __init__(self):
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25 """
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26 Constructor of Writer class
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27 """
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28 self.__name__ = self.__class__.__name__
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29 self.logger = logging.getLogger(self.__name__)
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30 self.logger.propagate = False
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31
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32 def write(self, data, filename, **_write_kwargs):
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33 """
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34 write API
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35
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36 :param filename: Name of file to write to
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37 :param data: data to write to file
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38 :return: data written to file
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39 """
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40
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41 t0 = time()
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42 self.logger.info(f'Executing "write" with filename={filename}, type(data)={type(data)}, kwargs={_write_kwargs}')
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43
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44 data = self._write(data, filename, **_write_kwargs)
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45
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46 self.logger.info(f'Finished "write" in {time()-t0:.3f} seconds\n')
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47
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48 return(data)
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49
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50 def _write(self, data, filename):
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51 with open(filename, 'a') as file:
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52 file.write(data)
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53 return(data)
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54
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55 class YAMLWriter(Writer):
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56 def _write(self, data, filename, force_overwrite=False):
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57 '''If `data` is a `dict`, write it to `filename`.
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58
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59 :param data: the dictionary to write to `filename`.
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60 :type data: dict
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61 :param filename: name of the file to write to.
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62 :type filename: str
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63 :param force_overwrite: flag to allow data in `filename` to be
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64 overwritten if it already exists.
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65 :type force_overwrite: bool
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66 :raises TypeError: if `data` is not a `dict`
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67 :raises RuntimeError: if `filename` already exists and
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68 `force_overwrite` is `False`.
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69 :return: the original input data
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70 :rtype: dict
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71 '''
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72
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73 import yaml
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74
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75 if not isinstance(data, (dict, list)):
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76 raise(TypeError(f'{self.__name__}.write: input data must be a dict or list.'))
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77
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78 if not force_overwrite:
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79 if os.path.isfile(filename):
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80 raise(RuntimeError(f'{self.__name__}: {filename} already exists.'))
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81
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82 with open(filename, 'w') as outf:
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83 yaml.dump(data, outf, sort_keys=False)
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84
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85 return(data)
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86
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87 class ExtractArchiveWriter(Writer):
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88 def _write(self, data, filename):
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89 '''Take a .tar archive represented as bytes in `data` and write the
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90 extracted archive to files.
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91
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92 :param data: the archive data
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93 :type data: bytes
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94 :param filename: the name of a directory to which the archive files will
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95 be written
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96 :type filename: str
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97 :return: the original `data`
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98 :rtype: bytes
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99 '''
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100
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101 from io import BytesIO
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102 import tarfile
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103
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104 tar = tarfile.open(fileobj=BytesIO(data))
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105 tar.extractall(path=filename)
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106
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107 return(data)
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108
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109
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110 class NexusWriter(Writer):
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111 def _write(self, data, filename, force_overwrite=False):
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112 '''Write `data` to a NeXus file
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113
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114 :param data: the data to write to `filename`.
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115 :param filename: name of the file to write to.
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116 :param force_overwrite: flag to allow data in `filename` to be
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117 overwritten, if it already exists.
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118 :return: the original input data
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119 '''
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120
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121 from nexusformat.nexus import NXobject
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122 import xarray as xr
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123
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124 if isinstance(data, NXobject):
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125 nxstructure = data
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126
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127 elif isinstance(data, xr.Dataset):
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128 nxstructure = self.get_nxdata_from_dataset(data)
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129
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130 elif isinstance(data, xr.DataArray):
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131 nxstructure = self.get_nxdata_from_dataarray(data)
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132
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133 else:
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134 raise(TypeError(f'{self.__name__}.write: unknown data format: {type(data).__name__}'))
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135
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136 mode = 'w' if force_overwrite else 'w-'
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137 nxstructure.save(filename, mode=mode)
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138
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139 return(data)
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140
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141
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142 def get_nxdata_from_dataset(self, dset):
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143 '''Return an instance of `nexusformat.nexus.NXdata` that represents the
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144 data and metadata attributes contained in `dset`.
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145
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146 :param dset: the input dataset to represent
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147 :type data: xarray.Dataset
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148 :return: `dset` represented as an instance of `nexusformat.nexus.NXdata`
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149 :rtype: nexusformat.nexus.NXdata
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150 '''
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151
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152 from nexusformat.nexus import NXdata, NXfield
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153
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154 nxdata_args = {'signal':None, 'axes':()}
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155
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156 for var in dset.data_vars:
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157 data_var = dset[var]
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158 nxfield = NXfield(data_var.data,
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159 name=data_var.name,
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160 attrs=data_var.attrs)
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161 if nxdata_args['signal'] is None:
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162 nxdata_args['signal'] = nxfield
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163 else:
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164 nxdata_args[var] = nxfield
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165
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166 for coord in dset.coords:
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167 coord_var = dset[coord]
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168 nxfield = NXfield(coord_var.data,
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169 name=coord_var.name,
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170 attrs=coord_var.attrs)
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171 nxdata_args['axes'] = (*nxdata_args['axes'], nxfield)
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172
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173 nxdata = NXdata(**nxdata_args)
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174 nxdata.attrs['xarray_attrs'] = json.dumps(dset.attrs)
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175
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176 return(nxdata)
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177
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178 def get_nxdata_from_dataarray(self, darr):
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179 '''Return an instance of `nexusformat.nexus.NXdata` that represents the
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180 data and metadata attributes contained in `darr`.
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181
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182 :param darr: the input dataset to represent
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183 :type darr: xarray.DataArray
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184 :return: `darr` represented as an instance of `nexusformat.nexus.NXdata`
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185 :rtype: nexusformat.nexus.NXdata
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186 '''
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187
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188 from nexusformat.nexus import NXdata, NXfield
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189
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190 nxdata_args = {'signal':None, 'axes':()}
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191
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192 nxdata_args['signal'] = NXfield(darr.data,
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193 name=darr.name,
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194 attrs=darr.attrs)
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195
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196
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197 for coord in darr.coords:
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198 coord_var = darr[coord]
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199 nxfield = NXfield(coord_var.data,
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200 name=coord_var.name,
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201 attrs=coord_var.attrs)
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202 nxdata_args['axes'] = (*nxdata_args['axes'], nxfield)
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203
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204 nxdata = NXdata(**nxdata_args)
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205 nxdata.attrs['xarray_attrs'] = json.dumps(darr.attrs)
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206
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207 return(nxdata)
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208
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209
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210 class OptionParser():
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211 '''User based option parser'''
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212 def __init__(self):
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213 self.parser = argparse.ArgumentParser(prog='PROG')
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214 self.parser.add_argument("--data", action="store",
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215 dest="data", default="", help="Input data")
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216 self.parser.add_argument("--filename", action="store",
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217 dest="filename", default="", help="Output file")
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218 self.parser.add_argument("--writer", action="store",
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219 dest="writer", default="Writer", help="Writer class name")
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220 self.parser.add_argument('--log-level', choices=logging._nameToLevel.keys(),
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221 dest='log_level', default='INFO', help='logging level')
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222
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223 def main():
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224 '''Main function'''
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225 optmgr = OptionParser()
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226 opts = optmgr.parser.parse_args()
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227 clsName = opts.writer
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228 try:
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229 writerCls = getattr(sys.modules[__name__],clsName)
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230 except:
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231 print(f'Unsupported writer {clsName}')
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232 sys.exit(1)
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233
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234 writer = writerCls()
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235 writer.logger.setLevel(getattr(logging, opts.log_level))
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236 log_handler = logging.StreamHandler()
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237 log_handler.setFormatter(logging.Formatter('{name:20}: {message}', style='{'))
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238 writer.logger.addHandler(log_handler)
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239 data = writer.write(opts.data, opts.filename)
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240 print(f"Writer {writer} writes to {opts.filename}, data {data}")
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241
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242 if __name__ == '__main__':
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243 main()