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| 58 | <div class="version"> |
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| 59 | 7.1 |
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| 148 | <hr/> |
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| 151 | <div itemprop="articleBody"> |
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| 152 | |
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| 153 | <h1>Source code for UioFiles</h1><div class="highlight"><pre> |
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| 154 | <span></span><span class="ch">#!/usr/bin/env python</span> |
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| 155 | <span class="c1"># -*- coding: utf-8 -*-</span> |
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| 156 | <span class="c1">#*******************************************************************************</span> |
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| 157 | <span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span> |
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| 158 | <span class="c1">#</span> |
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| 159 | <span class="c1"># @Date: October 2014</span> |
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| 160 | <span class="c1">#</span> |
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| 161 | <span class="c1"># @Change History:</span> |
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| 162 | <span class="c1">#</span> |
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| 163 | <span class="c1"># November 2015 - Leopold Haimberger (University of Vienna):</span> |
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| 164 | <span class="c1"># - modified method list_files to work with glob instead of listdir</span> |
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| 165 | <span class="c1"># - added pattern search in method list_files</span> |
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| 166 | <span class="c1">#</span> |
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[2625ca8] | 167 | <span class="c1"># February - December 2018 - Anne Philipp (University of Vienna):</span> |
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[274f9ef] | 168 | <span class="c1"># - applied PEP8 style guide</span> |
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| 169 | <span class="c1"># - added documentation</span> |
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| 170 | <span class="c1"># - optimisation of method list_files since it didn't work correctly</span> |
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| 171 | <span class="c1"># for sub directories</span> |
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| 172 | <span class="c1"># - additional speed up of method list_files</span> |
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| 173 | <span class="c1"># - modified the class so that it is initiated with a pattern instead</span> |
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| 174 | <span class="c1"># of suffixes. Gives more precision in selection of files.</span> |
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[2625ca8] | 175 | <span class="c1"># - added delete method</span> |
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[274f9ef] | 176 | <span class="c1">#</span> |
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| 177 | <span class="c1"># @License:</span> |
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[2625ca8] | 178 | <span class="c1"># (C) Copyright 2014-2019.</span> |
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| 179 | <span class="c1"># Anne Philipp, Leopold Haimberger</span> |
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[274f9ef] | 180 | <span class="c1">#</span> |
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[2625ca8] | 181 | <span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span> |
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| 182 | <span class="c1"># International License. To view a copy of this license, visit</span> |
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| 183 | <span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span> |
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| 184 | <span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span> |
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[274f9ef] | 185 | <span class="c1">#*******************************************************************************</span> |
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| 186 | |
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| 187 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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| 188 | <span class="c1"># MODULES</span> |
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| 189 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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| 190 | <span class="kn">import</span> <span class="nn">os</span> |
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| 191 | <span class="kn">import</span> <span class="nn">sys</span> |
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| 192 | <span class="kn">import</span> <span class="nn">fnmatch</span> |
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| 193 | |
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[2625ca8] | 194 | <span class="c1"># software specific modules from flex_extract</span> |
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[274f9ef] | 195 | <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'../'</span><span class="p">)</span> |
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| 196 | <span class="kn">from</span> <span class="nn">mods.tools</span> <span class="k">import</span> <span class="n">silent_remove</span><span class="p">,</span> <span class="n">get_list_as_string</span> |
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| 197 | |
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| 198 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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| 199 | <span class="c1"># CLASS</span> |
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| 200 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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| 201 | |
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| 202 | <div class="viewcode-block" id="UioFiles"><a class="viewcode-back" href="../api.html#UioFiles.UioFiles">[docs]</a><span class="k">class</span> <span class="nc">UioFiles</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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[2625ca8] | 203 | <span class="sd">'''Collection of files matching a specific pattern.</span> |
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| 204 | |
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| 205 | <span class="sd"> The pattern can contain regular expressions for the files.</span> |
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| 206 | <span class="sd"> The files are listed and can be transformed to a single string or</span> |
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| 207 | <span class="sd"> they can be deleted.</span> |
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| 208 | |
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| 209 | <span class="sd"> Attributes</span> |
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| 210 | <span class="sd"> ----------</span> |
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| 211 | <span class="sd"> path : str</span> |
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| 212 | <span class="sd"> Directory where to list the files.</span> |
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| 213 | |
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| 214 | <span class="sd"> pattern : str</span> |
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| 215 | <span class="sd"> Regular expression pattern. For example: '\*.grb'</span> |
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| 216 | |
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| 217 | <span class="sd"> files : list of str</span> |
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| 218 | <span class="sd"> List of files matching the pattern in the path.</span> |
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[274f9ef] | 219 | <span class="sd"> '''</span> |
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| 220 | <span class="c1"># --------------------------------------------------------------------------</span> |
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[2625ca8] | 221 | <span class="c1"># CLASS METHODS</span> |
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[274f9ef] | 222 | <span class="c1"># --------------------------------------------------------------------------</span> |
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| 223 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">pattern</span><span class="p">):</span> |
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| 224 | <span class="sd">'''Assignes a specific pattern for these files.</span> |
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| 225 | |
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| 226 | <span class="sd"> Parameters</span> |
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| 227 | <span class="sd"> ----------</span> |
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[2625ca8] | 228 | <span class="sd"> path : str</span> |
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[274f9ef] | 229 | <span class="sd"> Directory where to list the files.</span> |
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| 230 | |
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[2625ca8] | 231 | <span class="sd"> pattern : str</span> |
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[274f9ef] | 232 | <span class="sd"> Regular expression pattern. For example: '\*.grb'</span> |
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| 233 | |
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| 234 | <span class="sd"> Return</span> |
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| 235 | <span class="sd"> ------</span> |
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| 236 | |
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| 237 | <span class="sd"> '''</span> |
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| 238 | |
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| 239 | <span class="bp">self</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span> |
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| 240 | <span class="bp">self</span><span class="o">.</span><span class="n">pattern</span> <span class="o">=</span> <span class="n">pattern</span> |
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| 241 | <span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">[]</span> |
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| 242 | |
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[2625ca8] | 243 | <span class="bp">self</span><span class="o">.</span><span class="n">_list_files</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">)</span> |
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[274f9ef] | 244 | |
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| 245 | <span class="k">return</span> |
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| 246 | |
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[2625ca8] | 247 | |
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| 248 | <span class="k">def</span> <span class="nf">_list_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span> |
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[274f9ef] | 249 | <span class="sd">'''Lists all files in the directory with the matching</span> |
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| 250 | <span class="sd"> regular expression pattern.</span> |
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| 251 | |
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| 252 | <span class="sd"> Parameters</span> |
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| 253 | <span class="sd"> ----------</span> |
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[2625ca8] | 254 | <span class="sd"> path : str</span> |
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[274f9ef] | 255 | <span class="sd"> Path to the files.</span> |
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| 256 | |
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| 257 | <span class="sd"> Return</span> |
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| 258 | <span class="sd"> ------</span> |
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| 259 | |
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| 260 | <span class="sd"> '''</span> |
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| 261 | <span class="c1"># Get the absolute path</span> |
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| 262 | <span class="n">path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> |
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| 263 | |
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| 264 | <span class="c1"># get all files in the dir and subdir as absolut path</span> |
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| 265 | <span class="k">for</span> <span class="n">root</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> |
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| 266 | <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">filenames</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pattern</span><span class="p">):</span> |
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| 267 | <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">filename</span><span class="p">))</span> |
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| 268 | |
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| 269 | <span class="k">return</span> |
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| 270 | |
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[2625ca8] | 271 | |
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[274f9ef] | 272 | <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 273 | <span class="sd">'''Converts the list of files into a single string.</span> |
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| 274 | <span class="sd"> The entries are sepereated by "," sign.</span> |
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| 275 | |
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| 276 | <span class="sd"> Parameters</span> |
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| 277 | <span class="sd"> ----------</span> |
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| 278 | |
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| 279 | <span class="sd"> Return</span> |
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| 280 | <span class="sd"> ------</span> |
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[2625ca8] | 281 | <span class="sd"> files_string : str</span> |
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[274f9ef] | 282 | <span class="sd"> The content of the list as a single string.</span> |
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| 283 | <span class="sd"> '''</span> |
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| 284 | |
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| 285 | <span class="n">filenames</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">]</span> |
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| 286 | <span class="n">files_string</span> <span class="o">=</span> <span class="n">get_list_as_string</span><span class="p">(</span><span class="n">filenames</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">', '</span><span class="p">)</span> |
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| 287 | |
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| 288 | <span class="k">return</span> <span class="n">files_string</span> |
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| 289 | |
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[2625ca8] | 290 | |
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[274f9ef] | 291 | <div class="viewcode-block" id="UioFiles.delete_files"><a class="viewcode-back" href="../api.html#UioFiles.UioFiles.delete_files">[docs]</a> <span class="k">def</span> <span class="nf">delete_files</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 292 | <span class="sd">'''Deletes the files.</span> |
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| 293 | |
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| 294 | <span class="sd"> Parameters</span> |
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| 295 | <span class="sd"> ----------</span> |
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| 296 | |
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| 297 | <span class="sd"> Return</span> |
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| 298 | <span class="sd"> ------</span> |
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| 299 | |
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| 300 | <span class="sd"> '''</span> |
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| 301 | |
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| 302 | <span class="k">for</span> <span class="n">old_file</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">:</span> |
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| 303 | <span class="n">silent_remove</span><span class="p">(</span><span class="n">old_file</span><span class="p">)</span> |
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| 304 | |
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| 305 | <span class="k">return</span></div></div> |
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| 306 | </pre></div> |
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| 307 | |
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| 308 | </div> |
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| 309 | |
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| 310 | </div> |
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| 311 | <footer> |
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| 312 | |
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| 313 | |
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| 314 | <hr/> |
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| 315 | |
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| 316 | <div role="contentinfo"> |
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| 317 | <p> |
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[f66f990] | 318 | © Copyright 2018, Anne Philipp and Leopold Haimberger. |
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[274f9ef] | 319 | |
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| 320 | </p> |
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| 321 | </div> |
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| 322 | Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. |
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| 323 | |
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| 324 | </footer> |
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| 326 | </div> |
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