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58              <div class="version">
59                7.1
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83              <p class="caption"><span class="caption-text">Table of Contents:</span></p>
84<ul>
85<li class="toctree-l1"><a class="reference internal" href="../downloads.html">Downloads</a></li>
86<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
87<li class="toctree-l1"><a class="reference internal" href="../program_structure.html">Program Structure</a></li>
88<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
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134      <li><a href="../index.html">Docs</a> &raquo;</li>
135       
136          <li><a href="index.html">Module code</a> &raquo;</li>
137       
138      <li>UioFiles</li>
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152           
153  <h1>Source code for UioFiles</h1><div class="highlight"><pre>
154<span></span><span class="ch">#!/usr/bin/env python</span>
155<span class="c1"># -*- coding: utf-8 -*-</span>
156<span class="c1">#*******************************************************************************</span>
157<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
158<span class="c1">#</span>
159<span class="c1"># @Date: October 2014</span>
160<span class="c1">#</span>
161<span class="c1"># @Change History:</span>
162<span class="c1">#</span>
163<span class="c1">#    November 2015 - Leopold Haimberger (University of Vienna):</span>
164<span class="c1">#        - modified method list_files to work with glob instead of listdir</span>
165<span class="c1">#        - added pattern search in method list_files</span>
166<span class="c1">#</span>
167<span class="c1">#    February 2018 - Anne Philipp (University of Vienna):</span>
168<span class="c1">#        - applied PEP8 style guide</span>
169<span class="c1">#        - added documentation</span>
170<span class="c1">#        - optimisation of method list_files since it didn&#39;t work correctly</span>
171<span class="c1">#          for sub directories</span>
172<span class="c1">#        - additional speed up of method list_files</span>
173<span class="c1">#        - modified the class so that it is initiated with a pattern instead</span>
174<span class="c1">#          of suffixes. Gives more precision in selection of files.</span>
175<span class="c1">#</span>
176<span class="c1"># @License:</span>
177<span class="c1">#    (C) Copyright 2014-2018.</span>
178<span class="c1">#</span>
179<span class="c1">#    This software is licensed under the terms of the Apache Licence Version 2.0</span>
180<span class="c1">#    which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.</span>
181<span class="c1">#</span>
182<span class="c1"># @Class Decription:</span>
183<span class="c1">#    The class is for file manipulation. It is initiated with a regular</span>
184<span class="c1">#    expression pattern for this instance and can produce a list of Files</span>
185<span class="c1">#    from the given file pattern. These files can be deleted.</span>
186<span class="c1">#</span>
187<span class="c1"># @Class Content:</span>
188<span class="c1">#    - __init__</span>
189<span class="c1">#    - __str__</span>
190<span class="c1">#    - __list_files__</span>
191<span class="c1">#    - delete_files</span>
192<span class="c1">#</span>
193<span class="c1"># @Class Attributes:</span>
194<span class="c1">#    - pattern</span>
195<span class="c1">#    - files</span>
196<span class="c1">#</span>
197<span class="c1">#*******************************************************************************</span>
198
199<span class="c1"># ------------------------------------------------------------------------------</span>
200<span class="c1"># MODULES</span>
201<span class="c1"># ------------------------------------------------------------------------------</span>
202<span class="kn">import</span> <span class="nn">os</span>
203<span class="kn">import</span> <span class="nn">sys</span>
204<span class="kn">import</span> <span class="nn">fnmatch</span>
205
206<span class="c1"># software specific module from flex_extract</span>
207<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">&#39;../&#39;</span><span class="p">)</span>
208<span class="c1">#import profiling</span>
209<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>
210
211<span class="c1"># ------------------------------------------------------------------------------</span>
212<span class="c1"># CLASS</span>
213<span class="c1"># ------------------------------------------------------------------------------</span>
214
215<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>
216    <span class="sd">&#39;&#39;&#39;Class to manipulate files. At initialisation it has the pattern</span>
217<span class="sd">    which stores a regular expression pattern for the files, the path</span>
218<span class="sd">    to the files and the files already.</span>
219<span class="sd">    &#39;&#39;&#39;</span>
220    <span class="c1"># --------------------------------------------------------------------------</span>
221    <span class="c1"># CLASS FUNCTIONS</span>
222    <span class="c1"># --------------------------------------------------------------------------</span>
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>
224        <span class="sd">&#39;&#39;&#39;Assignes a specific pattern for these files.</span>
225
226<span class="sd">        Parameters</span>
227<span class="sd">        ----------</span>
228<span class="sd">        path : :obj:`string`</span>
229<span class="sd">            Directory where to list the files.</span>
230
231<span class="sd">        pattern : :obj:`string`</span>
232<span class="sd">            Regular expression pattern. For example: &#39;\*.grb&#39;</span>
233
234<span class="sd">        Return</span>
235<span class="sd">        ------</span>
236
237<span class="sd">        &#39;&#39;&#39;</span>
238
239        <span class="bp">self</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span>
240        <span class="bp">self</span><span class="o">.</span><span class="n">pattern</span> <span class="o">=</span> <span class="n">pattern</span>
241        <span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">[]</span>
242
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>
244
245        <span class="k">return</span>
246
247    <span class="c1">#@profiling.timefn</span>
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>
249        <span class="sd">&#39;&#39;&#39;Lists all files in the directory with the matching</span>
250<span class="sd">        regular expression pattern.</span>
251
252<span class="sd">        Parameters</span>
253<span class="sd">        ----------</span>
254<span class="sd">        path : :obj:`string`</span>
255<span class="sd">            Path to the files.</span>
256
257<span class="sd">        Return</span>
258<span class="sd">        ------</span>
259
260<span class="sd">        &#39;&#39;&#39;</span>
261        <span class="c1"># Get the absolute path</span>
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>
263
264        <span class="c1"># get all files in the dir and subdir as absolut path</span>
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>
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>
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>
268
269        <span class="k">return</span>
270
271    <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
272        <span class="sd">&#39;&#39;&#39;Converts the list of files into a single string.</span>
273<span class="sd">        The entries are sepereated by &quot;,&quot; sign.</span>
274
275<span class="sd">        Parameters</span>
276<span class="sd">        ----------</span>
277
278<span class="sd">        Return</span>
279<span class="sd">        ------</span>
280<span class="sd">        files_string : :obj:`string`</span>
281<span class="sd">            The content of the list as a single string.</span>
282<span class="sd">        &#39;&#39;&#39;</span>
283
284        <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>
285        <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">&#39;, &#39;</span><span class="p">)</span>
286
287        <span class="k">return</span> <span class="n">files_string</span>
288
289<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>
290        <span class="sd">&#39;&#39;&#39;Deletes the files.</span>
291
292<span class="sd">        Parameters</span>
293<span class="sd">        ----------</span>
294
295<span class="sd">        Return</span>
296<span class="sd">        ------</span>
297
298<span class="sd">        &#39;&#39;&#39;</span>
299
300        <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>
301            <span class="n">silent_remove</span><span class="p">(</span><span class="n">old_file</span><span class="p">)</span>
302
303        <span class="k">return</span></div></div>
304</pre></div>
305
306           </div>
307           
308          </div>
309          <footer>
310 
311
312  <hr/>
313
314  <div role="contentinfo">
315    <p>
316        &copy; Copyright 2018, Anne Philipp and Leopold Haimberger.
317
318    </p>
319  </div>
320  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>.
321
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323
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326
327    </section>
328
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330 
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338            VERSION:'7.1 alpha',
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341            FILE_SUFFIX:'.html',
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