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<h1>Source code for UioFiles</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
<span class="c1">#</span>
<span class="c1"># @Date: October 2014</span>
<span class="c1">#</span>
<span class="c1"># @Change History:</span>
<span class="c1">#</span>
<span class="c1"># November 2015 - Leopold Haimberger (University of Vienna):</span>
<span class="c1"># - modified method list_files to work with glob instead of listdir</span>
<span class="c1"># - added pattern search in method list_files</span>
<span class="c1">#</span>
<span class="c1"># February - December 2018 - Anne Philipp (University of Vienna):</span>
<span class="c1"># - applied PEP8 style guide</span>
<span class="c1"># - added documentation</span>
<span class="c1"># - optimisation of method list_files since it didn&#39;t work correctly</span>
<span class="c1"># for sub directories</span>
<span class="c1"># - additional speed up of method list_files</span>
<span class="c1"># - modified the class so that it is initiated with a pattern instead</span>
<span class="c1"># of suffixes. Gives more precision in selection of files.</span>
<span class="c1"># - added delete method</span>
<span class="c1">#</span>
<span class="c1"># @License:</span>
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
<span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># ------------------------------------------------------------------------------</span>
<span class="c1"># MODULES</span>
<span class="c1"># ------------------------------------------------------------------------------</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">fnmatch</span>
<span class="c1"># software specific modules from flex_extract</span>
<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>
<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>
<span class="c1"># ------------------------------------------------------------------------------</span>
<span class="c1"># CLASS</span>
<span class="c1"># ------------------------------------------------------------------------------</span>
<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>
<span class="sd">&#39;&#39;&#39;Collection of files matching a specific pattern.</span>
<span class="sd"> The pattern can contain regular expressions for the files.</span>
<span class="sd"> The files are listed and can be transformed to a single string or</span>
<span class="sd"> they can be deleted.</span>
<span class="sd"> Attributes</span>
<span class="sd"> ----------</span>
<span class="sd"> path : str</span>
<span class="sd"> Directory where to list the files.</span>
<span class="sd"> pattern : str</span>
<span class="sd"> Regular expression pattern. For example: &#39;\*.grb&#39;</span>
<span class="sd"> files : list of str</span>
<span class="sd"> List of files matching the pattern in the path.</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="c1"># --------------------------------------------------------------------------</span>
<span class="c1"># CLASS METHODS</span>
<span class="c1"># --------------------------------------------------------------------------</span>
<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>
<span class="sd">&#39;&#39;&#39;Assignes a specific pattern for these files.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> path : str</span>
<span class="sd"> Directory where to list the files.</span>
<span class="sd"> pattern : str</span>
<span class="sd"> Regular expression pattern. For example: &#39;\*.grb&#39;</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pattern</span> <span class="o">=</span> <span class="n">pattern</span>
<span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">[]</span>
<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>
<span class="k">return</span>
<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>
<span class="sd">&#39;&#39;&#39;Lists all files in the directory with the matching</span>
<span class="sd"> regular expression pattern.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> path : str</span>
<span class="sd"> Path to the files.</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="c1"># Get the absolute path</span>
<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>
<span class="c1"># get all files in the dir and subdir as absolut path</span>
<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>
<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>
<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>
<span class="k">return</span>
<span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&#39;&#39;&#39;Converts the list of files into a single string.</span>
<span class="sd"> The entries are sepereated by &quot;,&quot; sign.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
<span class="sd"> files_string : str</span>
<span class="sd"> The content of the list as a single string.</span>
<span class="sd"> &#39;&#39;&#39;</span>
<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>
<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>
<span class="k">return</span> <span class="n">files_string</span>
<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>
<span class="sd">&#39;&#39;&#39;Deletes the files.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
<span class="sd"> &#39;&#39;&#39;</span>
<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>
<span class="n">silent_remove</span><span class="p">(</span><span class="n">old_file</span><span class="p">)</span>
<span class="k">return</span></div></div>
</pre></div>
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<h1>All modules for which code is available</h1>
<ul><li><a href="ControlFile.html">ControlFile</a></li>
<li><a href="EcFlexpart.html">EcFlexpart</a></li>
<li><a href="GribUtil.html">GribUtil</a></li>
<li><a href="MarsRetrieval.html">MarsRetrieval</a></li>
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<li><a href="install.html">install</a></li>
<li><a href="prepare_flexpart.html">prepare_flexpart</a></li>
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Auto Generated Documentation
============================
.. automodule:: disaggregation
:members:
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Auto Generated Documentation
============================
.. contents::
:local:
Porgrams
--------
install
*******
.. automodule:: install
:members:
submit
******
.. automodule:: submit
:members:
Classes
-------
ControlFile
***********
.. automodule:: ControlFile
:members:
EcFlexpart
**********
.. automodule:: EcFlexpart
:members:
GribUtil
*********
.. automodule:: GribUtil
:members:
MarsRetrieval
*************
.. automodule:: MarsRetrieval
:members:
UioFiles
********
.. automodule:: UioFiles
:members:
Modules
-------
get_mars_data
*************
.. automodule:: get_mars_data
:members:
prepare_flexpart
****************
.. automodule:: prepare_flexpart
:members:
tools
*****
.. automodule:: tools
:members:
disaggregation
**************
.. automodule:: disaggregation
:members:
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============================
.. automodule:: disaggregation
:members:
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