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Commit 81c180c9 authored by Anne Tipka's avatar Anne Tipka :headphones:
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Merge branch current master branch from CTBTO's gitlab repo into dev branch from flexpart.eu repo

parents 6857073d 78963049
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.gitlab-ci.yml 0 → 100644
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image: python:3.7-alpine
pages:
stage: deploy
script:
- cp -r Documentation/html public
artifacts:
paths:
- public
only:
- master
Documentation/html/Documentation/Api/api_python.html
+ 37
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......@@ -2492,6 +2492,28 @@ command line.</p></li>
<div class="section" id="module-tools">
<span id="tools"></span><h3><a class="toc-backref" href="#id15">tools</a><a class="headerlink" href="#module-tools" title="Permalink to this headline"></a></h3>
<p>This module contains a collection of diverse tasks within flex_extract.</p>
<dl class="function">
<dt id="tools.check_for_string_in_file">
<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">check_for_string_in_file</code><span class="sig-paren">(</span><em class="sig-param">filepath</em>, <em class="sig-param">search_string</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#check_for_string_in_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.check_for_string_in_file" title="Permalink to this definition"></a></dt>
<dd><p>Search for a specific string in a file and return True if
the string was found.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filepath</strong> (<em>str</em>) – The full file path which is to be examined.</p></li>
<li><p><strong>search_string</strong> (<em>str</em>) – The string which is looked up for in the file.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True : String was found
False : String was not found</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>Boolean</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="tools.clean_up">
<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">clean_up</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#clean_up"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.clean_up" title="Permalink to this definition"></a></dt>
......@@ -2735,6 +2757,21 @@ then the Python type None is returned, otherwise the string itself.</p>
</dl>
</dd></dl>
<dl class="function">
<dt id="tools.overwrite_lines_in_file">
<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">overwrite_lines_in_file</code><span class="sig-paren">(</span><em class="sig-param">filepath</em>, <em class="sig-param">search_string</em>, <em class="sig-param">sub_string</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#overwrite_lines_in_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.overwrite_lines_in_file" title="Permalink to this definition"></a></dt>
<dd><p>Overwrites lines which contain the given search string with the
substitution string.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>search_string</strong> (<em>str</em>) – The string which is looked up for in the file.</p></li>
<li><p><strong>sub_string</strong> (<em>str</em>) – The string which overwrites the search string.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="tools.product">
<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">product</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwds</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.product" title="Permalink to this definition"></a></dt>
......
Documentation/html/Documentation/Input/setup.html
+ 15
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......@@ -234,9 +234,9 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<tbody>
<tr class="row-even"><td><p>TARGET</p></td>
<td><p>String</p></td>
<td><p>local, ecgate, cca, ccb</p></td>
<td><p>local, syslocal, ecgate, cca, ccb</p></td>
<td><p>None</p></td>
<td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
<td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here. Syslocal = seperates the executables and user application files during installation. Paths are selectable through INSTALLDIR and SYSINSTALLDIR</p></td>
</tr>
<tr class="row-odd"><td><p>MAKEFILE</p></td>
<td><p>String</p></td>
......@@ -274,13 +274,19 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<td><p>$HOME on ECMWF server and current flex_extract root path on local machine</p></td>
<td><p>Root path where flex_extract should be installed. It will always be $HOME on ECMWF servers and if not set for the local mode, it will be the current flex_extract root path on local servers. </p></td>
</tr>
<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
<tr class="row-odd"><td><p>SYSINSTALLDIR</p></td>
<td><p>String</p></td>
<td><p>a full path </p></td>
<td><p>None</p></td>
<td><p>This will be the same as INSTALLDIR if TARGET=local. Otherwise, the executable files are stored in this path. If it is choosen to be in a system path, don’t forget to start the script with admin rights. </p></td>
</tr>
<tr class="row-even"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
<td><p>installscript.template</p></td>
<td><p>installscript.template</p></td>
<td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed because it is already optimised for ECMWF servers. (Remote and Gateway mode)</p></td>
</tr>
<tr class="row-even"><td><p>CONTROLFILE</p></td>
<tr class="row-odd"><td><p>CONTROLFILE</p></td>
<td><p>String</p></td>
<td><p>any CONTROL file</p></td>
<td><p>CONTROL_EA5</p></td>
......@@ -401,6 +407,7 @@ we see again all possible command line parameters.</p>
usage: install.py <span class="o">[</span>-h<span class="o">]</span> <span class="o">[</span>--target INSTALL_TARGET<span class="o">]</span> <span class="o">[</span>--makefile MAKEFILE<span class="o">]</span>
<span class="o">[</span>--ecuid ECUID<span class="o">]</span> <span class="o">[</span>--ecgid ECGID<span class="o">]</span> <span class="o">[</span>--gateway GATEWAY<span class="o">]</span>
<span class="o">[</span>--destination DESTINATION<span class="o">]</span> <span class="o">[</span>--installdir INSTALLDIR<span class="o">]</span>
<span class="o">[</span>--sysinstalldir SYSINSTALLDIR<span class="o">]</span>
<span class="o">[</span>--job_template JOB_TEMPLATE<span class="o">]</span> <span class="o">[</span>--controlfile CONTROLFILE<span class="o">]</span>
Install flex_extract software locally or on ECMWF machines
......@@ -408,7 +415,7 @@ Install flex_extract software locally or on ECMWF machines
optional arguments:
-h, --help show this <span class="nb">help</span> message and <span class="nb">exit</span>
--target INSTALL_TARGET
Valid targets: <span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two
Valid targets: syslocal <span class="p">|</span> <span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two
are at ECMWF <span class="o">(</span>default: None<span class="o">)</span>
--makefile MAKEFILE Name of makefile to compile the Fortran
code. <span class="o">(</span>default depends on <span class="sb">`</span>target<span class="sb">`</span>: <span class="nb">local</span> - makefile_local_gfortran,
......@@ -422,6 +429,9 @@ optional arguments:
--installdir INSTALLDIR
Root directory where flex_extract will be installed
to. <span class="o">(</span>default: None<span class="o">)</span>
--sysinstalldir SYSINSTALLDIR
System installation path<span class="p">;</span> where executables are
stored. <span class="o">(</span>default: None<span class="o">)</span>
--job_template JOB_TEMPLATE
The rudimentary template file to create a batch job
template <span class="k">for</span> submission to ECMWF servers. <span class="o">(</span>default:
......
Documentation/html/Installation/local.html
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......@@ -103,6 +103,7 @@
<li class="toctree-l4"><a class="reference internal" href="#preparing-the-local-environment">Preparing the local environment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#testing-the-local-environment">Testing the local environment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#local-installation">Local installation</a></li>
<li class="toctree-l4"><a class="reference internal" href="#local-system-installation">Local system installation</a></li>
</ul>
</li>
</ul>
......@@ -394,14 +395,14 @@ and then install the <code class="docutils literal notranslate"><span class="pre
<span id="ref-install-local"></span><h2>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline"></a></h2>
<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during the
installation process. A suitable makefile (<code class="docutils literal notranslate"><span class="pre">makefile_local_gfortran</span></code>) for the compilation is set by default.
This may be overwritten by the <code class="docutils literal notranslate"><span class="pre">MAKEFILE</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p>
<p>However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>
This may be overwritten by the <code class="docutils literal notranslate"><span class="pre">MAKEFILE</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code>.</p>
<p>However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code>
For details on the makefile and how to adapt them, see <a class="reference internal" href="../Documentation/Input/fortran_makefile.html#ref-convert"><span class="std std-ref">Fortran Makefile</span></a>.</p>
<p>In the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, open the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script
<p>In the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, open the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> script
with an editor and adapt the installation parameters in the section labelled with
“AVAILABLE COMMANDLINE ARGUMENTS TO SET” as shown below:</p>
<div class="literal-block-wrapper docutils container" id="setup-sh">
<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-sh" title="Permalink to this code"></a></div>
<div class="literal-block-wrapper docutils container" id="setup-local-sh">
<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-local-sh" title="Permalink to this code"></a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
<span class="c1"># -----------------------------------------------------------------</span>
<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
......@@ -415,6 +416,7 @@ with an editor and adapt the installation parameters in the section labelled wit
<span class="nv">GATEWAY</span><span class="o">=</span>None
<span class="nv">DESTINATION</span><span class="o">=</span>None
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
<span class="nv">SYSINSTALLDIR</span><span class="o">=</span>None
<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">&#39;&#39;</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">&#39;CONTROL_EA5&#39;</span>
...
......@@ -422,11 +424,11 @@ with an editor and adapt the installation parameters in the section labelled wit
</div>
</div>
<p>Afterwards, type:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup_local.sh
</pre></div>
</div>
<p>to start the installation. You should see the following standard output.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup_local.sh</span>
WARNING: installdir has not been specified
flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in &lt;path-to-flex_extract&gt;/flex_extract_v7.1/Source/Fortran
Install flex_extract_v7.1 software at <span class="nb">local</span> in directory &lt;path-to-flex_extract&gt;/flex_extract_v7.1
......@@ -445,6 +447,58 @@ lrwxrwxrwx. <span class="m">1</span> &lt;username&gt; tmc <span class="m">20</sp
</pre></div>
</div>
</div>
<div class="section" id="local-system-installation">
<h2>Local system installation<a class="headerlink" href="#local-system-installation" title="Permalink to this headline"></a></h2>
<p>There is also the possibility to separate the software executables from the user application files. For doing so, the <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> parameter can be set to “syslocal” and the additional parameter <code class="docutils literal notranslate"><span class="pre">SYSINSTALLDIR</span></code> in the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> has to be specified. This new path will contain the Fortran and Python executables of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. If you chose to set a system path for this, please start the script as root.
The user directory for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, which basically consists of everything except the <code class="docutils literal notranslate"><span class="pre">Source</span></code> directory, will be installed into <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code>.
In this installation mode, an extra (hidden) <code class="docutils literal notranslate"><span class="pre">.setup.rc</span></code> file will be generated in the <code class="docutils literal notranslate"><span class="pre">Run</span></code> directory. It contains the necessary settings for running the local system mode.</p>
<p>Despite the change in the <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> parameter, the meaning of <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code> and the additional <code class="docutils literal notranslate"><span class="pre">SYSINSTALLDIR</span></code>, the steps for installation are the same as in the local installation mentioned above. For example, modify the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> file as follows:</p>
<div class="literal-block-wrapper docutils container" id="id1">
<div class="code-block-caption"><span class="caption-text">‘Example settings for a local system installation.’</span><a class="headerlink" href="#id1" title="Permalink to this code"></a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
<span class="c1"># -----------------------------------------------------------------</span>
<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
<span class="c1">#</span>
<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
<span class="c1">#</span>
<span class="nv">TARGET</span><span class="o">=</span><span class="s1">&#39;syslocal&#39;</span>
<span class="nv">MAKEFILE</span><span class="o">=</span>&lt;name_of_your_makefile&gt;
<span class="nv">ECUID</span><span class="o">=</span>None
<span class="nv">ECGID</span><span class="o">=</span>None
<span class="nv">GATEWAY</span><span class="o">=</span>None
<span class="nv">DESTINATION</span><span class="o">=</span>None
<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="nv">$HOME</span>
<span class="nv">SYSINSTALLDIR</span><span class="o">=</span>/usr/bin/
<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">&#39;&#39;</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">&#39;CONTROL_EA5&#39;</span>
...
</pre></div>
</div>
</div>
<p>Afterwards, type:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo ./setup_local.sh
</pre></div>
</div>
<p>to start the installation. You should see the following standard output.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>Flex_extract will be installed in &lt;<span class="nv">$HOME</span>&gt;
Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
Using makefile: makefile_local_gfortran
/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./rwgrib2.f90
/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./phgrreal.f90
/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./grphreal.f90
/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./ftrafo.f90
/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./calc_etadot.f90
/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./posnam.f90
/usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp
ln -sf calc_etadot_fast.out calc_etadot
lrwxrwxrwx. <span class="m">1</span> &lt;username&gt; tmc <span class="m">20</span> <span class="m">27</span>. Okt <span class="m">23</span>:25 ./calc_etadot -&gt; calc_etadot_fast.out
SUCCESS: INSTALLATION FINISHED!
</pre></div>
</div>
<p>You can now change into the user directory specified in <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code> and find a <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code> directory there.</p>
</div>
</div>
......
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......@@ -182,6 +182,8 @@
<span class="c1"># - outsourced the commandline argument assignments to control attributes</span>
<span class="c1"># June 2020 - Anne Philipp</span>
<span class="c1"># - update default makefile to None</span>
<span class="c1"># August 2020 - Leopold Haimberger</span>
<span class="c1"># - added a class parameter for system installation path</span>
<span class="c1">#</span>
<span class="c1"># @License:</span>
<span class="c1"># (C) Copyright 2014-2020.</span>
......@@ -565,6 +567,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">flexextractdir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span>
<span class="bp">self</span><span class="o">.</span><span class="n">exedir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span>
<span class="bp">self</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makefile</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">destination</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">gateway</span> <span class="o">=</span> <span class="kc">None</span>
......
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......@@ -275,7 +275,7 @@
<span class="c1"># send files to ECMWF server</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">submit</span><span class="p">(</span><span class="n">job_template</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">queue</span><span class="p">)</span>
<span class="n">exit_message</span> <span class="o">=</span> <span class="s1">&#39;FLEX_EXTRACT JOB SCRIPT IS SUBMITED!&#39;</span>
<span class="n">exit_message</span> <span class="o">=</span> <span class="s1">&#39;FLEX_EXTRACT JOB SCRIPT IS SUBMITTED!&#39;</span>
<span class="n">normal_exit</span><span class="p">(</span><span class="n">exit_message</span><span class="p">)</span>
......
Documentation/html/_modules/tools.html
+ 64
− 4
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......@@ -184,6 +184,10 @@
<span class="c1"># put_file_to_ecserver, submit_job_to_ecserver, get_informations,</span>
<span class="c1"># get_dimensions, execute_subprocess, none_or_int, none_or_str</span>
<span class="c1">#</span>
<span class="c1"># August 2020 - Leopold Haimberger (University of Vienna)</span>
<span class="c1"># - added function to check if a specific string is in a file</span>
<span class="c1"># - added function to overwrite lines in a file which contain specific string</span>
<span class="c1">#</span>
<span class="c1"># @License:</span>
<span class="c1"># (C) Copyright 2014-2020.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
......@@ -1071,6 +1075,62 @@
<span class="k">return</span> <span class="n">start_period</span><span class="p">,</span> <span class="n">end_period</span></div>
<div class="viewcode-block" id="check_for_string_in_file"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.check_for_string_in_file">[docs]</a><span class="k">def</span> <span class="nf">check_for_string_in_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">search_string</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Search for a specific string in a file and return True if</span>
<span class="sd"> the string was found.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> filepath : str</span>
<span class="sd"> The full file path which is to be examined.</span>
<span class="sd"> search_string : str</span>
<span class="sd"> The string which is looked up for in the file.</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
<span class="sd"> Boolean :</span>
<span class="sd"> True : String was found</span>
<span class="sd"> False : String was not found</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fio</span><span class="p">:</span>
<span class="k">if</span> <span class="n">search_string</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">True</span>
<span class="k">return</span> <span class="kc">False</span></div>
<div class="viewcode-block" id="overwrite_lines_in_file"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.overwrite_lines_in_file">[docs]</a><span class="k">def</span> <span class="nf">overwrite_lines_in_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">search_string</span><span class="p">,</span> <span class="n">sub_string</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Overwrites lines which contain the given search string with the</span>
<span class="sd"> substitution string.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> search_string : str</span>
<span class="sd"> The string which is looked up for in the file.</span>
<span class="sd"> sub_string : str</span>
<span class="sd"> The string which overwrites the search string.</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">fio</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
<span class="k">if</span> <span class="n">search_string</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">sub_string</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
<span class="k">return</span></div>
</pre></div>
</div>
......
Documentation/html/_sources/Documentation/Input/setup.rst.txt
+ 6
− 1
View file @ 81c180c9
......@@ -164,6 +164,7 @@ we see again all possible command line parameters.
usage: install.py [-h] [--target INSTALL_TARGET] [--makefile MAKEFILE]
[--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY]
[--destination DESTINATION] [--installdir INSTALLDIR]
[--sysinstalldir SYSINSTALLDIR]
[--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE]
Install flex_extract software locally or on ECMWF machines
......@@ -171,7 +172,7 @@ we see again all possible command line parameters.
optional arguments:
-h, --help show this help message and exit
--target INSTALL_TARGET
Valid targets: local | ecgate | cca , the latter two
Valid targets: syslocal | local | ecgate | cca , the latter two
are at ECMWF (default: None)
--makefile MAKEFILE Name of makefile to compile the Fortran
code. (default depends on `target`: local - makefile_local_gfortran,
......@@ -185,6 +186,9 @@ we see again all possible command line parameters.
--installdir INSTALLDIR
Root directory where flex_extract will be installed
to. (default: None)
--sysinstalldir SYSINSTALLDIR
System installation path; where executables are
stored. (default: None)
--job_template JOB_TEMPLATE
The rudimentary template file to create a batch job
template for submission to ECMWF servers. (default:
......@@ -197,6 +201,7 @@ we see again all possible command line parameters.
.. toctree::
:hidden:
:maxdepth: 2
Documentation/html/_sources/Installation/local.rst.txt
+ 69
− 6
View file @ 81c180c9
......@@ -265,20 +265,20 @@ Local installation
The Fortran program called ``calc_etadot`` will be compiled during the
installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default.
This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``.
This may be overwritten by the ``MAKEFILE`` parameter in ``setup_local.sh``.
However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh``
However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup_local.sh``
For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`.
In the root directory of ``flex_extract``, open the ``setup.sh`` script
In the root directory of ``flex_extract``, open the ``setup_local.sh`` script
with an editor and adapt the installation parameters in the section labelled with
"AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:
.. code-block:: bash
:caption: 'Example settings for a local installation.'
:name: setup.sh
:name: setup_local.sh
...
# -----------------------------------------------------------------
......@@ -293,6 +293,7 @@ with an editor and adapt the installation parameters in the section labelled wit
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
SYSINSTALLDIR=None
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
......@@ -302,14 +303,14 @@ Afterwards, type:
.. code-block:: bash
$ ./setup.sh
$ ./setup_local.sh
to start the installation. You should see the following standard output.
.. code-block:: bash
# Output of setup.sh
# Output of setup_local.sh
WARNING: installdir has not been specified
flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1
......@@ -326,3 +327,65 @@ to start the installation. You should see the following standard output.
lrwxrwxrwx. 1 <username> tmc 20 Aug 12 10:59 ./calc_etadot -> calc_etadot_fast.out
Local system installation
=========================
There is also the possibility to separate the software executables from the user application files. For doing so, the ``TARGET`` parameter can be set to "syslocal" and the additional parameter ``SYSINSTALLDIR`` in the ``setup_local.sh`` has to be specified. This new path will contain the Fortran and Python executables of ``flex_extract``. If you chose to set a system path for this, please start the script as root.
The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.
In this installation mode, an extra (hidden) ``.setup.rc`` file will be generated in the ``Run`` directory. It contains the necessary settings for running the local system mode.
Despite the change in the ``TARGET`` parameter, the meaning of ``INSTALLDIR`` and the additional ``SYSINSTALLDIR``, the steps for installation are the same as in the local installation mentioned above. For example, modify the ``setup_local.sh`` file as follows:
.. code-block:: bash
:caption: 'Example settings for a local system installation.'
:name: setup_local.sh
...
# -----------------------------------------------------------------
# AVAILABLE COMMANDLINE ARGUMENTS TO SET
#
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='syslocal'
MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=$HOME
SYSINSTALLDIR=/usr/bin/
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
Afterwards, type:
.. code-block:: bash
$ sudo ./setup_local.sh
to start the installation. You should see the following standard output.
.. code-block:: bash
Flex_extract will be installed in <$HOME>
Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
Using makefile: makefile_local_gfortran
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90
/usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp
ln -sf calc_etadot_fast.out calc_etadot
lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out
SUCCESS: INSTALLATION FINISHED!
You can now change into the user directory specified in ``INSTALLDIR`` and find a ``flex_extract_vX.X`` directory there.
Documentation/html/genindex.html
+ 6
− 2
View file @ 81c180c9
......@@ -272,6 +272,8 @@
<li><a href="Documentation/Api/api_python.html#checks.check_dates">check_dates() (in module checks)</a>
</li>
<li><a href="Documentation/Api/api_python.html#get_mars_data.check_dates_for_nonflux_fc_times">check_dates_for_nonflux_fc_times() (in module get_mars_data)</a>
</li>
<li><a href="Documentation/Api/api_python.html#tools.check_for_string_in_file">check_for_string_in_file() (in module tools)</a>
</li>
<li><a href="Documentation/Api/api_python.html#checks.check_grid">check_grid() (in module checks)</a>
</li>
......@@ -649,13 +651,15 @@
</li>
<li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.omegadiff">omegadiff (ControlFile.ControlFile attribute)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.oper">oper (ControlFile.ControlFile attribute)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.outputdir">outputdir (ControlFile.ControlFile attribute)</a>
</li>
<li><a href="Documentation/Api/api_python.html#EcFlexpart.EcFlexpart.outputfilelist">outputfilelist (EcFlexpart.EcFlexpart attribute)</a>
</li>
<li><a href="Documentation/Api/api_python.html#tools.overwrite_lines_in_file">overwrite_lines_in_file() (in module tools)</a>
</li>
</ul></td>
</tr></table>
......
Documentation/html/objects.inv
+ 0
− 0
View file @ 81c180c9
No preview for this file type
Documentation/html/searchindex.js
+ 1
− 1
View file @ 81c180c9
This diff is collapsed.
For_developers/InstallationParameter.xls
+ 0
− 0
View file @ 81c180c9
No preview for this file type
For_developers/Sphinx/Source/Documentation/Input/setup.rst
+ 6
− 1
View file @ 81c180c9
......@@ -164,6 +164,7 @@ we see again all possible command line parameters.
usage: install.py [-h] [--target INSTALL_TARGET] [--makefile MAKEFILE]
[--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY]
[--destination DESTINATION] [--installdir INSTALLDIR]
[--sysinstalldir SYSINSTALLDIR]
[--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE]
Install flex_extract software locally or on ECMWF machines
......@@ -171,7 +172,7 @@ we see again all possible command line parameters.
optional arguments:
-h, --help show this help message and exit
--target INSTALL_TARGET
Valid targets: local | ecgate | cca , the latter two
Valid targets: syslocal | local | ecgate | cca , the latter two
are at ECMWF (default: None)
--makefile MAKEFILE Name of makefile to compile the Fortran
code. (default depends on `target`: local - makefile_local_gfortran,
......@@ -185,6 +186,9 @@ we see again all possible command line parameters.
--installdir INSTALLDIR
Root directory where flex_extract will be installed
to. (default: None)
--sysinstalldir SYSINSTALLDIR
System installation path; where executables are
stored. (default: None)
--job_template JOB_TEMPLATE
The rudimentary template file to create a batch job
template for submission to ECMWF servers. (default:
......@@ -197,6 +201,7 @@ we see again all possible command line parameters.
.. toctree::
:hidden:
:maxdepth: 2
For_developers/Sphinx/Source/Installation/local.rst
+ 69
− 6
View file @ 81c180c9
......@@ -265,20 +265,20 @@ Local installation
The Fortran program called ``calc_etadot`` will be compiled during the
installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default.
This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``.
This may be overwritten by the ``MAKEFILE`` parameter in ``setup_local.sh``.
However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh``
However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup_local.sh``
For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`.
In the root directory of ``flex_extract``, open the ``setup.sh`` script
In the root directory of ``flex_extract``, open the ``setup_local.sh`` script
with an editor and adapt the installation parameters in the section labelled with
"AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:
.. code-block:: bash
:caption: 'Example settings for a local installation.'
:name: setup.sh
:name: setup_local.sh
...
# -----------------------------------------------------------------
......@@ -293,6 +293,7 @@ with an editor and adapt the installation parameters in the section labelled wit
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
SYSINSTALLDIR=None
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
......@@ -302,14 +303,14 @@ Afterwards, type:
.. code-block:: bash
$ ./setup.sh
$ ./setup_local.sh
to start the installation. You should see the following standard output.
.. code-block:: bash
# Output of setup.sh
# Output of setup_local.sh
WARNING: installdir has not been specified
flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1
......@@ -326,3 +327,65 @@ to start the installation. You should see the following standard output.
lrwxrwxrwx. 1 <username> tmc 20 Aug 12 10:59 ./calc_etadot -> calc_etadot_fast.out
Local system installation
=========================
There is also the possibility to separate the software executables from the user application files. For doing so, the ``TARGET`` parameter can be set to "syslocal" and the additional parameter ``SYSINSTALLDIR`` in the ``setup_local.sh`` has to be specified. This new path will contain the Fortran and Python executables of ``flex_extract``. If you chose to set a system path for this, please start the script as root.
The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.
In this installation mode, an extra (hidden) ``.setup.rc`` file will be generated in the ``Run`` directory. It contains the necessary settings for running the local system mode.
Despite the change in the ``TARGET`` parameter, the meaning of ``INSTALLDIR`` and the additional ``SYSINSTALLDIR``, the steps for installation are the same as in the local installation mentioned above. For example, modify the ``setup_local.sh`` file as follows:
.. code-block:: bash
:caption: 'Example settings for a local system installation.'
:name: setup_local.sh
...
# -----------------------------------------------------------------
# AVAILABLE COMMANDLINE ARGUMENTS TO SET
#
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='syslocal'
MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=$HOME
SYSINSTALLDIR=/usr/bin/
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
Afterwards, type:
.. code-block:: bash
$ sudo ./setup_local.sh
to start the installation. You should see the following standard output.
.. code-block:: bash
Flex_extract will be installed in <$HOME>
Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
Using makefile: makefile_local_gfortran
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90
/usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90
/usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp
ln -sf calc_etadot_fast.out calc_etadot
lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out
SUCCESS: INSTALLATION FINISHED!
You can now change into the user directory specified in ``INSTALLDIR`` and find a ``flex_extract_vX.X`` directory there.
README.md
+ 4
− 3
View file @ 81c180c9
......@@ -2,7 +2,7 @@
`flex_extract` is a software package to support retrieving meteorological fields from the European Centre for Medium-Range Weather Forecasts' (ECMWF) Meteorological Archival and Retrieval System (MARS) as input for the `FLEXTRA`/`FLEXPART` Atmospheric Transport Modelling system.
`FLEXPART` (“FLEXible PARTicle dispersion model”, http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.
`FLEXPART` ("FLEXible PARTicle dispersion model", http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.
## Installation and Usage
......@@ -16,10 +16,10 @@ https://www.flexpart.eu/wiki/FpInputMetEcmwf
## Authors
Anne Philipp, Leopold Haimberger and Petra Seibert
Anne Tipka (formerly Philipp), Leopold Haimberger and Petra Seibert
## License
(C) Copyright 2014-2019.
(C) Copyright 2014-2020.
SPDX-License-Identifier: CC-BY-4.0
......@@ -27,3 +27,4 @@ Anne Philipp, Leopold Haimberger and Petra Seibert
International License. To view a copy of this license, visit
http://creativecommons.org/licenses/by/4.0/ or send a letter to
Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
Run/run_local.sh
+ 1
− 1
View file @ 81c180c9
......@@ -11,7 +11,7 @@
# guarantee necessary parameters were set and consistent.
#
# @Licence:
# (C) Copyright 2014-2019.
# (C) Copyright 2014-2020.
#
# SPDX-License-Identifier: CC-BY-4.0
#
......
Source/Python/Classes/ControlFile.py
+ 3
− 0
View file @ 81c180c9
......@@ -20,6 +20,8 @@
# - outsourced the commandline argument assignments to control attributes
# June 2020 - Anne Philipp
# - update default makefile to None
# August 2020 - Leopold Haimberger
# - added a class parameter for system installation path
#
# @License:
# (C) Copyright 2014-2020.
......@@ -403,6 +405,7 @@ class ControlFile(object):
self.flexextractdir = _config.PATH_FLEXEXTRACT_DIR
self.exedir = _config.PATH_FORTRAN_SRC
self.installdir = None
self.sysinstalldir = None
self.makefile = None
self.destination = None
self.gateway = None
......
Source/Python/Mods/tools.py
+ 64
− 4
View file @ 81c180c9
......@@ -22,6 +22,10 @@
# put_file_to_ecserver, submit_job_to_ecserver, get_informations,
# get_dimensions, execute_subprocess, none_or_int, none_or_str
#
# August 2020 - Leopold Haimberger (University of Vienna)
# - added function to check if a specific string is in a file
# - added function to overwrite lines in a file which contain specific string
#
# @License:
# (C) Copyright 2014-2020.
# Anne Philipp, Leopold Haimberger
......@@ -909,3 +913,59 @@ def generate_retrieval_period_boundary(c):
return start_period, end_period
def check_for_string_in_file(filepath, search_string):
"""
Search for a specific string in a file and return True if
the string was found.
Parameters
----------
filepath : str
The full file path which is to be examined.
search_string : str
The string which is looked up for in the file.
Return
------
Boolean :
True : String was found
False : String was not found
"""
with open(filepath, 'r') as fio:
for line in fio:
if search_string in line:
return True
return False
def overwrite_lines_in_file(filepath, search_string, sub_string):
"""
Overwrites lines which contain the given search string with the
substitution string.
Parameters
----------
search_string : str
The string which is looked up for in the file.
sub_string : str
The string which overwrites the search string.
Return
------
"""
with open(filepath, 'r') as fio:
data = fio.readlines()
with open(filepath, 'w') as fio:
for line in data:
if search_string in line:
fio.write(sub_string)
else:
fio.write(line)
return
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