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<h1>Source code for dgenies</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">flask</span> <span class="k">import</span> <span class="n">Flask</span>
<span class="kn">from</span> <span class="nn">.config_reader</span> <span class="k">import</span> <span class="n">AppConfigReader</span>
<span class="kn">from</span> <span class="nn">.lib.crons</span> <span class="k">import</span> <span class="n">Crons</span>
<span class="n">VERSION</span> <span class="o">=</span> <span class="s2">&quot;1.0.1&quot;</span>
<span class="n">app</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">app_title</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">APP_DATA</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">config_reader</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">mailer</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">app_folder</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">MODE</span> <span class="o">=</span> <span class="s2">&quot;webserver&quot;</span>
<span class="n">DEBUG</span> <span class="o">=</span> <span class="kc">False</span>
<div class="viewcode-block" id="launch"><a class="viewcode-back" href="../dgenies.html#dgenies.launch">[docs]</a><span class="k">def</span> <span class="nf">launch</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s2">&quot;webserver&quot;</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">global</span> <span class="n">app</span><span class="p">,</span> <span class="n">app_title</span><span class="p">,</span> <span class="n">app_folder</span><span class="p">,</span> <span class="n">APP_DATA</span><span class="p">,</span> <span class="n">config_reader</span><span class="p">,</span> <span class="n">mailer</span><span class="p">,</span> <span class="n">MODE</span><span class="p">,</span> <span class="n">DEBUG</span>
<span class="n">app_folder</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">dirname</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">realpath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span>
<span class="n">MODE</span> <span class="o">=</span> <span class="n">mode</span>
<span class="n">DEBUG</span> <span class="o">=</span> <span class="n">debug</span>
<span class="c1"># Init config reader:</span>
<span class="n">config_reader</span> <span class="o">=</span> <span class="n">AppConfigReader</span><span class="p">()</span>
<span class="n">UPLOAD_FOLDER</span> <span class="o">=</span> <span class="n">config_reader</span><span class="o">.</span><span class="n">upload_folder</span>
<span class="n">APP_DATA</span> <span class="o">=</span> <span class="n">config_reader</span><span class="o">.</span><span class="n">app_data</span>
<span class="n">app_title</span> <span class="o">=</span> <span class="s2">&quot;D-GENIES - Dotplot large Genomes in an Interactive, Efficient and Simple way&quot;</span>
<span class="c1"># Init Flask:</span>
<span class="n">app</span> <span class="o">=</span> <span class="n">Flask</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">static_url_path</span><span class="o">=</span><span class="s1">&#39;/static&#39;</span><span class="p">)</span>
<span class="n">app</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;UPLOAD_FOLDER&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">UPLOAD_FOLDER</span>
<span class="n">app</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;MAX_CONTENT_LENGTH&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">config_reader</span><span class="o">.</span><span class="n">max_upload_file_size</span>
<span class="n">app</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;SECRET_KEY&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;dsqdsq-255sdA-fHfg52-25Asd5&#39;</span>
<span class="c1"># Init mail:</span>
<span class="k">if</span> <span class="n">MODE</span> <span class="o">==</span> <span class="s2">&quot;webserver&quot;</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">.lib.mailer</span> <span class="k">import</span> <span class="n">Mailer</span>
<span class="n">mailer</span> <span class="o">=</span> <span class="n">Mailer</span><span class="p">(</span><span class="n">app</span><span class="p">)</span>
<span class="c1"># Create data dir if not exists</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">config_reader</span><span class="o">.</span><span class="n">app_data</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">config_reader</span><span class="o">.</span><span class="n">app_data</span><span class="p">)</span>
<span class="k">if</span> <span class="n">config_reader</span><span class="o">.</span><span class="n">debug</span> <span class="ow">and</span> <span class="n">config_reader</span><span class="o">.</span><span class="n">log_dir</span> <span class="o">!=</span> <span class="s2">&quot;stdout&quot;</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">config_reader</span><span class="o">.</span><span class="n">log_dir</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">config_reader</span><span class="o">.</span><span class="n">log_dir</span><span class="p">)</span>
<span class="c1"># Crons:</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s1">&#39;DISABLE_CRONS&#39;</span><span class="p">)</span> <span class="o">!=</span> <span class="s2">&quot;True&quot;</span> <span class="ow">and</span> <span class="n">MODE</span> <span class="o">==</span> <span class="s2">&quot;webserver&quot;</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Starting crons...&quot;</span><span class="p">)</span>
<span class="n">crons</span> <span class="o">=</span> <span class="n">Crons</span><span class="p">(</span><span class="n">app_folder</span><span class="p">,</span> <span class="n">config_reader</span><span class="o">.</span><span class="n">debug</span> <span class="ow">or</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s1">&#39;LOGS&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="s2">&quot;True&quot;</span><span class="p">)</span>
<span class="n">crons</span><span class="o">.</span><span class="n">start_all</span><span class="p">()</span>
<span class="kn">from</span> <span class="nn">dgenies</span> <span class="k">import</span> <span class="n">views</span>
<span class="k">return</span> <span class="n">app</span></div>
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<h1>Source code for dgenies.lib.crons</h1><div class="highlight"><pre>
<span></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">re</span>
<span class="kn">import</span> <span class="nn">getpass</span>
<span class="kn">import</span> <span class="nn">psutil</span>
<span class="kn">from</span> <span class="nn">crontab</span> <span class="k">import</span> <span class="n">CronTab</span>
<span class="kn">from</span> <span class="nn">dgenies.config_reader</span> <span class="k">import</span> <span class="n">AppConfigReader</span>
<div class="viewcode-block" id="Crons"><a class="viewcode-back" href="../../../dgenies.lib.html#dgenies.lib.crons.Crons">[docs]</a><span class="k">class</span> <span class="nc">Crons</span><span class="p">:</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">base_dir</span><span class="p">,</span> <span class="n">debug</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">base_dir</span> <span class="o">=</span> <span class="n">base_dir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">debug</span> <span class="o">=</span> <span class="n">debug</span>
<span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span> <span class="o">=</span> <span class="n">CronTab</span><span class="p">(</span><span class="n">user</span><span class="o">=</span><span class="n">getpass</span><span class="o">.</span><span class="n">getuser</span><span class="p">())</span>
<span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">AppConfigReader</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">local_scheduler_pid_file</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">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">config_dir</span><span class="p">,</span> <span class="s2">&quot;.local_scheduler_pid&quot;</span><span class="p">)</span>
<div class="viewcode-block" id="Crons.clear"><a class="viewcode-back" href="../../../dgenies.lib.html#dgenies.lib.crons.Crons.clear">[docs]</a> <span class="k">def</span> <span class="nf">clear</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">kill_scheduler</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="c1"># Remove old crons:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span><span class="o">.</span><span class="n">remove_all</span><span class="p">(</span><span class="n">comment</span><span class="o">=</span><span class="s2">&quot;dgenies&quot;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span><span class="o">.</span><span class="n">write</span><span class="p">()</span>
<span class="k">if</span> <span class="n">kill_scheduler</span><span class="p">:</span>
<span class="c1"># Kill local scheduler:</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">local_scheduler_pid_file</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">local_scheduler_pid_file</span><span class="p">)</span> <span class="k">as</span> <span class="n">p_f</span><span class="p">:</span>
<span class="n">pid</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">p_f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">))</span>
<span class="k">if</span> <span class="n">psutil</span><span class="o">.</span><span class="n">pid_exists</span><span class="p">(</span><span class="n">pid</span><span class="p">):</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">psutil</span><span class="o">.</span><span class="n">Process</span><span class="p">(</span><span class="n">pid</span><span class="p">)</span>
<span class="n">p</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span></div>
<div class="viewcode-block" id="Crons.start_all"><a class="viewcode-back" href="../../../dgenies.lib.html#dgenies.lib.crons.Crons.start_all">[docs]</a> <span class="k">def</span> <span class="nf">start_all</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">clear</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">init_clean_cron</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">init_launch_local_cron</span><span class="p">()</span></div>
<span class="nd">@staticmethod</span>
<span class="k">def</span> <span class="nf">_get_python_exec</span><span class="p">():</span>
<span class="n">pyexec</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">executable</span>
<span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;^(.+)/lib/(python[^/]+)/((site-packages/bin/python)|())$&quot;</span><span class="p">,</span> <span class="n">pyexec</span><span class="p">)</span>
<span class="k">if</span> <span class="n">match</span><span class="p">:</span>
<span class="n">pyexec</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%s</span><span class="s2">/bin/</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">2</span><span class="p">))</span>
<span class="k">return</span> <span class="n">pyexec</span>
<div class="viewcode-block" id="Crons.init_clean_cron"><a class="viewcode-back" href="../../../dgenies.lib.html#dgenies.lib.crons.Crons.init_clean_cron">[docs]</a> <span class="k">def</span> <span class="nf">init_clean_cron</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Clean cron is launched at 1h00am each day</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">clean_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">cron_clean_time</span>
<span class="n">clean_freq</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">cron_clean_freq</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">base_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">job</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span><span class="o">.</span><span class="n">new</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_get_python_exec</span><span class="p">()</span> <span class="o">+</span>
<span class="s2">&quot; </span><span class="si">{0}</span><span class="s2">/bin/clean_jobs.py &gt; </span><span class="si">{1}</span><span class="s2">/clean.log 2&gt;&amp;1&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">base_dir</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">log_dir</span><span class="p">),</span>
<span class="n">comment</span><span class="o">=</span><span class="s2">&quot;dgenies&quot;</span><span class="p">)</span>
<span class="n">job</span><span class="o">.</span><span class="n">day</span><span class="o">.</span><span class="n">every</span><span class="p">(</span><span class="n">clean_freq</span><span class="p">)</span>
<span class="n">job</span><span class="o">.</span><span class="n">hour</span><span class="o">.</span><span class="n">on</span><span class="p">(</span><span class="n">clean_time</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">job</span><span class="o">.</span><span class="n">minute</span><span class="o">.</span><span class="n">on</span><span class="p">(</span><span class="n">clean_time</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span><span class="o">.</span><span class="n">write</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Crons: base_dir must not be None&quot;</span><span class="p">)</span></div>
<div class="viewcode-block" id="Crons.init_launch_local_cron"><a class="viewcode-back" href="../../../dgenies.lib.html#dgenies.lib.crons.Crons.init_launch_local_cron">[docs]</a> <span class="k">def</span> <span class="nf">init_launch_local_cron</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Try to launch local scheduler (if not already launched)</span>
<span class="sd"> :return:</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">base_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">pyexec</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_python_exec</span><span class="p">()</span>
<span class="n">logs</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">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">log_dir</span><span class="p">,</span> <span class="s2">&quot;local_scheduler.log&quot;</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">debug</span> <span class="k">else</span> <span class="s2">&quot;/dev/null&quot;</span>
<span class="n">job</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span><span class="o">.</span><span class="n">new</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{0}</span><span class="s2">/bin/start_local_scheduler.sh </span><span class="si">{0}</span><span class="s2"> </span><span class="si">{1}</span><span class="s2"> </span><span class="si">{2}</span><span class="s2"> </span><span class="si">{3}</span><span class="s2"> &gt; /dev/null 2&gt;&amp;1 &amp;&quot;</span><span class="o">.</span>
<span class="nb">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">base_dir</span><span class="p">,</span> <span class="n">pyexec</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">local_scheduler_pid_file</span><span class="p">,</span> <span class="n">logs</span><span class="p">),</span>
<span class="n">comment</span><span class="o">=</span><span class="s2">&quot;dgenies&quot;</span><span class="p">)</span>
<span class="n">job</span><span class="o">.</span><span class="n">minute</span><span class="o">.</span><span class="n">every</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">my_cron</span><span class="o">.</span><span class="n">write</span><span class="p">()</span></div></div>
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