deploy: f803ba7

Author: TorecLuik

.doctrees/biomero.doctree

@@ -215,17 +215,22 @@ <h1>Source code for biomero.views</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="JobAccounting.update_view_table"><a class="viewcode-back" href="../../biomero.html#biomero.views.JobAccounting.update_view_table">[docs]</a>    <span class="nd">@retry_on_database_conflict</span><span class="p">(</span><span class="n">max_retries</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
     <span class="k">def</span><span class="w"> </span><span class="nf">update_view_table</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_id</span><span class="p">,</span> <span class="n">user</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">task_id</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Update the view table with new job information.&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Update the view table with new job information.</span>
+
+<span class="sd">        Uses merge (upsert) so that if SLURM recycles a job ID the new</span>
+<span class="sd">        task_id/user/group overwrites the stale row instead of silently</span>
+<span class="sd">        failing and leaving the old mapping in place.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">with</span> <span class="n">EngineManager</span><span class="o">.</span><span class="n">get_session</span><span class="p">()</span> <span class="k">as</span> <span class="n">session</span><span class="p">:</span>
             <span class="k">try</span><span class="p">:</span>
                 <span class="n">new_job</span> <span class="o">=</span> <span class="n">JobView</span><span class="p">(</span><span class="n">slurm_job_id</span><span class="o">=</span><span class="n">job_id</span><span class="p">,</span> <span class="n">user</span><span class="o">=</span><span class="n">user</span><span class="p">,</span> <span class="n">group</span><span class="o">=</span><span class="n">group</span><span class="p">,</span> <span class="n">task_id</span><span class="o">=</span><span class="n">task_id</span><span class="p">)</span>
-                <span class="n">session</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">new_job</span><span class="p">)</span>
+                <span class="n">session</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">new_job</span><span class="p">)</span>
                 <span class="n">session</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
-                <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Inserted job into view table: job_id=</span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2">, user=</span><span class="si">{</span><span class="n">user</span><span class="si">}</span><span class="s2">, group=</span><span class="si">{</span><span class="n">group</span><span class="si">}</span><span class="s2">, task_id=</span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+                <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Upserted job into view table: job_id=</span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2">, user=</span><span class="si">{</span><span class="n">user</span><span class="si">}</span><span class="s2">, group=</span><span class="si">{</span><span class="n">group</span><span class="si">}</span><span class="s2">, task_id=</span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
             <span class="k">except</span> <span class="n">IntegrityError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
                 <span class="n">session</span><span class="o">.</span><span class="n">rollback</span><span class="p">()</span>
-                <span class="c1"># Handle the case where the job already exists in the table if necessary</span>
-                <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Database conflict inserting job (will retry): job_id=</span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2">, user=</span><span class="si">{</span><span class="n">user</span><span class="si">}</span><span class="s2">, group=</span><span class="si">{</span><span class="n">group</span><span class="si">}</span><span class="s2">, error=</span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></div>
+                <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Database conflict upserting job (will retry): job_id=</span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2">, user=</span><span class="si">{</span><span class="n">user</span><span class="si">}</span><span class="s2">, group=</span><span class="si">{</span><span class="n">group</span><span class="si">}</span><span class="s2">, error=</span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+                <span class="k">raise</span></div>
 
 <div class="viewcode-block" id="JobAccounting.get_jobs"><a class="viewcode-back" href="../../biomero.html#biomero.views.JobAccounting.get_jobs">[docs]</a>    <span class="k">def</span><span class="w"> </span><span class="nf">get_jobs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">user</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">group</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Retrieve jobs for a specific user and/or group.</span>

.doctrees/environment.pickle

@@ -2358,6 +2358,9 @@ <h1>biomero package<a class="headerlink" href="#biomero-package" title="Permalin
 <dt class="sig sig-object py" id="biomero.views.JobAccounting.update_view_table">
 <span class="sig-name descname"><span class="pre">update_view_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">job_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">user</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">group</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">task_id</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/biomero/views.html#JobAccounting.update_view_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biomero.views.JobAccounting.update_view_table" title="Permalink to this definition"></a></dt>
 <dd><p>Update the view table with new job information.</p>
+<p>Uses merge (upsert) so that if SLURM recycles a job ID the new
+task_id/user/group overwrites the stale row instead of silently
+failing and leaving the old mapping in place.</p>
 </dd></dl>
 
 </dd></dl>