deploy: abe5302

_modules/biomero/slurm_client.html

@@ -336,7 +336,7 @@ <h1>Source code for biomero.slurm_client</h1><div class="highlight"><pre>
     <span class="n">_DEFAULT_SLURM_GIT_SCRIPT_PATH</span> <span class="o">=</span> <span class="s2">&quot;slurm-scripts&quot;</span>
     <span class="n">_OUT_SEP</span> <span class="o">=</span> <span class="s2">&quot;--split--&quot;</span>
     <span class="n">_VERSION_CMD</span> <span class="o">=</span> <span class="s2">&quot;ls -h </span><span class="se">\&quot;</span><span class="si">{slurm_images_path}</span><span class="s2">/</span><span class="si">{image_path}</span><span class="se">\&quot;</span><span class="s2"> | grep -oP &#39;(?&lt;=\-|\_)(v.+|latest)(?=.simg|.sif)&#39;&quot;</span>
-    <span class="n">_CONVERTER_VERSION_CMD</span> <span class="o">=</span> <span class="s2">&quot;ls -h </span><span class="se">\&quot;</span><span class="si">{converter_path}</span><span class="se">\&quot;</span><span class="s2"> | grep -oP &#39;(convert_.+)(?=.simg|.sif)&#39; | awk &#39;{n=split($0, a, </span><span class="se">\&quot;</span><span class="s2">_</span><span class="se">\&quot;</span><span class="s2">); last=a[n]; sub(</span><span class="se">\&quot;</span><span class="s2">_</span><span class="se">\&quot;</span><span class="s2">last</span><span class="se">\&quot;</span><span class="s2">$</span><span class="se">\&quot;</span><span class="s2">, </span><span class="se">\&quot;\&quot;</span><span class="s2">, $0); print $0, last}&#39;&quot;</span>
+    <span class="n">_CONVERTER_VERSION_CMD</span> <span class="o">=</span> <span class="s2">&quot;ls -h </span><span class="se">\&quot;</span><span class="si">{converter_path}</span><span class="se">\&quot;</span><span class="s2"> | grep -oP &#39;(convert_.+)(?=.simg|.sif)&#39; | awk &#39;{{n=split($0, a, </span><span class="se">\&quot;</span><span class="s2">_</span><span class="se">\&quot;</span><span class="s2">); last=a[n]; sub(</span><span class="se">\&quot;</span><span class="s2">_</span><span class="se">\&quot;</span><span class="s2">last</span><span class="se">\&quot;</span><span class="s2">$</span><span class="se">\&quot;</span><span class="s2">, </span><span class="se">\&quot;\&quot;</span><span class="s2">, $0); print $0, last}}&#39;&quot;</span>
     <span class="c1"># Note, grep returns exitcode 1 if no match is found!</span>
     <span class="c1"># This will translate into a UnexpectedExit error, so mute that if you</span>
     <span class="c1"># don&#39;t care about empty.</span>
@@ -598,8 +598,10 @@ <h1>Source code for biomero.slurm_client</h1><div class="highlight"><pre>
         <span class="n">cmd</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_CONVERTER_VERSION_CMD</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
             <span class="n">converter_path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">slurm_converters_path</span><span class="p">),</span>
         <span class="n">r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">run_commands</span><span class="p">([</span><span class="n">cmd</span><span class="p">])</span>
-        <span class="c1"># split lines further into a k,v dict</span>
-        <span class="n">result_dict</span> <span class="o">=</span> <span class="p">{</span><span class="n">line</span><span class="o">.</span><span class="n">rsplit</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]:</span> <span class="n">line</span><span class="o">.</span><span class="n">rsplit</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">r</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)}</span>
+        <span class="n">result_dict</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">ok</span><span class="p">:</span>
+            <span class="c1"># split lines further into a k,v dict</span>
+            <span class="n">result_dict</span> <span class="o">=</span> <span class="p">{</span><span class="n">line</span><span class="o">.</span><span class="n">rsplit</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]:</span> <span class="n">line</span><span class="o">.</span><span class="n">rsplit</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">r</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)}</span>
         <span class="k">return</span> <span class="n">result_dict</span></div>
 
 <div class="viewcode-block" id="SlurmClient.setup_converters"><a class="viewcode-back" href="../../biomero.html#biomero.slurm_client.SlurmClient.setup_converters">[docs]</a>    <span class="k">def</span> <span class="nf">setup_converters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>