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jordibc committed Mar 25, 2024
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18 changes: 16 additions & 2 deletions _modules/ete4/smartview/gui/server.html
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Expand Up @@ -801,11 +801,20 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>

<span class="sd"> It retrieves all that from a previously saved pickle file in /tmp.&quot;&quot;&quot;</span>
<span class="c1"># Called when tree has been deleted from memory.</span>
<span class="n">tree_data</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;/tmp/</span><span class="si">{</span><span class="n">tid</span><span class="si">}</span><span class="s1">.pickle&#39;</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">tree_data</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;/tmp/</span><span class="si">{</span><span class="n">tid</span><span class="si">}</span><span class="s1">.pickle&#39;</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">FileNotFoundError</span><span class="p">,</span> <span class="ne">EOFError</span><span class="p">,</span> <span class="n">pickle</span><span class="o">.</span><span class="n">UnpicklingError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Tree </span><span class="si">{</span><span class="n">tid</span><span class="si">}</span><span class="s1"> cannot be recovered from disk. Loading placeholder.&#39;</span><span class="p">)</span>
<span class="n">tree_data</span> <span class="o">=</span> <span class="n">TreeData</span><span class="p">()</span>
<span class="n">tree_data</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Placeholder tree&#39;</span>
<span class="n">tree_data</span><span class="o">.</span><span class="n">tree</span> <span class="o">=</span> <span class="n">Tree</span><span class="p">(</span><span class="s1">&#39;(could,not,load,tree);&#39;</span><span class="p">)</span>
<span class="n">ops</span><span class="o">.</span><span class="n">update_sizes_all</span><span class="p">(</span><span class="n">tree_data</span><span class="o">.</span><span class="n">tree</span><span class="p">)</span>

<span class="n">tree_data</span><span class="o">.</span><span class="n">style</span> <span class="o">=</span> <span class="n">copy_style</span><span class="p">(</span><span class="n">TreeStyle</span><span class="p">())</span>
<span class="n">tree_data</span><span class="o">.</span><span class="n">layouts</span> <span class="o">=</span> <span class="n">retrieve_layouts</span><span class="p">(</span><span class="n">tree_data</span><span class="o">.</span><span class="n">layouts</span><span class="p">)</span>
<span class="n">tree_data</span><span class="o">.</span><span class="n">active</span> <span class="o">=</span> <span class="n">drawer_module</span><span class="o">.</span><span class="n">get_empty_active</span><span class="p">()</span>
<span class="n">tree_data</span><span class="o">.</span><span class="n">timer</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span> <span class="c1"># to track if it is active</span>

<span class="k">return</span> <span class="n">tree_data</span></div>


Expand Down Expand Up @@ -1634,7 +1643,12 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>
<span class="n">data</span><span class="o">.</span><span class="n">style</span> <span class="o">=</span> <span class="kc">None</span> <span class="c1"># since it can&#39;t be pickled</span>
<span class="n">data</span><span class="o">.</span><span class="n">layouts</span> <span class="o">=</span> <span class="n">layouts</span> <span class="c1"># same</span>
<span class="n">data</span><span class="o">.</span><span class="n">active</span> <span class="o">=</span> <span class="kc">None</span> <span class="c1"># same</span>
<span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;/tmp/</span><span class="si">{</span><span class="n">tid</span><span class="si">}</span><span class="s1">.pickle&#39;</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;/tmp/</span><span class="si">{</span><span class="n">tid</span><span class="si">}</span><span class="s1">.pickle&#39;</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
<span class="k">except</span> <span class="p">(</span><span class="n">pickle</span><span class="o">.</span><span class="n">PicklingError</span><span class="p">,</span> <span class="ne">PermissionError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Tree </span><span class="si">{</span><span class="n">tid</span><span class="si">}</span><span class="s1"> not saved to file.&#39;</span><span class="p">)</span>
<span class="c1"># So changing to ultrametric and back will not work,</span>
<span class="c1"># because it is done by re-reading from the dumped file.</span>
<span class="n">thr_write</span> <span class="o">=</span> <span class="n">Thread</span><span class="p">(</span><span class="n">daemon</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="n">write_tree_data</span><span class="p">)</span> <span class="c1"># so we are not delayed</span>
<span class="n">thr_write</span><span class="o">.</span><span class="n">start</span><span class="p">()</span> <span class="c1"># by big trees</span>

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2 changes: 1 addition & 1 deletion reference/reference_smartview.html
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Expand Up @@ -92,7 +92,7 @@ <h1><a class="toc-backref" href="#id1" role="doc-backlink">Smartview (web graphi

<dl class="py class">
<dt class="sig sig-object py" id="ete4.smartview.gui.server.TreeData">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TreeData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree:</span> <span class="pre">ete4.core.tree.Tree</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style:</span> <span class="pre">ete4.smartview.renderer.treestyle.TreeStyle</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer:</span> <span class="pre">float</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ultrametric:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active:</span> <span class="pre">&lt;function</span> <span class="pre">namedtuple</span> <span class="pre">at</span> <span class="pre">0x73cad0542a20&gt;</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/smartview/gui/server.html#TreeData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.TreeData" title="Link to this definition"></a></dt>
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TreeData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree:</span> <span class="pre">ete4.core.tree.Tree</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style:</span> <span class="pre">ete4.smartview.renderer.treestyle.TreeStyle</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer:</span> <span class="pre">float</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ultrametric:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active:</span> <span class="pre">&lt;function</span> <span class="pre">namedtuple</span> <span class="pre">at</span> <span class="pre">0x7f98a5d42a20&gt;</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/smartview/gui/server.html#TreeData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.TreeData" title="Link to this definition"></a></dt>
<dd><dl class="py method">
<dt class="sig sig-object py" id="ete4.smartview.gui.server.TreeData.__init__">
<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="reference_tree.html#ete4.Tree" title="ete4.core.tree.Tree"><span class="pre">Tree</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#ete4.smartview.renderer.treestyle.TreeStyle" title="ete4.smartview.renderer.treestyle.TreeStyle"><span class="pre">TreeStyle</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ultrametric</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">namedtuple</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#ete4.smartview.gui.server.TreeData.__init__" title="Link to this definition"></a></dt>
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2 changes: 1 addition & 1 deletion searchindex.js
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