deploy: 2c9cc51

_modules/ete4/smartview/gui/server.html

@@ -694,9 +694,10 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>
     <span class="s2">&quot;Add tree to app.trees and initialize it if not there, and return it&quot;</span>
     <span class="k">try</span><span class="p">:</span>
         <span class="n">tid</span><span class="p">,</span> <span class="n">subtree</span> <span class="o">=</span> <span class="n">get_tid</span><span class="p">(</span><span class="n">tree_id</span><span class="p">)</span>
-        <span class="n">tree_data</span> <span class="o">=</span> <span class="n">app</span><span class="o">.</span><span class="n">trees</span><span class="p">[</span><span class="n">tid</span><span class="p">]</span>
 
-        <span class="k">if</span> <span class="n">tree_data</span><span class="o">.</span><span class="n">tree</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">tid</span> <span class="ow">in</span> <span class="n">app</span><span class="o">.</span><span class="n">trees</span><span class="p">:</span>
+            <span class="n">tree_data</span> <span class="o">=</span> <span class="n">app</span><span class="o">.</span><span class="n">trees</span><span class="p">[</span><span class="n">tid</span><span class="p">]</span>
+
             <span class="c1"># Reinitialize if layouts have to be reapplied</span>
             <span class="k">if</span> <span class="ow">not</span> <span class="n">tree_data</span><span class="o">.</span><span class="n">initialized</span><span class="p">:</span>
                 <span class="n">initialize_tree_style</span><span class="p">(</span><span class="n">tree_data</span><span class="p">)</span>
@@ -712,7 +713,7 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>
 
             <span class="k">return</span> <span class="n">tree_data</span><span class="o">.</span><span class="n">tree</span><span class="p">[</span><span class="n">subtree</span><span class="p">]</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">tree_data</span><span class="o">.</span><span class="n">name</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">layouts</span> <span class="o">=</span> <span class="n">retrieve_tree</span><span class="p">(</span><span class="n">tid</span><span class="p">)</span>
+            <span class="n">tree_data</span> <span class="o">=</span> <span class="n">app</span><span class="o">.</span><span class="n">trees</span><span class="p">[</span><span class="n">tid</span><span class="p">]</span> <span class="o">=</span> <span class="n">retrieve_tree_data</span><span class="p">(</span><span class="n">tid</span><span class="p">)</span>
 
             <span class="k">if</span> <span class="n">tree_data</span><span class="o">.</span><span class="n">ultrametric</span><span class="p">:</span>
                 <span class="n">tree_data</span><span class="o">.</span><span class="n">tree</span><span class="o">.</span><span class="n">to_ultrametric</span><span class="p">()</span>
@@ -778,24 +779,19 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>
 
 
 
-<div class="viewcode-block" id="retrieve_tree">
-<a class="viewcode-back" href="../../../../reference/reference_smartview.html#ete4.smartview.gui.server.retrieve_tree">[docs]</a>
-<span class="k">def</span> <span class="nf">retrieve_tree</span><span class="p">(</span><span class="n">tid</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Retrieve tree from file and return its name, tree structure, and layouts.</span>
+<div class="viewcode-block" id="retrieve_tree_data">
+<a class="viewcode-back" href="../../../../reference/reference_smartview.html#ete4.smartview.gui.server.retrieve_tree_data">[docs]</a>
+<span class="k">def</span> <span class="nf">retrieve_tree_data</span><span class="p">(</span><span class="n">tid</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Retrieve and return tree data from file.</span>
 
 <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">tmpfile</span> <span class="o">=</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="c1"># beautiful...</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">handle</span><span class="p">:</span>
-        <span class="n">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="n">handle</span><span class="p">)</span>
-
-    <span class="n">name</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;name&quot;</span><span class="p">]</span>
-    <span class="n">tree</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;tree&quot;</span><span class="p">]</span>
-    <span class="n">layouts</span> <span class="o">=</span> <span class="n">retrieve_layouts</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s2">&quot;layouts&quot;</span><span class="p">])</span>
-
-    <span class="n">app</span><span class="o">.</span><span class="n">trees</span><span class="p">[</span><span class="n">tid</span><span class="p">]</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">name</span><span class="p">,</span> <span class="n">tree</span><span class="p">,</span> <span class="n">layouts</span></div>
+    <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="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>
 
 
 
@@ -1617,12 +1613,14 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>
     <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">tree</span> <span class="o">=</span> <span class="n">tree</span>
 
-    <span class="k">def</span> <span class="nf">write_tree</span><span class="p">():</span>
+    <span class="k">def</span> <span class="nf">write_tree_data</span><span class="p">():</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Write tree data as a temporary pickle file.&quot;&quot;&quot;</span>
-        <span class="n">obj</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">name</span><span class="p">,</span> <span class="s1">&#39;layouts&#39;</span><span class="p">:</span> <span class="n">layouts</span><span class="p">,</span> <span class="s1">&#39;tree&#39;</span><span class="p">:</span> <span class="n">tree</span> <span class="p">}</span>
-        <span class="k">with</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">as</span> <span class="n">handle</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">obj</span><span class="p">,</span> <span class="n">handle</span><span class="p">)</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</span><span class="p">)</span>  <span class="c1"># so we are not delayed</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="n">tree_data</span><span class="p">)</span>
+        <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="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>
 
     <span class="k">return</span> <span class="n">tid</span></div>

genindex.html

@@ -1537,7 +1537,7 @@ <h2 id="R">R</h2>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.retrieve_layouts">retrieve_layouts() (in module ete4.smartview.gui.server)</a>
 </li>
-      <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.retrieve_tree">retrieve_tree() (in module ete4.smartview.gui.server)</a>
+      <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.retrieve_tree_data">retrieve_tree_data() (in module ete4.smartview.gui.server)</a>
 </li>
       <li><a href="reference/reference_tree.html#ete4.Tree.reverse_children">reverse_children() (Tree method)</a>
 </li>