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SINTEF · Oct 23, 2023 · 9e7d0c7 · 9e7d0c7
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diff --git a/latest/CHANGELOG/CHANGELOG.md b/latest/CHANGELOG/CHANGELOG.md
@@ -10,17 +10,21 @@
 
 **Fixed bugs:**
 
+- Wrong OPTIMADEStructureAttributes datamodel [\#164](https://github.com/SINTEF/oteapi-optimade/issues/164)
+- OPTIMADE plugin produces empty instances of http://onto-ns.com/meta/1.0/OPTIMADEStructureSpecies  [\#162](https://github.com/SINTEF/oteapi-optimade/issues/162)
 - Pipeline figure not being shown in docs [\#144](https://github.com/SINTEF/oteapi-optimade/issues/144)
 - Updated DLite installation pathway [\#136](https://github.com/SINTEF/oteapi-optimade/issues/136)
 - `Segmentation fault` from dlite in CI [\#115](https://github.com/SINTEF/oteapi-optimade/issues/115)
 - init file missing in the new `dlite` module [\#113](https://github.com/SINTEF/oteapi-optimade/issues/113)
 
 **Closed issues:**
 
+- Make the JSON-serialisation of entities human readable [\#160](https://github.com/SINTEF/oteapi-optimade/issues/160)
 - Use ruff instead of pylint \(and isort\) [\#156](https://github.com/SINTEF/oteapi-optimade/issues/156)
 
 **Merged pull requests:**
 
+- Update data models [\#169](https://github.com/SINTEF/oteapi-optimade/pull/169) ([CasperWA](https://github.com/CasperWA))
 - Move from pylint \(& isort\) to ruff [\#157](https://github.com/SINTEF/oteapi-optimade/pull/157) ([CasperWA](https://github.com/CasperWA))
 - Use relative link, which works only in production [\#145](https://github.com/SINTEF/oteapi-optimade/pull/145) ([CasperWA](https://github.com/CasperWA))
 - Avoid DLite v0.4.0 [\#139](https://github.com/SINTEF/oteapi-optimade/pull/139) ([CasperWA](https://github.com/CasperWA))

diff --git a/latest/CHANGELOG/index.html b/latest/CHANGELOG/index.html
@@ -1071,17 +1071,21 @@ <h2 id="unreleased-changes-2023-10-23"><a href="https://github.com/SINTEF/oteapi
 </ul>
 <p><strong>Fixed bugs:</strong></p>
 <ul>
+<li>Wrong OPTIMADEStructureAttributes datamodel <a href="https://github.com/SINTEF/oteapi-optimade/issues/164">#164</a></li>
+<li>OPTIMADE plugin produces empty instances of http://onto-ns.com/meta/1.0/OPTIMADEStructureSpecies  <a href="https://github.com/SINTEF/oteapi-optimade/issues/162">#162</a></li>
 <li>Pipeline figure not being shown in docs <a href="https://github.com/SINTEF/oteapi-optimade/issues/144">#144</a></li>
 <li>Updated DLite installation pathway <a href="https://github.com/SINTEF/oteapi-optimade/issues/136">#136</a></li>
 <li><code>Segmentation fault</code> from dlite in CI <a href="https://github.com/SINTEF/oteapi-optimade/issues/115">#115</a></li>
 <li>init file missing in the new <code>dlite</code> module <a href="https://github.com/SINTEF/oteapi-optimade/issues/113">#113</a></li>
 </ul>
 <p><strong>Closed issues:</strong></p>
 <ul>
+<li>Make the JSON-serialisation of entities human readable <a href="https://github.com/SINTEF/oteapi-optimade/issues/160">#160</a></li>
 <li>Use ruff instead of pylint (and isort) <a href="https://github.com/SINTEF/oteapi-optimade/issues/156">#156</a></li>
 </ul>
 <p><strong>Merged pull requests:</strong></p>
 <ul>
+<li>Update data models <a href="https://github.com/SINTEF/oteapi-optimade/pull/169">#169</a> (<a href="https://github.com/CasperWA">CasperWA</a>)</li>
 <li>Move from pylint (&amp; isort) to ruff <a href="https://github.com/SINTEF/oteapi-optimade/pull/157">#157</a> (<a href="https://github.com/CasperWA">CasperWA</a>)</li>
 <li>Use relative link, which works only in production <a href="https://github.com/SINTEF/oteapi-optimade/pull/145">#145</a> (<a href="https://github.com/CasperWA">CasperWA</a>)</li>
 <li>Avoid DLite v0.4.0 <a href="https://github.com/SINTEF/oteapi-optimade/pull/139">#139</a> (<a href="https://github.com/CasperWA">CasperWA</a>)</li>

diff --git a/latest/api_reference/dlite/parse/index.html b/latest/api_reference/dlite/parse/index.html
@@ -1142,22 +1142,22 @@ <h2 id="oteapi_optimade.dlite.parse.OPTIMADEDLiteParseStrategy" class="doc doc-h
 
         <span class="n">entities_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span> <span class="o">/</span> <span class="s2">&quot;entities&quot;</span>
 
-        <span class="n">dlite</span><span class="o">.</span><span class="n">storage_path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">entities_path</span> <span class="o">/</span> <span class="s2">&quot;*.json&quot;</span><span class="p">))</span>
+        <span class="n">dlite</span><span class="o">.</span><span class="n">storage_path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">entities_path</span> <span class="o">/</span> <span class="s2">&quot;*.yaml&quot;</span><span class="p">))</span>
 
         <span class="c1"># JSONAPIResourceLinks = dlite.Instance.from_url(</span>
-        <span class="c1">#     f&quot;json://{entities_path}/JSONAPIResourceLinks.json&quot;</span>
+        <span class="c1">#     f&quot;yaml://{entities_path}/JSONAPIResourceLinks.yaml&quot;</span>
         <span class="c1"># )</span>
         <span class="n">OPTIMADEStructure</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructure.json&quot;</span>
+            <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructure.yaml&quot;</span>
         <span class="p">)</span>
         <span class="n">OPTIMADEStructureAssembly</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAssembly.json&quot;</span>
+            <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAssembly.yaml&quot;</span>
         <span class="p">)</span>
         <span class="n">OPTIMADEStructureAttributes</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAttributes.json&quot;</span>
+            <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAttributes.yaml&quot;</span>
         <span class="p">)</span>
         <span class="n">OPTIMADEStructureSpecies</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureSpecies.json&quot;</span>
+            <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureSpecies.yaml&quot;</span>
         <span class="p">)</span>
 
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parse_config</span><span class="o">.</span><span class="n">configuration</span><span class="o">.</span><span class="n">return_object</span><span class="p">:</span>
@@ -1288,12 +1288,16 @@ <h2 id="oteapi_optimade.dlite.parse.OPTIMADEDLiteParseStrategy" class="doc doc-h
 
             <span class="c1"># Attributes</span>
             <span class="n">new_structure_attributes</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
-                <span class="n">structure</span><span class="o">.</span><span class="n">attributes</span><span class="o">.</span><span class="n">dict</span><span class="p">(</span><span class="n">exclude</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;species&quot;</span><span class="p">,</span> <span class="s2">&quot;assemblies&quot;</span><span class="p">})</span>
+                <span class="n">structure</span><span class="o">.</span><span class="n">attributes</span><span class="o">.</span><span class="n">dict</span><span class="p">(</span>
+                    <span class="n">exclude</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;species&quot;</span><span class="p">,</span> <span class="s2">&quot;assemblies&quot;</span><span class="p">,</span> <span class="s2">&quot;nelements&quot;</span><span class="p">,</span> <span class="s2">&quot;nsites&quot;</span><span class="p">}</span>
+                <span class="p">)</span>
             <span class="p">)</span>
             <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">new_structure_attributes</span><span class="p">):</span>
                 <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">):</span>
                     <span class="n">new_structure_attributes</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
 
+            <span class="c1"># Structure features values are Enum values, so we need to convert them to</span>
+            <span class="c1"># their string (true) values</span>
             <span class="n">new_structure_attributes</span><span class="p">[</span><span class="s2">&quot;structure_features&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
                 <span class="n">_</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">new_structure_attributes</span><span class="p">[</span><span class="s2">&quot;structure_features&quot;</span><span class="p">]</span>
             <span class="p">]</span>
@@ -1439,22 +1443,22 @@ <h3 id="oteapi_optimade.dlite.parse.OPTIMADEDLiteParseStrategy.get" class="doc d
 
     <span class="n">entities_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span> <span class="o">/</span> <span class="s2">&quot;entities&quot;</span>
 
-    <span class="n">dlite</span><span class="o">.</span><span class="n">storage_path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">entities_path</span> <span class="o">/</span> <span class="s2">&quot;*.json&quot;</span><span class="p">))</span>
+    <span class="n">dlite</span><span class="o">.</span><span class="n">storage_path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">entities_path</span> <span class="o">/</span> <span class="s2">&quot;*.yaml&quot;</span><span class="p">))</span>
 
     <span class="c1"># JSONAPIResourceLinks = dlite.Instance.from_url(</span>
-    <span class="c1">#     f&quot;json://{entities_path}/JSONAPIResourceLinks.json&quot;</span>
+    <span class="c1">#     f&quot;yaml://{entities_path}/JSONAPIResourceLinks.yaml&quot;</span>
     <span class="c1"># )</span>
     <span class="n">OPTIMADEStructure</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-        <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructure.json&quot;</span>
+        <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructure.yaml&quot;</span>
     <span class="p">)</span>
     <span class="n">OPTIMADEStructureAssembly</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-        <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAssembly.json&quot;</span>
+        <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAssembly.yaml&quot;</span>
     <span class="p">)</span>
     <span class="n">OPTIMADEStructureAttributes</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-        <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAttributes.json&quot;</span>
+        <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureAttributes.yaml&quot;</span>
     <span class="p">)</span>
     <span class="n">OPTIMADEStructureSpecies</span> <span class="o">=</span> <span class="n">dlite</span><span class="o">.</span><span class="n">Instance</span><span class="o">.</span><span class="n">from_url</span><span class="p">(</span>
-        <span class="sa">f</span><span class="s2">&quot;json://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureSpecies.json&quot;</span>
+        <span class="sa">f</span><span class="s2">&quot;yaml://</span><span class="si">{</span><span class="n">entities_path</span><span class="si">}</span><span class="s2">/OPTIMADEStructureSpecies.yaml&quot;</span>
     <span class="p">)</span>
 
     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parse_config</span><span class="o">.</span><span class="n">configuration</span><span class="o">.</span><span class="n">return_object</span><span class="p">:</span>
@@ -1585,12 +1589,16 @@ <h3 id="oteapi_optimade.dlite.parse.OPTIMADEDLiteParseStrategy.get" class="doc d
 
         <span class="c1"># Attributes</span>
         <span class="n">new_structure_attributes</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
-            <span class="n">structure</span><span class="o">.</span><span class="n">attributes</span><span class="o">.</span><span class="n">dict</span><span class="p">(</span><span class="n">exclude</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;species&quot;</span><span class="p">,</span> <span class="s2">&quot;assemblies&quot;</span><span class="p">})</span>
+            <span class="n">structure</span><span class="o">.</span><span class="n">attributes</span><span class="o">.</span><span class="n">dict</span><span class="p">(</span>
+                <span class="n">exclude</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;species&quot;</span><span class="p">,</span> <span class="s2">&quot;assemblies&quot;</span><span class="p">,</span> <span class="s2">&quot;nelements&quot;</span><span class="p">,</span> <span class="s2">&quot;nsites&quot;</span><span class="p">}</span>
+            <span class="p">)</span>
         <span class="p">)</span>
         <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">new_structure_attributes</span><span class="p">):</span>
             <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">):</span>
                 <span class="n">new_structure_attributes</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
 
+        <span class="c1"># Structure features values are Enum values, so we need to convert them to</span>
+        <span class="c1"># their string (true) values</span>
         <span class="n">new_structure_attributes</span><span class="p">[</span><span class="s2">&quot;structure_features&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
             <span class="n">_</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">new_structure_attributes</span><span class="p">[</span><span class="s2">&quot;structure_features&quot;</span><span class="p">]</span>
         <span class="p">]</span>