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_modules/oaklib/implementations/sqldb/sql_implementation.html

@@ -212,6 +212,7 @@ <h1>Source code for oaklib.implementations.sqldb.sql_implementation</h1><div cla
     <span class="n">DEFINITION</span><span class="p">,</span>
     <span class="n">LANGUAGE_TAG</span><span class="p">,</span>
     <span class="n">METADATA_MAP</span><span class="p">,</span>
+    <span class="n">METADATA_STATEMENT</span><span class="p">,</span>
     <span class="n">PRED_CURIE</span><span class="p">,</span>
     <span class="n">PREFIX_MAP</span><span class="p">,</span>
     <span class="n">RELATIONSHIP</span><span class="p">,</span>
@@ -758,6 +759,33 @@ <h1>Source code for oaklib.implementations.sqldb.sql_implementation</h1><div cla
         <span class="bp">self</span><span class="o">.</span><span class="n">add_missing_property_values</span><span class="p">(</span><span class="n">curie</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
         <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
 
+    <span class="k">def</span> <span class="nf">entities_metadata_statements</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">curies</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">CURIE</span><span class="p">],</span>
+        <span class="n">predicates</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="n">PRED_CURIE</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">include_nested_metadata</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Iterator</span><span class="p">[</span><span class="n">METADATA_STATEMENT</span><span class="p">]:</span>
+        <span class="n">q</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">Statements</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">include_nested_metadata</span><span class="p">:</span>
+            <span class="n">subquery</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">RdfTypeStatement</span><span class="o">.</span><span class="n">subject</span><span class="p">)</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                <span class="n">RdfTypeStatement</span><span class="o">.</span><span class="n">object</span> <span class="o">==</span> <span class="s2">&quot;owl:AnnotationProperty&quot;</span>
+            <span class="p">)</span>
+            <span class="n">annotation_properties</span> <span class="o">=</span> <span class="p">{</span><span class="n">row</span><span class="o">.</span><span class="n">subject</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">subquery</span><span class="p">}</span>
+            <span class="n">annotation_properties</span> <span class="o">=</span> <span class="n">annotation_properties</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="n">STANDARD_ANNOTATION_PROPERTIES</span><span class="p">)</span>
+            <span class="n">q</span> <span class="o">=</span> <span class="n">q</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">Statements</span><span class="o">.</span><span class="n">predicate</span><span class="o">.</span><span class="n">in_</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">annotation_properties</span><span class="p">)))</span>
+        <span class="n">q</span> <span class="o">=</span> <span class="n">q</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">Statements</span><span class="o">.</span><span class="n">subject</span><span class="o">.</span><span class="n">in_</span><span class="p">(</span><span class="n">curies</span><span class="p">))</span>
+        <span class="k">if</span> <span class="n">predicates</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">q</span> <span class="o">=</span> <span class="n">q</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">Statements</span><span class="o">.</span><span class="n">predicate</span><span class="o">.</span><span class="n">in_</span><span class="p">(</span><span class="n">predicates</span><span class="p">))</span>
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">q</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">row</span><span class="o">.</span><span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">v</span> <span class="o">=</span> <span class="n">_python_value</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">row</span><span class="o">.</span><span class="n">datatype</span><span class="p">)</span>
+            <span class="k">elif</span> <span class="n">row</span><span class="o">.</span><span class="n">object</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">v</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">object</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">v</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="k">yield</span> <span class="n">row</span><span class="o">.</span><span class="n">subject</span><span class="p">,</span> <span class="n">row</span><span class="o">.</span><span class="n">predicate</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> <span class="n">row</span><span class="o">.</span><span class="n">datatype</span><span class="p">,</span> <span class="p">{}</span>
+
     <span class="k">def</span> <span class="nf">ontologies</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">CURIE</span><span class="p">]:</span>
         <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">OntologyNode</span><span class="p">):</span>
             <span class="k">yield</span> <span class="n">row</span><span class="o">.</span><span class="n">id</span>

_modules/oaklib/interfaces/basic_ontology_interface.html

@@ -1682,7 +1682,11 @@ <h1>Source code for oaklib.interfaces.basic_ontology_interface</h1><div class="h
 <div class="viewcode-block" id="BasicOntologyInterface.entities_metadata_statements">
 <a class="viewcode-back" href="../../../packages/interfaces/basic.html#oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.entities_metadata_statements">[docs]</a>
     <span class="k">def</span> <span class="nf">entities_metadata_statements</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span> <span class="n">curies</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">CURIE</span><span class="p">],</span> <span class="n">predicates</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="n">PRED_CURIE</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">curies</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">CURIE</span><span class="p">],</span>
+        <span class="n">predicates</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="n">PRED_CURIE</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">include_nested_metadata</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Iterator</span><span class="p">[</span><span class="n">METADATA_STATEMENT</span><span class="p">]:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Retrieve metadata statements (entity annotations) for a collection of entities.</span>

packages/interfaces/basic.html

@@ -1530,7 +1530,7 @@
 
 <dl class="py method">
 <dt class="sig sig-object py" id="oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.entities_metadata_statements">
-<span class="sig-name descname"><span class="pre">entities_metadata_statements</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">curies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">Iterator</span><span class="p"><span class="pre">[</span></span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../../_modules/oaklib/interfaces/basic_ontology_interface.html#BasicOntologyInterface.entities_metadata_statements"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.entities_metadata_statements" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">entities_metadata_statements</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">curies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">predicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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_nested_metadata</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</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">Iterator</span><span class="p"><span class="pre">[</span></span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../../_modules/oaklib/interfaces/basic_ontology_interface.html#BasicOntologyInterface.entities_metadata_statements"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.entities_metadata_statements" title="Link to this definition"></a></dt>
 <dd><p>Retrieve metadata statements (entity annotations) for a collection of entities.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>