Deploying to gh-pages from @ 45f58a5 🚀

_sources/validation_codes_dictionary.md.txt

@@ -172,6 +172,18 @@
 
 **Description:** Predicate specified in Input Edge is not defined as a predicate in specified version of Biolink. Replace with a proper predicate!
 
+### error.query_graph.nodes.uninformative
+
+**Message:** Missing informative node information
+
+**Description:** Query graph must have at least one node with identifiers and/or categories available for query!
+
+### error.query_graph.nodes.dangling
+
+**Message:** Dangling nodes
+
+**Description:** At least one query node is unused in the query graph!
+
 ### error.query_graph.node.category.missing
 
 **Message:** Category is missing from node
@@ -350,13 +362,25 @@
 
 ### error.knowledge_graph.nodes.empty
 
-**Message:** No nodes found!
+**Message:** No nodes found
 
 **Description:** Knowledge graph in TRAPI messages must have a 'nodes' key and non-empty associated value!
 
+### error.knowledge_graph.nodes.uninformative
+
+**Message:** Missing informative node information!
+
+**Description:** All nodes in a knowledge graph must have categories!
+
+### error.knowledge_graph.nodes.dangling
+
+**Message:** Dangling nodes
+
+**Description:** At least one query node is unused in the knowledge graph!
+
 ### error.knowledge_graph.edges.empty
 
-**Message:** No edges found!
+**Message:** No edges found
 
 **Description:** Knowledge graph in TRAPI messages must have a 'edges' key and non-empty associated value!
 

genindex.html

@@ -144,10 +144,10 @@ <h2 id="C">C</h2>
 </li>
       <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BiolinkValidator.check_biolink_model_compliance">check_biolink_model_compliance() (reasoner_validator.biolink.BiolinkValidator method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BiolinkValidator.check_biolink_model_compliance_of_input_edge">check_biolink_model_compliance_of_input_edge() (reasoner_validator.biolink.BiolinkValidator method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reasoner_validator.html#reasoner_validator.validator.TRAPIResponseValidator.check_compliance_of_trapi_response">check_compliance_of_trapi_response() (reasoner_validator.validator.TRAPIResponseValidator method)</a>
 </li>
       <li><a href="reasoner_validator.trapi.mapping.html#reasoner_validator.trapi.mapping.MappingValidator.check_dangling_references">check_dangling_references() (reasoner_validator.trapi.mapping.MappingValidator method)</a>
@@ -161,6 +161,8 @@ <h2 id="C">C</h2>
       <li><a href="reasoner_validator.validation_codes.html#reasoner_validator.validation_codes.CodeDictionary">CodeDictionary (class in reasoner_validator.validation_codes)</a>
 </li>
       <li><a href="reasoner_validator.validation_codes.html#reasoner_validator.validation_codes.CodeDictionary.CONTEXT">CONTEXT (reasoner_validator.validation_codes.CodeDictionary attribute)</a>
+</li>
+      <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BiolinkValidator.count_node">count_node() (reasoner_validator.biolink.BiolinkValidator method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -273,6 +275,8 @@ <h2 id="H">H</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reasoner_validator.report.html#reasoner_validator.report.ValidationReporter.has_critical">has_critical() (reasoner_validator.report.ValidationReporter method)</a>
+</li>
+      <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BiolinkValidator.has_dangling_nodes">has_dangling_nodes() (reasoner_validator.biolink.BiolinkValidator method)</a>
 </li>
       <li><a href="reasoner_validator.report.html#reasoner_validator.report.ValidationReporter.has_errors">has_errors() (reasoner_validator.report.ValidationReporter method)</a>
 </li>
@@ -283,6 +287,8 @@ <h2 id="H">H</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reasoner_validator.html#reasoner_validator.validator.TRAPIResponseValidator.has_valid_knowledge_graph">has_valid_knowledge_graph() (reasoner_validator.validator.TRAPIResponseValidator method)</a>
+</li>
+      <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BiolinkValidator.has_valid_node_information">has_valid_node_information() (reasoner_validator.biolink.BiolinkValidator method)</a>
 </li>
       <li><a href="reasoner_validator.html#reasoner_validator.validator.TRAPIResponseValidator.has_valid_query_graph">has_valid_query_graph() (reasoner_validator.validator.TRAPIResponseValidator method)</a>
 </li>
@@ -321,6 +327,10 @@ <h2 id="K">K</h2>
 
 <h2 id="L">L</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="reasoner_validator.report.html#reasoner_validator.report.TRAPIGraphType.label">label() (reasoner_validator.report.TRAPIGraphType method)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reasoner_validator.trapi.html#reasoner_validator.trapi.load_schema">load_schema() (in module reasoner_validator.trapi)</a>
 </li>
@@ -494,6 +504,8 @@ <h2 id="R">R</h2>
         <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BMTWrapper.reset_biolink_version">(reasoner_validator.biolink.BMTWrapper method)</a>
 </li>
       </ul></li>
+      <li><a href="reasoner_validator.biolink.html#reasoner_validator.biolink.BiolinkValidator.reset_node_info">reset_node_info() (reasoner_validator.biolink.BiolinkValidator method)</a>
+</li>
       <li><a href="reasoner_validator.trapi.html#reasoner_validator.trapi.TRAPISchemaValidator.reset_trapi_version">reset_trapi_version() (reasoner_validator.trapi.TRAPISchemaValidator method)</a>
 </li>
   </ul></td>

reasoner_validator.biolink.html

@@ -61,15 +61,19 @@
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.build_source_trail"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.build_source_trail()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.check_biolink_model_compliance"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.check_biolink_model_compliance()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.check_biolink_model_compliance_of_input_edge"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.check_biolink_model_compliance_of_input_edge()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.count_node"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.count_node()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_biolink_version"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.get_biolink_version()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_node_categories"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.get_node_categories()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_node_identifiers"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.get_node_identifiers()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_result"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.get_result()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_target_provenance"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.get_target_provenance()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.has_dangling_nodes"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.has_dangling_nodes()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.has_valid_node_information"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.has_valid_node_information()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.merge"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.merge()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.minimum_required_biolink_version"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.minimum_required_biolink_version()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.report_header"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.report_header()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.reset_biolink_version"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.reset_biolink_version()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.reset_node_info"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.reset_node_info()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.set_nodes"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.set_nodes()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.to_dict"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.to_dict()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.validate_attribute_constraints"><code class="docutils literal notranslate"><span class="pre">BiolinkValidator.validate_attribute_constraints()</span></code></a></li>
@@ -273,7 +277,7 @@
 <td><p>Get copy of all messages as a Python data structure.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_node_categories" title="reasoner_validator.biolink.BiolinkValidator.get_node_categories"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_node_categories</span></code></a>(node_id)</p></td>
-<td><p>Categories by 'node_id'.</p></td>
+<td><p>Categories by 'node_id'. :param node_id: :return: For a given node_id, returns the associated categories;          None if node_id is currently unknown or has no categories.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="#reasoner_validator.biolink.BiolinkValidator.get_node_identifiers" title="reasoner_validator.biolink.BiolinkValidator.get_node_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_node_identifiers</span></code></a>()</p></td>
 <td><p><dl class="field-list simple">
@@ -415,13 +419,25 @@
 </table>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p><strong>get_bmt</strong></p></td>
+<tr class="row-odd"><td><p><strong>count_node</strong></p></td>
+<td></td>
+</tr>
+<tr class="row-even"><td><p><strong>get_bmt</strong></p></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><strong>get_message_type_tag</strong></p></td>
+<tr class="row-odd"><td><p><strong>get_message_type_tag</strong></p></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><strong>report_header</strong></p></td>
+<tr class="row-even"><td><p><strong>has_dangling_nodes</strong></p></td>
+<td></td>
+</tr>
+<tr class="row-odd"><td><p><strong>has_valid_node_information</strong></p></td>
+<td></td>
+</tr>
+<tr class="row-even"><td><p><strong>report_header</strong></p></td>
+<td></td>
+</tr>
+<tr class="row-odd"><td><p><strong>reset_node_info</strong></p></td>
 <td></td>
 </tr>
 <tr class="row-even"><td><p><strong>validate_input_edge_node</strong></p></td>
@@ -490,6 +506,11 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.count_node">
+<span class="sig-name descname"><span class="pre">count_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.count_node" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.get_biolink_version">
 <span class="sig-name descname"><span class="pre">get_biolink_version</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.get_biolink_version" title="Permalink to this definition"></a></dt>
@@ -508,7 +529,10 @@
 <span class="sig-name descname"><span class="pre">get_node_categories</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">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><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.get_node_categories" title="Permalink to this definition"></a></dt>
 <dd><p>Categories by ‘node_id’.
 :param node_id:
-:return: For a given node_id, returns the associated categories; None if node_id is currently unknown</p>
+:return: For a given node_id, returns the associated categories;</p>
+<blockquote>
+<div><p>None if node_id is currently unknown or has no categories.</p>
+</div></blockquote>
 </dd></dl>
 
 <dl class="py method">
@@ -540,6 +564,16 @@
 :return: Tuple[Optional[str], Optional[str], Optional[str]] of ara_source, kp_source, kp_source_type</p>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.has_dangling_nodes">
+<span class="sig-name descname"><span class="pre">has_dangling_nodes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.has_dangling_nodes" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.has_valid_node_information">
+<span class="sig-name descname"><span class="pre">has_valid_node_information</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="reasoner_validator.report.html#reasoner_validator.report.TRAPIGraphType" title="reasoner_validator.report.TRAPIGraphType"><span class="pre">TRAPIGraphType</span></a></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">bool</span></span></span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.has_valid_node_information" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.merge">
 <span class="sig-name descname"><span class="pre">merge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reporter</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.merge" title="Permalink to this definition"></a></dt>
@@ -578,11 +612,17 @@
 :return: None</p>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.reset_node_info">
+<span class="sig-name descname"><span class="pre">reset_node_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="reasoner_validator.report.html#reasoner_validator.report.TRAPIGraphType" title="reasoner_validator.report.TRAPIGraphType"><span class="pre">TRAPIGraphType</span></a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.reset_node_info" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="reasoner_validator.biolink.BiolinkValidator.set_nodes">
 <span class="sig-name descname"><span class="pre">set_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#reasoner_validator.biolink.BiolinkValidator.set_nodes" title="Permalink to this definition"></a></dt>
 <dd><p>Records additional nodes, uniquely by node_id, with specified categories.
-:param nodes: Dict, node_id indexed node categories
+:param nodes: Dict, node_id indexed node categories. A given node_id is
+tagged with “None” if the categories are missing?
 :return: None</p>
 </dd></dl>