Merge branch 'main' of https://github.com/isamplesorg/vocabularyTemplate

isamplesorg · Dec 21, 2023 · a3fe9e6 · a3fe9e6
2 parents 4f2bb4d + 5eacda4
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Showing 6 changed files with 23 additions and 22 deletions.
diff --git a/cache/vocabularies.db b/cache/vocabularies.db
diff --git a/docs/test_feature_type.html b/docs/test_feature_type.html
@@ -56,27 +56,27 @@ <h2 id="toc-title">Table of contents</h2>
 <p>getObject subject: https://w3id.org/isample/vocabulary/sampledfeature/1.0/testfeaturevocabulary</p>
 <p>getObject predicate: http://www.w3.org/2004/02/skos/core#prefLabel</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb425ca12b0&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc8fd01580&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/sampledfeature/1.0/testfeaturevocabulary</p>
 <p>getObject predicate: http://purl.org/dc/terms/modified</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb426d884a0&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc9028cc50&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/sampledfeature/1.0/testfeaturevocabulary</p>
 <p>getObject predicate: http://www.w3.org/2004/02/skos/core#definition</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb425ccd6d0&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc8f1f9b20&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/sampledfeature/1.0/testfeaturevocabulary</p>
 <p>getObject predicate: http://www.w3.org/2000/01/rdf-schema#comment</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb426d88800&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc9028d880&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/sampledfeature/1.0/testfeaturevocabulary</p>
 <p>getObject predicate: http://www.w3.org/2004/02/skos/core#historyNote</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb425ccc5c0&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc8f1f9d60&gt;</p>
 <p><span id="ConceptScheme"></span></p>
 <section id="concept-scheme-conceptscheme" class="level1" data-number="1">
 <h1 data-number="1"><span class="header-section-number">1</span> <strong>Concept scheme:</strong> ConceptScheme</h1>

diff --git a/docs/test_feature_type.md b/docs/test_feature_type.md
@@ -12,7 +12,7 @@ getObject predicate: http://www.w3.org/2004/02/skos/core#prefLabel
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb425ca12b0>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc8fd01580>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -27,7 +27,7 @@ getObject predicate: http://purl.org/dc/terms/modified
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb426d884a0>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc9028cc50>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -42,7 +42,7 @@ getObject predicate: http://www.w3.org/2004/02/skos/core#definition
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb425ccd6d0>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc8f1f9b20>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -57,7 +57,7 @@ getObject predicate: http://www.w3.org/2000/01/rdf-schema#comment
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb426d88800>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc9028d880>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -72,7 +72,7 @@ getObject predicate: http://www.w3.org/2004/02/skos/core#historyNote
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fb425ccc5c0>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7efc8f1f9d60>
 
 ---
 comment: | 

diff --git a/docs/test_sample_type.html b/docs/test_sample_type.html
@@ -56,27 +56,27 @@ <h2 id="toc-title">Table of contents</h2>
 <p>getObject subject: https://w3id.org/isample/vocabulary/specimentype/1.0/testvocabulary</p>
 <p>getObject predicate: http://www.w3.org/2004/02/skos/core#prefLabel</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3d711040&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94df6cfdd0&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/specimentype/1.0/testvocabulary</p>
 <p>getObject predicate: http://purl.org/dc/terms/modified</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3c9e8200&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94df750770&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/specimentype/1.0/testvocabulary</p>
 <p>getObject predicate: http://www.w3.org/2004/02/skos/core#definition</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3b929940&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94de699160&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/specimentype/1.0/testvocabulary</p>
 <p>getObject predicate: http://www.w3.org/2000/01/rdf-schema#comment</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3c9e8710&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94df751160&gt;</p>
 <p>getObject prefixes: PREFIX skos: <a href="http://www.w3.org/2004/02/skos/core#" class="uri">http://www.w3.org/2004/02/skos/core#</a> PREFIX owl: <a href="http://www.w3.org/2002/07/owl#" class="uri">http://www.w3.org/2002/07/owl#</a> PREFIX rdf: <a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class="uri">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a> PREFIX rdfs: <a href="http://www.w3.org/2000/01/rdf-schema#" class="uri">http://www.w3.org/2000/01/rdf-schema#</a></p>
 <p>getObject subject: https://w3id.org/isample/vocabulary/specimentype/1.0/testvocabulary</p>
 <p>getObject predicate: http://www.w3.org/2004/02/skos/core#historyNote</p>
 <p>length of qres: 0</p>
-<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3b929d60&gt;</p>
+<p>qres: &lt;rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94de698350&gt;</p>
 <p><span id="ConceptScheme"></span></p>
 <section id="concept-scheme-conceptscheme" class="level1" data-number="1">
 <h1 data-number="1"><span class="header-section-number">1</span> <strong>Concept scheme:</strong> ConceptScheme</h1>

diff --git a/docs/test_sample_type.md b/docs/test_sample_type.md
@@ -12,7 +12,7 @@ getObject predicate: http://www.w3.org/2004/02/skos/core#prefLabel
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3d711040>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94df6cfdd0>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -27,7 +27,7 @@ getObject predicate: http://purl.org/dc/terms/modified
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3c9e8200>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94df750770>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -42,7 +42,7 @@ getObject predicate: http://www.w3.org/2004/02/skos/core#definition
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3b929940>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94de699160>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -57,7 +57,7 @@ getObject predicate: http://www.w3.org/2000/01/rdf-schema#comment
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3c9e8710>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94df751160>
 
 getObject prefixes: 
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
@@ -72,7 +72,7 @@ getObject predicate: http://www.w3.org/2004/02/skos/core#historyNote
 
 length of qres: 0
 
-qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7fcc3b929d60>
+qres: <rdflib.plugins.sparql.processor.SPARQLResult object at 0x7f94de698350>
 
 ---
 comment: | 

diff --git a/tools/navocab/__init__.py b/tools/navocab/__init__.py
@@ -72,7 +72,7 @@ def __init__(
         storage_uri=DEFAULT_STORE,
         store_identifier=STORE_IDENTIFIER,
 #        purge_existing=False,
-        purge_existing=False  # change to true to get rid of previous loads
+        purge_existing=True  # change to true to get rid of previous loads
     ):
         self.origin = None
         self.storage_uri = storage_uri
@@ -93,6 +93,7 @@ def _initialize_store(self, purge=False):
 
 
         if purge:
+            L.debug("navocab init: purging %s", self.store_identifier)
             graph.destroy(self.storage_uri)
 
         graph.open(self.storage_uri, create=True)
@@ -142,6 +143,7 @@ def load(
         # First check for extension_vocab rdfs:subPropertyOf extended_vocab
         # if not present, then compute and add it for later use.
         # What vocabulary did we just load?
+        L.debug("bindings: %s", bindings.items())
         q = (
             VocabularyStore._PFX
             + """SELECT ?s
@@ -150,7 +152,6 @@ def load(
         }"""
         )
         qres = g_loaded.query(q)
-        L.info("Navocab.load.query result: %s", qres)
         loaded_vocabulary = self._result_single_value(qres, abbreviate=False)
         if loaded_vocabulary is not None:
             L.info("Loaded vocabulary %s", loaded_vocabulary)