Merge pull request #86 from opendata-mvcr/enhancement/85-subclassof-b…

…roader

Enhancement/85 subclassof broader

ontology/termit-model.ttl

@@ -267,3 +267,7 @@ termit-pojem:je-publikován
 
 termit-pojem:má-můj-poslední-komentář
         a               owl:ObjectProperty.
+
+rdfs:subClassOf
+        a rdf:Property ;
+        rdfs:subPropertyOf  <http://www.w3.org/2004/02/skos/core#broader> .

pom.xml

@@ -20,7 +20,7 @@
     <repositories>
         <repository>
             <id>kbss</id>
-            <url>http://kbss.felk.cvut.cz/m2repo</url>
+            <url>https://kbss.felk.cvut.cz/m2repo</url>
         </repository>
     </repositories>
 

src/main/java/cz/cvut/kbss/termit/dto/TermDto.java

@@ -9,6 +9,7 @@
 import cz.cvut.kbss.termit.model.AbstractTerm;
 import cz.cvut.kbss.termit.model.Term;
 
+import java.util.Collection;
 import java.util.LinkedHashSet;
 import java.util.Objects;
 import java.util.Set;
@@ -56,4 +57,12 @@ public Set<TermDto> getParentTerms() {
     public void setParentTerms(Set<TermDto> parentTerms) {
         this.parentTerms = parentTerms;
     }
+
+    public void addParentTerms(Collection<TermDto> parents) {
+        Objects.requireNonNull(parents);
+        if (parentTerms == null) {
+            this.parentTerms = new LinkedHashSet<>();
+        }
+        parentTerms.addAll(parents);
+    }
 }

src/main/java/cz/cvut/kbss/termit/model/Term.java

@@ -6,6 +6,7 @@
 import cz.cvut.kbss.jopa.model.annotations.*;
 import cz.cvut.kbss.jopa.model.descriptors.Descriptor;
 import cz.cvut.kbss.jopa.vocabulary.DC;
+import cz.cvut.kbss.jopa.vocabulary.RDFS;
 import cz.cvut.kbss.jopa.vocabulary.SKOS;
 import cz.cvut.kbss.jsonld.annotation.JsonLdAttributeOrder;
 import cz.cvut.kbss.termit.dto.TermInfo;
@@ -33,7 +34,7 @@
 @Configurable
 @Audited
 @OWLClass(iri = SKOS.CONCEPT)
-@JsonLdAttributeOrder({"uri", "label", "description", "subTerms"})
+@JsonLdAttributeOrder({"uri", "label", "description", "parentTerms", "superTypes", "subTerms"})
 public class Term extends AbstractTerm implements HasTypes {
 
     /**
@@ -42,8 +43,7 @@ public class Term extends AbstractTerm implements HasTypes {
     public static final List<String> EXPORT_COLUMNS = Collections
             .unmodifiableList(
                     Arrays.asList("IRI", "Label", "Alternative Labels", "Hidden Labels", "Definition", "Description",
-                            "Types", "Sources", "Parent term",
-                            "SubTerms", "Draft"));
+                            "Types", "Sources", "Parent term", "SubTerms", "Draft"));
 
     @Autowired
     @Transient
@@ -64,6 +64,10 @@ public class Term extends AbstractTerm implements HasTypes {
     @OWLObjectProperty(iri = SKOS.BROADER, fetch = FetchType.EAGER)
     private Set<Term> parentTerms;
 
+    @OWLObjectProperty(iri = RDFS.SUB_CLASS_OF, fetch = FetchType.EAGER)
+    // TODO Replace with TermInfo when new the new model with TermInfo being entity is merged from KBSS
+    private Set<Term> superTypes;
+
     @Inferred
     @OWLObjectProperty(iri = Vocabulary.s_p_ma_zdroj_definice_termu, fetch = FetchType.EAGER)
     private TermDefinitionSource definitionSource;
@@ -144,6 +148,14 @@ public void addParentTerm(Term term) {
         parentTerms.add(term);
     }
 
+    public Set<Term> getSuperTypes() {
+        return superTypes;
+    }
+
+    public void setSuperTypes(Set<Term> superTypes) {
+        this.superTypes = superTypes;
+    }
+
     public Set<String> getSources() {
         return sources;
     }
@@ -270,7 +282,8 @@ public void toExcel(Row row) {
      * term at all
      */
     public boolean hasParentInSameVocabulary() {
-        return parentTerms != null && parentTerms.stream().anyMatch(p -> p.getGlossary().equals(getGlossary()));
+        return parentTerms != null && parentTerms.stream().anyMatch(p -> p.getGlossary().equals(getGlossary()))
+                || superTypes != null && superTypes.stream().anyMatch(p -> p.getGlossary().equals(getGlossary()));
     }
 
     @Override

src/main/java/cz/cvut/kbss/termit/persistence/DescriptorFactory.java

@@ -248,7 +248,9 @@ public Descriptor termDescriptor(URI vocabularyUri) {
         persistenceUtils.getCanonicalContainerContexts().forEach(parentDescriptor::addContext);
         // Allow indefinite length of the ancestor chain
         parentDescriptor.addAttributeDescriptor(fieldSpec(Term.class, "parentTerms"), parentDescriptor);
+        parentDescriptor.addAttributeDescriptor(fieldSpec(Term.class, "superTypes"), parentDescriptor);
         descriptor.addAttributeDescriptor(fieldSpec(Term.class, "parentTerms"), parentDescriptor);
+        descriptor.addAttributeDescriptor(fieldSpec(Term.class, "superTypes"), parentDescriptor);
         // Definition source is inferred. That means it is in a special context in GraphDB. Therefore, we need to use
         // the default context to prevent JOPA from thinking the value has changed on merge
         descriptor.addAttributeContext(fieldSpec(Term.class, "definitionSource"), null);

src/main/java/cz/cvut/kbss/termit/persistence/dao/TermDao.java

@@ -324,7 +324,14 @@ private <T extends AbstractTerm> List<T> findAllFrom(Set<URI> contexts, Pageable
             final Descriptor descriptor = descriptorFactory.termDescriptor((URI) null);
             resolveWorkspaceAndCanonicalContexts().forEach(descriptor::addContext);
             query.setDescriptor(descriptor);
-            return executeQueryAndLoadSubTerms(query, contexts);
+            final List<T> result = executeQueryAndLoadSubTerms(query, contexts);
+            if (TermDto.class.isAssignableFrom(resultType)) {
+                result.forEach(t -> {
+                    final TermDto dto = (TermDto) t;
+                    dto.addParentTerms(loadInferredParentTerms(dto, contexts, dto.getParentTerms()));
+                });
+            }
+            return result;
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
@@ -409,12 +416,32 @@ private List<TermDto> findAllFrom(Set<URI> contexts, String searchString, Pageab
             final Descriptor descriptor = descriptorFactory.termDescriptor((URI) null);
             contexts.forEach(descriptor::addContext);
             query.setDescriptor(descriptor);
-            return executeQueryAndLoadSubTerms(query, contexts);
+            final List<TermDto> result = executeQueryAndLoadSubTerms(query, contexts);
+            result.forEach(t -> {
+                t.addParentTerms(loadInferredParentTerms(t, contexts, t.getParentTerms()));
+            });
+            return result;
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
     }
 
+    private List<TermDto> loadInferredParentTerms(TermDto term, Set<URI> graphs, Set<TermDto> exclude) {
+        return em.createNativeQuery("SELECT DISTINCT ?parent WHERE {" +
+                "GRAPH ?g { " +
+                "?parent a ?type ." +
+                "}" +
+                "?term ?broader ?parent ." +    // Let broader be outside of the graph to include inference
+                "FILTER (?g IN (?graphs))" +
+                "FILTER (?parent NOT IN (?exclude))" +
+                "}", TermDto.class).setParameter("type", typeUri)
+                .setParameter("term", term)
+                .setParameter("broader", URI.create(SKOS.BROADER))
+                .setParameter("graphs", graphs)
+                .setParameter("exclude", exclude != null ? exclude : Collections.emptyList())
+                .getResultList();
+    }
+
     /**
      * Returns true if the vocabulary does not contain any terms.
      *
@@ -463,12 +490,13 @@ private void loadAdditionTermMetadata(AbstractTerm term, Set<URI> graphs) {
      */
     private Set<TermInfo> loadSubTermInfo(AbstractTerm parent, Set<URI> graphs) {
         final Stream<TermInfo> subTermsStream = em.createNativeQuery("SELECT ?entity ?label ?vocabulary WHERE {" +
-                "GRAPH ?g { ?entity ?broader ?parent ;" +
-                "a ?type ;" +
+                "GRAPH ?g { " +
+                "?entity a ?type ;" +
                 "?hasLabel ?label ." +
                 "FILTER (lang(?label) = ?labelLang) ." +
                 "}" +
-                "?entity ?inVocabulary ?vocabulary ." +
+                "?entity ?broader ?parent ; " + // Let broader be outside of the graph to allow including inferences
+                "?inVocabulary ?vocabulary ." +
                 "FILTER (?g in (?graphs))" +
                 "} ORDER BY LCASE(?label)", "TermInfo")
                 .setParameter("type", typeUri)
@@ -582,7 +610,10 @@ private List<TermDto> findAllImpl(String searchString, URI vocabularyIri) {
                     .setParameter("searchString", searchString, config.get(ConfigParam.LANGUAGE));
             query.setDescriptor(descriptorFactory.termDescriptor(vocabularyIri));
             final List<TermDto> terms = executeQueryAndLoadSubTerms(query, Collections.singleton(vocabularyCtx));
-            terms.forEach(t -> loadParentSubTerms(t, vocabularyCtx));
+            terms.forEach(t -> {
+                loadParentSubTerms(t, vocabularyCtx);
+                t.addParentTerms(loadInferredParentTerms(t, Collections.singleton(vocabularyCtx), t.getParentTerms()));
+            });
             return terms;
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
@@ -641,19 +672,17 @@ public List<Term> findAllSubTerms(Term parent) {
         graphs.forEach(descriptor::addContext);
         final TypedQuery<Term> query = em.createNativeQuery("SELECT DISTINCT ?term WHERE {" +
                 "GRAPH ?g { " +
-                "?term ?broader ?parent ;" +
-                "a ?type ;" +
-                "?hasLabel ?label . " +
-                "FILTER (lang(?label) = ?labelLang) ." +
+                "?term a ?type ." +
                 "}" +
+                "?term ?broader ?parent ." +    // Let broader be outside of the graph to include inference
                 "FILTER (?g in (?graphs))" +
-                "} ORDER BY LCASE(?label)", Term.class).setParameter("type", typeUri)
+                "}", Term.class).setParameter("type", typeUri)
                 .setParameter("broader", URI.create(SKOS.BROADER))
                 .setParameter("parent", parent)
-                .setParameter("hasLabel", LABEL_PROP)
                 .setParameter("graphs", graphs)
-                .setParameter("labelLang", config.get(ConfigParam.LANGUAGE))
                 .setDescriptor(descriptor);
-        return executeQueryAndLoadSubTerms(query, graphs);
+        final List<Term> terms = executeQueryAndLoadSubTerms(query, graphs);
+        terms.sort(Comparator.comparing(t -> t.getLabel().get(config.get(ConfigParam.LANGUAGE))));
+        return terms;
     }
 }

src/test/java/cz/cvut/kbss/termit/model/TermTest.java

@@ -297,4 +297,16 @@ void toExcelHandlesNullAltLabelsAttribute() {
                                               .forEach(v -> assertThat(row.getCell(3).getStringCellValue(),
                                                       containsString(v))));
     }
+
+    @Test
+    void hasParentInSameVocabularyIncludesSuperTypesAsParents() {
+        final Term sut = Generator.generateTermWithId();
+        final URI vocabularyUri = Generator.generateUri();
+        sut.setGlossary(vocabularyUri);
+        final Term parent = Generator.generateTermWithId();
+        parent.setGlossary(vocabularyUri);
+        sut.setSuperTypes(Collections.singleton(parent));
+
+        assertTrue(sut.hasParentInSameVocabulary());
+    }
 }

src/test/java/cz/cvut/kbss/termit/persistence/DescriptorFactoryTest.java

@@ -161,4 +161,18 @@ private Set<URI> generateCanonicalContainer() {
         });
         return statements.stream().map(s -> URI.create(s.getObject().stringValue())).collect(Collectors.toSet());
     }
+
+    @Test
+    void termDescriptorCreatesDescriptorWithSuperTypesContextsContainingWorkspaceVocabulariesAndCanonicalCacheContainerContexts() throws Exception {
+        final FieldSpecification<Term, Term> superTypesFieldSpec = mock(FieldSpecification.class);
+        when(superTypesFieldSpec.getJavaField()).thenReturn(Term.class.getDeclaredField("superTypes"));
+        final Set<URI> workspaceVocabularies = IntStream.range(0, 3).mapToObj(i -> Generator.generateUri()).collect(Collectors.toSet());
+        final WorkspaceMetadata wsMetadata = workspaceMetadataProvider.getCurrentWorkspaceMetadata();
+        doReturn(workspaceVocabularies).when(wsMetadata).getVocabularyContexts();
+        final Set<URI> canonicalVocabularies = generateCanonicalContainer();
+        final Descriptor result = sut.termDescriptor(term);
+        final Set<URI> parentContexts = result.getAttributeDescriptor(superTypesFieldSpec).getContexts();
+        assertThat(parentContexts, hasItems(workspaceVocabularies.toArray(new URI[]{})));
+        assertThat(parentContexts, hasItems(canonicalVocabularies.toArray(new URI[]{})));
+    }
 }

src/test/java/cz/cvut/kbss/termit/persistence/dao/TermDaoTest.java

@@ -727,4 +727,33 @@ void subTermLoadingSortsThemByLabel() {
             assertEquals(child.getUri(), next.getUri());
         }
     }
+
+    @Test
+    void findAllBySearchStringAndVocabularyLoadsInferredParentTerms() {
+        final Term term = Generator.generateTermWithId(vocabulary.getUri());
+        final String searchString = "test";
+        term.getLabel().set(Constants.DEFAULT_LANGUAGE, searchString + " value");
+        final Term parent = Generator.generateTermWithId(vocabulary.getUri());
+        vocabulary.getGlossary().addRootTerm(parent);
+        transactional(() -> {
+            em.persist(term, descriptorFactory.termDescriptor(vocabulary));
+            em.persist(parent, descriptorFactory.termDescriptor(vocabulary));
+            em.merge(vocabulary.getGlossary(), descriptorFactory.glossaryDescriptor(vocabulary));
+            addTermInVocabularyRelationship(term, vocabulary.getUri());
+            addTermInVocabularyRelationship(parent, vocabulary.getUri());
+            insertInferredBroaderRelationship(term, parent, em);
+        });
+
+        final List<TermDto> result = sut.findAll(searchString, vocabulary);
+        assertEquals(1, result.size());
+        assertThat(result.get(0).getParentTerms(), hasItem(new TermDto(parent)));
+    }
+
+    static void insertInferredBroaderRelationship(Term child, Term parent, EntityManager em) {
+        final Repository repo = em.unwrap(Repository.class);
+        try (final RepositoryConnection conn = repo.getConnection()) {
+            final ValueFactory vf = conn.getValueFactory();
+            conn.add(vf.createIRI(child.getUri().toString()), vf.createIRI(SKOS.BROADER), vf.createIRI(parent.getUri().toString()));
+        }
+    }
 }

src/test/java/cz/cvut/kbss/termit/persistence/dao/TermDaoWorkspacesTest.java

@@ -847,4 +847,74 @@ void findAllRootsReturnsCorrectPageContent() {
         final List<TermDto> result = sut.findAllRoots(PageRequest.of(1, pageSize));
         assertEquals(expected, result);
     }
+
+    @Test
+    void updateSupportsTermWithSupertypeInCanonicalContainer() {
+        final Term term = Generator.generateTermWithId();
+        final Term superType = Generator.generateTermWithId();
+        persistTermIntoCanonicalContainer(superType);
+        final EntityDescriptor termDescriptor = new EntityDescriptor(vocabulary.getUri());
+        transactional(() -> {
+            em.persist(term, termDescriptor);
+            Generator.addTermInVocabularyRelationship(term, vocabulary.getUri(), em);
+        });
+
+        term.setSuperTypes(Collections.singleton(superType));
+        // This is normally inferred
+        term.setVocabulary(vocabulary.getUri());
+        transactional(() -> sut.update(term));
+        final Term result = em.find(Term.class, term.getUri());
+        assertEquals(term, result);
+        assertEquals(term, result);
+        assertThat(result.getSuperTypes(), hasItem(superType));
+    }
+
+    @Test
+    void findAllInCurrentWorkspaceBySearchStringLoadsInferredParentTerms() {
+        final String searchString = "search";
+        final Term term = Generator.generateTermWithId();
+        final Term parent = Generator.generateTermWithId();
+        term.getLabel().set(Constants.DEFAULT_LANGUAGE, searchString + " string label");
+        term.setGlossary(vocabulary.getGlossary().getUri());
+        final Vocabulary anotherVocabularyInWs = Generator.generateVocabularyWithId();
+        saveVocabulary(anotherVocabularyInWs);
+        parent.setGlossary(anotherVocabularyInWs.getGlossary().getUri());
+        transactional(() -> {
+            em.persist(term, new EntityDescriptor(vocabulary.getUri()));
+            vocabulary.getGlossary().addRootTerm(term);
+            em.merge(vocabulary.getGlossary(), descriptorFactory.glossaryDescriptor(vocabulary));
+            Generator.addTermInVocabularyRelationship(term, vocabulary.getUri(), em);
+            em.persist(parent, new EntityDescriptor(anotherVocabularyInWs.getUri()));
+            Generator.addTermInVocabularyRelationship(parent, anotherVocabularyInWs.getUri(), em);
+            TermDaoTest.insertInferredBroaderRelationship(term, parent, em);
+        });
+
+        final List<TermDto> result = sut.findAll(searchString);
+        assertEquals(1, result.size());
+        assertThat(result.get(0).getParentTerms(), hasItem(new TermDto(parent)));
+    }
+
+    @Test
+    void findAllByPageableLoadsInferredParentTerms() {
+        final Term term = Generator.generateTermWithId();
+        final Term parent = Generator.generateTermWithId();
+        term.setGlossary(vocabulary.getGlossary().getUri());
+        final Vocabulary anotherVocabularyInWs = Generator.generateVocabularyWithId();
+        saveVocabulary(anotherVocabularyInWs);
+        parent.setGlossary(anotherVocabularyInWs.getGlossary().getUri());
+        transactional(() -> {
+            em.persist(term, new EntityDescriptor(vocabulary.getUri()));
+            vocabulary.getGlossary().addRootTerm(term);
+            em.merge(vocabulary.getGlossary(), descriptorFactory.glossaryDescriptor(vocabulary));
+            Generator.addTermInVocabularyRelationship(term, vocabulary.getUri(), em);
+            em.persist(parent, new EntityDescriptor(anotherVocabularyInWs.getUri()));
+            Generator.addTermInVocabularyRelationship(parent, anotherVocabularyInWs.getUri(), em);
+            TermDaoTest.insertInferredBroaderRelationship(term, parent, em);
+        });
+
+        final List<TermDto> results = sut.findAll(Constants.DEFAULT_PAGE_SPEC);
+        final Optional<TermDto> res = results.stream().filter(t -> t.getUri().equals(term.getUri())).findFirst();
+        assertTrue(res.isPresent());
+        assertThat(res.get().getParentTerms(), hasItem(new TermDto(parent)));
+    }
 }