Merge pull request #222 from kbss-cvut/development

2.16.3 Release

pom.xml

@@ -7,11 +7,11 @@
  <parent>
  <groupId>org.springframework.boot</groupId>
  <artifactId>spring-boot-starter-parent</artifactId>
- <version>2.7.8</version>
+ <version>2.7.9</version>
  </parent>
 
  <artifactId>termit</artifactId>
- <version>2.16.2</version>
+ <version>2.16.3</version>
  <name>TermIt</name>
  <description>Terminology manager based on Semantic Web technologies.</description>
  <packaging>${packaging}</packaging>
@@ -25,10 +25,10 @@
 
  <properties>
  <java.version>11</java.version>
- <org.apache.tika.tika-core.version>2.6.0</org.apache.tika.tika-core.version>
+ <org.apache.tika.tika-core.version>2.7.0</org.apache.tika.tika-core.version>
  <org.mapstruct.version>1.5.3.Final</org.mapstruct.version>
- <cz.cvut.kbss.jopa.version>0.20.2</cz.cvut.kbss.jopa.version>
- <cz.cvut.kbss.jsonld.version>0.11.1</cz.cvut.kbss.jsonld.version>
+ <cz.cvut.kbss.jopa.version>0.21.1</cz.cvut.kbss.jopa.version>
+ <cz.cvut.kbss.jsonld.version>0.12.0</cz.cvut.kbss.jsonld.version>
  <org.aspectj.version>1.9.7</org.aspectj.version>
 
  <!-- Default value for deployment type property which should otherwise specified on command line -->
@@ -250,7 +250,7 @@
  <dependency>
  <groupId>org.jsoup</groupId>
  <artifactId>jsoup</artifactId>
- <version>1.15.3</version>
+ <version>1.15.4</version>
  </dependency>
 
  <!-- Flexmark for handling Markdown -->
@@ -295,7 +295,7 @@
  <dependency>
  <groupId>net.bull.javamelody</groupId>
  <artifactId>javamelody-spring-boot-starter</artifactId>
- <version>1.91.0</version>
+ <version>1.92.0</version>
  </dependency>
 
  <!-- Caching -->
@@ -431,9 +431,9 @@
  </configuration>
  </plugin>
  <plugin>
- <groupId>org.codehaus.mojo</groupId>
+ <groupId>dev.aspectj</groupId>
  <artifactId>aspectj-maven-plugin</artifactId>
- <version>1.14.0</version>
+ <version>1.13.1</version>
  <configuration>
  <complianceLevel>${java.version}</complianceLevel>
  <source>${java.version}</source>

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

@@ -17,8 +17,10 @@
  */
 package cz.cvut.kbss.termit.dto;
 
+import cz.cvut.kbss.jopa.model.MultilingualString;
 import cz.cvut.kbss.jopa.model.annotations.*;
 import cz.cvut.kbss.jopa.vocabulary.RDFS;
+import cz.cvut.kbss.ontodriver.model.LangString;
 import cz.cvut.kbss.termit.model.util.HasTypes;
 
 import java.io.Serializable;
@@ -35,9 +37,9 @@
  @VariableResult(name = "x",
  type = URI.class),
  @VariableResult(name = "label",
- type = String.class),
+ type = LangString.class),
  @VariableResult(name = "comment",
- type = String.class),
+ type = LangString.class),
  @VariableResult(name = "type",
  type = String.class)
  })})
@@ -48,21 +50,25 @@ public class RdfsResource implements Serializable, HasTypes {
  private URI uri;
 
  @OWLAnnotationProperty(iri = RDFS.LABEL)
- private String label;
+ private MultilingualString label;
 
  @OWLAnnotationProperty(iri = RDFS.COMMENT)
- private String comment;
+ private MultilingualString comment;
 
  @Types
  private Set<String> types;
 
  public RdfsResource() {
  }
 
- public RdfsResource(URI uri, String label, String comment, String type) {
+ public RdfsResource(URI uri, LangString label, LangString comment, String type) {
  this.uri = uri;
- this.label = label;
- this.comment = comment;
+ if (label != null) {
+ this.label = MultilingualString.create(label.getValue(), label.getLanguage().orElse(null));
+ }
+ if (comment != null) {
+ this.comment = MultilingualString.create(comment.getValue(), comment.getLanguage().orElse(null));
+ }
  this.types = Collections.singleton(type);
  }
 
@@ -74,19 +80,19 @@ public void setUri(URI uri) {
  this.uri = uri;
  }
 
- public String getLabel() {
+ public MultilingualString getLabel() {
  return label;
  }
 
- public void setLabel(String label) {
+ public void setLabel(MultilingualString label) {
  this.label = label;
  }
 
- public String getComment() {
+ public MultilingualString getComment() {
  return comment;
  }
 
- public void setComment(String comment) {
+ public void setComment(MultilingualString comment) {
  this.comment = comment;
  }
 
@@ -123,7 +129,7 @@ public int hashCode() {
  public String toString() {
  return "RdfsResource{" +
  "uri=" + uri +
- ", label='" + label + '\'' +
+ ", label=" + label +
  ", types=" + types +
  '}';
  }

src/main/java/cz/cvut/kbss/termit/dto/readonly/ReadOnlyTerm.java

@@ -184,13 +184,4 @@ public Map<String, Set<String>> getProperties() {
  public void setProperties(final Map<String, Set<String>> properties) {
  this.properties = properties;
  }
-
- @Override
- public String toString() {
- return "ReadOnlyTerm{" +
- getLabel() +
- " <" + getUri() + '>' +
- ", types=" + getTypes() +
- '}';
- }
 }

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

@@ -7,6 +7,7 @@
 import cz.cvut.kbss.termit.model.util.AssetVisitor;
 import cz.cvut.kbss.termit.model.util.HasTypes;
 import cz.cvut.kbss.termit.model.util.SupportsSnapshots;
+import cz.cvut.kbss.termit.util.Utils;
 import cz.cvut.kbss.termit.util.Vocabulary;
 import cz.cvut.kbss.termit.validation.PrimaryNotBlank;
 
@@ -157,4 +158,13 @@ public boolean equals(Object o) {
  public int hashCode() {
  return Objects.hash(getUri());
  }
+
+ @Override
+ public String toString() {
+ return getClass().getSimpleName() + "{" +
+ getLabel() + ' ' +
+ Utils.uriToString(getUri()) +
+ ", types=" + getTypes() +
+ '}';
+ }
 }

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

@@ -383,13 +383,4 @@ public void splitExternalAndInternalParents() {
  this.parentTerms = parents;
  this.externalParentTerms = externalParents;
  }
-
- @Override
- public String toString() {
- return "Term{" +
- getLabel() +
- " <" + getUri() + '>' +
- ", types=" + getTypes() +
- '}';
- }
 }

src/main/java/cz/cvut/kbss/termit/persistence/context/VocabularyContextMapper.java

@@ -14,7 +14,7 @@ public interface VocabularyContextMapper {
  /**
  * Gets identifier of the repository context in which the specified vocabulary is stored.
  *
- * @param vocabulary Vocabulary whose context to retrieve
+ * @param vocabulary Vocabulary whose context to retrieve. A reference is sufficient
  * @return Repository context identifier
  */
  default URI getVocabularyContext(Vocabulary vocabulary) {

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

@@ -38,10 +38,7 @@
 
 import java.io.ByteArrayOutputStream;
 import java.net.URI;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
+import java.util.*;
 import java.util.stream.Collectors;
 
 @Repository
@@ -65,7 +62,7 @@ public DataDao(EntityManager em, Configuration config) {
  * @return List of properties, ordered by label
  */
  public List<RdfsResource> findAllProperties() {
- return em.createNativeQuery("SELECT ?x ?label ?comment ?type WHERE {" +
+ final List<RdfsResource> result = em.createNativeQuery("SELECT ?x ?label ?comment ?type WHERE {" +
  "BIND (?property as ?type)" +
  "?x a ?type ." +
  "OPTIONAL { ?x ?has-label ?label . }" +
@@ -74,6 +71,25 @@ public List<RdfsResource> findAllProperties() {
  .setParameter("property", URI.create(RDF.PROPERTY))
  .setParameter("has-label", RDFS_LABEL)
  .setParameter("has-comment", URI.create(RDFS.COMMENT)).getResultList();
+ return consolidateTranslations(result);
+ }
+
+ private static List<RdfsResource> consolidateTranslations(List<RdfsResource> queryResult) {
+ final Map<URI, RdfsResource> map = new LinkedHashMap<>(queryResult.size());
+ queryResult.forEach(r -> {
+ if (!map.containsKey(r.getUri())) {
+ map.put(r.getUri(), r);
+ } else {
+ final RdfsResource res = map.get(r.getUri());
+ if (r.getLabel() != null) {
+ res.getLabel().getValue().putAll(r.getLabel().getValue());
+ }
+ if (r.getComment() != null) {
+ res.getComment().getValue().putAll(r.getComment().getValue());
+ }
+ }
+ });
+ return new ArrayList<>(map.values());
  }
 
  /**
@@ -101,14 +117,14 @@ public void persist(RdfsResource instance) {
  */
  public Optional<RdfsResource> find(URI id) {
  Objects.requireNonNull(id);
- final List<RdfsResource> resources = em.createNativeQuery("SELECT ?x ?label ?comment ?type WHERE {" +
+ final List<RdfsResource> resources = consolidateTranslations(em.createNativeQuery("SELECT ?x ?label ?comment ?type WHERE {" +
  "BIND (?id AS ?x)" +
  "?x a ?type ." +
  "OPTIONAL { ?x ?has-label ?label .}" +
  "OPTIONAL { ?x ?has-comment ?comment . }" +
  "}", "RdfsResource").setParameter("id", id)
  .setParameter("has-label", RDFS_LABEL)
- .setParameter("has-comment", URI.create(RDFS.COMMENT)).getResultList();
+ .setParameter("has-comment", URI.create(RDFS.COMMENT)).getResultList());
  if (resources.isEmpty()) {
  return Optional.empty();
  }

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

@@ -250,6 +250,12 @@ private void evictCachedSubTerms(Set<? extends AbstractTerm> originalParents,
  newCopy.forEach(t -> subTermsCache.evict(t.getUri()));
  }
 
+ /**
+ * Finds all terms in the specified vocabulary, regardless of their position in the term hierarchy.
+ *
+ * @param vocabulary Vocabulary whose terms to retrieve. A reference is sufficient
+ * @return List of vocabulary term DTOs
+ */
  public List<TermDto> findAll(Vocabulary vocabulary) {
  Objects.requireNonNull(vocabulary);
  try {

src/main/java/cz/cvut/kbss/termit/persistence/validation/Validator.java

@@ -5,6 +5,7 @@
 import cz.cvut.kbss.jopa.model.MultilingualString;
 import cz.cvut.kbss.termit.exception.TermItException;
 import cz.cvut.kbss.termit.model.validation.ValidationResult;
+import cz.cvut.kbss.termit.persistence.context.VocabularyContextMapper;
 import cz.cvut.kbss.termit.util.Configuration;
 import cz.cvut.kbss.termit.util.Utils;
 import org.apache.jena.rdf.model.Literal;
@@ -13,6 +14,7 @@
 import org.apache.jena.rdf.model.RDFNode;
 import org.apache.jena.util.FileUtils;
 import org.eclipse.rdf4j.model.IRI;
+import org.eclipse.rdf4j.model.ValueFactory;
 import org.eclipse.rdf4j.repository.Repository;
 import org.eclipse.rdf4j.repository.RepositoryConnection;
 import org.eclipse.rdf4j.rio.turtle.TurtleWriter;
@@ -54,13 +56,17 @@ public class Validator implements VocabularyContentValidator {
  private static final Set<String> MODEL_RULES_TO_ADD = Set.of("m1.ttl", "m2.ttl");
 
  private final EntityManager em;
+ private final VocabularyContextMapper vocabularyContextMapper;
 
  private com.github.sgov.server.Validator validator;
  private Model validationModel;
 
  @Autowired
- public Validator(EntityManager em, Configuration config) {
+ public Validator(EntityManager em,
+ VocabularyContextMapper vocabularyContextMapper,
+ Configuration config) {
  this.em = em;
+ this.vocabularyContextMapper = vocabularyContextMapper;
  initValidator(config.getPersistence().getLanguage());
  }
 
@@ -149,9 +155,11 @@ private Model getModelFromRdf4jRepository(final Collection<URI> vocabularyIris)
  final ByteArrayOutputStream baos = new ByteArrayOutputStream();
  final OutputStreamWriter writer = new OutputStreamWriter(baos, StandardCharsets.UTF_8);
  final Repository repository = em.unwrap(Repository.class);
+ final ValueFactory vf = repository.getValueFactory();
  try (final RepositoryConnection c = repository.getConnection()) {
  final List<IRI> iris = new ArrayList<>();
- vocabularyIris.forEach(i -> iris.add(repository.getValueFactory().createIRI(i.toString())));
+ vocabularyIris.forEach(
+ i -> iris.add(vf.createIRI(vocabularyContextMapper.getVocabularyContext(i).toString())));
  c.export(new TurtleWriter(writer), iris.toArray(new IRI[]{}));
  writer.close();
  }

src/main/java/cz/cvut/kbss/termit/service/business/TermService.java

@@ -79,7 +79,7 @@ public TermService(VocabularyExporters exporters, VocabularyService vocabularySe
  * If export into the specified media type is not supported, an empty {@link Optional} is returned.
  *
  * @param vocabulary Vocabulary to export
- * @param config Expected media type of the export
+ * @param config  Expected media type of the export
  * @return Exported resource wrapped in an {@code Optional}
  */
  public Optional<TypeAwareResource> exportGlossary(Vocabulary vocabulary, ExportConfig config) {
@@ -91,7 +91,7 @@ public Optional<TypeAwareResource> exportGlossary(Vocabulary vocabulary, ExportC
  /**
  * Retrieves all terms from the specified vocabulary.
  *
- * @param vocabulary Vocabulary whose terms will be returned
+ * @param vocabulary Vocabulary whose terms will be returned. A reference is sufficient
  * @return Matching terms
  */
  public List<TermDto> findAll(Vocabulary vocabulary) {
@@ -394,7 +394,7 @@ public void remove(Term term) {
  * during the analysis).
  *
  * @param term Term to analyze
- * @param vocabularyContext Identifier of the vocabulary used for analysis
+ * @param vocabularyContext Identifier of the repository context of the vocabulary used for analysis
  */
  public void analyzeTermDefinition(AbstractTerm term, URI vocabularyContext) {
  Objects.requireNonNull(term);