Merge pull request #263 from kbss-cvut/development

[3.0.4] Release
kbss-cvut · Apr 15, 2024 · 6be4c40 · 6be4c40
2 parents e427b5d + 6b53d4d
commit 6be4c40
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Showing 17 changed files with 131 additions and 73 deletions.
diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,7 @@
     </parent>
 
     <artifactId>termit</artifactId>
-    <version>3.0.3</version>
+    <version>3.0.4</version>
     <name>TermIt</name>
     <description>Terminology manager based on Semantic Web technologies.</description>
     <packaging>${packaging}</packaging>

diff --git a/src/main/java/cz/cvut/kbss/termit/persistence/dao/acl/AccessControlListDao.java b/src/main/java/cz/cvut/kbss/termit/persistence/dao/acl/AccessControlListDao.java
@@ -113,7 +113,7 @@ public void persist(AccessControlList acl) {
      */
     public void update(AccessControlList acl) {
         Objects.requireNonNull(acl);
-        final AccessControlList original = em.find(AccessControlList.class, acl.getUri());
+        final AccessControlList original = em.find(AccessControlList.class, acl.getUri(), descriptor());
         assert original != null;
         removeOrphanRecords(original, acl);
         em.merge(acl, descriptor());

diff --git a/src/main/java/cz/cvut/kbss/termit/rest/handler/RestExceptionHandler.java b/src/main/java/cz/cvut/kbss/termit/rest/handler/RestExceptionHandler.java
@@ -60,19 +60,19 @@ public class RestExceptionHandler {
 
     private static final Logger LOG = LoggerFactory.getLogger(RestExceptionHandler.class);
 
-    private static void logException(TermItException ex) {
+    private static void logException(TermItException ex, HttpServletRequest request) {
         if (shouldSuppressLogging(ex)) {
             return;
         }
-        logException("Exception caught.", ex);
+        logException("Exception caught when processing request to '" + request.getRequestURI() + "'.", ex);
     }
 
     private static boolean shouldSuppressLogging(TermItException ex) {
         return ex.getClass().getAnnotation(SuppressibleLogging.class) != null;
     }
 
-    private static void logException(Throwable ex) {
-        logException("Exception caught.", ex);
+    private static void logException(Throwable ex, HttpServletRequest request) {
+        logException("Exception caught when processing request to '" + request.getRequestURI() + "'.", ex);
     }
 
     private static void logException(String message, Throwable ex) {
@@ -85,7 +85,7 @@ private static ErrorInfo errorInfo(HttpServletRequest request, Throwable e) {
 
     @ExceptionHandler(PersistenceException.class)
     public ResponseEntity<ErrorInfo> persistenceException(HttpServletRequest request, PersistenceException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e.getCause()), HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
@@ -97,7 +97,7 @@ public ResponseEntity<ErrorInfo> jopaException(HttpServletRequest request, OWLPe
 
     @ExceptionHandler(ResourceExistsException.class)
     public ResponseEntity<ErrorInfo> resourceExistsException(HttpServletRequest request, ResourceExistsException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.CONFLICT);
     }
 
@@ -115,40 +115,40 @@ public ResponseEntity<ErrorInfo> usernameNotFound(HttpServletRequest request, Us
 
     @ExceptionHandler(AuthorizationException.class)
     public ResponseEntity<ErrorInfo> authorizationException(HttpServletRequest request, AuthorizationException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.FORBIDDEN);
     }
 
     @ExceptionHandler(ValidationException.class)
     public ResponseEntity<ErrorInfo> validationException(HttpServletRequest request, ValidationException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.CONFLICT);
     }
 
     @ExceptionHandler(WebServiceIntegrationException.class)
     public ResponseEntity<ErrorInfo> webServiceIntegrationException(HttpServletRequest request,
                                                                     WebServiceIntegrationException e) {
-        logException(e.getCause());
+        logException(e.getCause(), request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
     @ExceptionHandler(AnnotationGenerationException.class)
     public ResponseEntity<ErrorInfo> annotationGenerationException(HttpServletRequest request,
                                                                    AnnotationGenerationException e) {
-        logException(e.getCause());
+        logException(e.getCause(), request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
     @ExceptionHandler(TermItException.class)
     public ResponseEntity<ErrorInfo> termItException(HttpServletRequest request,
                                                      TermItException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
     @ExceptionHandler(JsonLdException.class)
     public ResponseEntity<ErrorInfo> jsonLdException(HttpServletRequest request, JsonLdException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(
                 ErrorInfo.createWithMessage("Error when processing JSON-LD.", request.getRequestURI()),
                 HttpStatus.INTERNAL_SERVER_ERROR);
@@ -157,14 +157,14 @@ public ResponseEntity<ErrorInfo> jsonLdException(HttpServletRequest request, Jso
     @ExceptionHandler(UnsupportedOperationException.class)
     public ResponseEntity<ErrorInfo> unsupportedAssetOperationException(HttpServletRequest request,
                                                                         UnsupportedOperationException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.CONFLICT);
     }
 
     @ExceptionHandler(VocabularyImportException.class)
     public ResponseEntity<ErrorInfo> vocabularyImportException(HttpServletRequest request,
                                                                VocabularyImportException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(
                 ErrorInfo.createWithMessageAndMessageId(e.getMessage(), e.getMessageId(), request.getRequestURI()),
                 HttpStatus.CONFLICT);
@@ -173,26 +173,26 @@ public ResponseEntity<ErrorInfo> vocabularyImportException(HttpServletRequest re
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> unsupportedImportMediaTypeException(HttpServletRequest request,
                                                                          UnsupportedImportMediaTypeException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.UNSUPPORTED_MEDIA_TYPE);
     }
 
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> assetRemovalException(HttpServletRequest request, AssetRemovalException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.CONFLICT);
     }
 
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> invalidParameter(HttpServletRequest request, InvalidParameterException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.UNPROCESSABLE_ENTITY);
     }
 
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> maxUploadSizeExceededException(HttpServletRequest request,
                                                                     MaxUploadSizeExceededException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(ErrorInfo.createWithMessageAndMessageId(
                 e.getMessage(),
                 "error.file.maxUploadSizeExceeded", request.getRequestURI()), HttpStatus.BAD_REQUEST);
@@ -201,29 +201,29 @@ public ResponseEntity<ErrorInfo> maxUploadSizeExceededException(HttpServletReque
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> snapshotNotEditableException(HttpServletRequest request,
                                                                   SnapshotNotEditableException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(ErrorInfo.createWithMessage(e.getMessage(), request.getRequestURI()),
-                HttpStatus.CONFLICT);
+                                    HttpStatus.CONFLICT);
     }
 
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> unsupportedSearchFacetException(HttpServletRequest request,
                                                                      UnsupportedSearchFacetException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.BAD_REQUEST);
     }
 
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> invalidLanguageConstantException(HttpServletRequest request,
                                                                       InvalidLanguageConstantException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(errorInfo(request, e), HttpStatus.BAD_REQUEST);
     }
 
     @ExceptionHandler
     public ResponseEntity<ErrorInfo> vocabularyImportException(HttpServletRequest request,
                                                                InvalidTermStateException e) {
-        logException(e);
+        logException(e, request);
         return new ResponseEntity<>(
                 ErrorInfo.createWithMessageAndMessageId(e.getMessage(), e.getMessageId(), request.getRequestURI()),
                 HttpStatus.CONFLICT);

diff --git a/src/main/java/cz/cvut/kbss/termit/service/IdentifierResolver.java b/src/main/java/cz/cvut/kbss/termit/service/IdentifierResolver.java
@@ -98,7 +98,7 @@ public static String normalize(String value) {
         return value.toLowerCase()
                     .trim()
                     .replaceAll("[\\s/\\\\]", Character.toString(REPLACEMENT_CHARACTER))
-                    .replaceAll("[(?&),]", "");
+                    .replaceAll("[(?&$#),]", "");
     }
 
     /**
@@ -169,7 +169,7 @@ public URI generateDerivedIdentifier(URI baseUri, String namespaceSeparator, Str
 
     /**
      * Generates a synthetic identifier using the specified base URL.
-     *
+     * <p>
      * This particular implementation uses the current system time in millis to generate the locally unique part of the identifier.
      *
      * @param base URL base

diff --git a/src/main/java/cz/cvut/kbss/termit/service/business/readonly/ReadOnlyTermService.java b/src/main/java/cz/cvut/kbss/termit/service/business/readonly/ReadOnlyTermService.java
@@ -87,13 +87,20 @@ private ReadOnlyTerm create(final Term term) {
 
     public List<ReadOnlyTerm> findSubTerms(ReadOnlyTerm parent) {
         Objects.requireNonNull(parent);
-        final Term arg = new Term(parent.getUri());
+        final Term arg = toTerm(parent);
         if (parent.getSubTerms() != null) {
             arg.setSubTerms(parent.getSubTerms());
         }
         return termService.findSubTerms(arg).stream().map(this::create).collect(Collectors.toList());
     }
 
+    private static Term toTerm(ReadOnlyTerm roTerm) {
+        final Term t = new Term(roTerm.getUri());
+        // Ensure vocabulary is set on the Term instance as it may be referenced later
+        t.setVocabulary(roTerm.getVocabulary());
+        return t;
+    }
+
     /**
      * Gets comments related to the specified term created in the specified time interval.
      *
@@ -132,13 +139,13 @@ public List<TermOccurrence> getDefinitionallyRelatedTargeting(Term instance) {
 
     public List<Snapshot> findSnapshots(ReadOnlyTerm asset) {
         Objects.requireNonNull(asset);
-        final Term arg = new Term(asset.getUri());
+        final Term arg = toTerm(asset);
         return termService.findSnapshots(arg);
     }
 
     public ReadOnlyTerm findVersionValidAt(ReadOnlyTerm asset, Instant at) {
         Objects.requireNonNull(asset);
-        final Term arg = new Term(asset.getUri());
+        final Term arg = toTerm(asset);
         return create(termService.findVersionValidAt(arg, at));
     }
 }
diff --git a/src/main/java/cz/cvut/kbss/termit/service/changetracking/MetamodelBasedChangeCalculator.java b/src/main/java/cz/cvut/kbss/termit/service/changetracking/MetamodelBasedChangeCalculator.java
@@ -60,10 +60,10 @@ public Collection<UpdateChangeRecord> calculateChanges(Asset<?> changed, Asset<?
             final Object updateValue = EntityPropertiesUtils.getAttributeValue(att, changed);
             if (att.isAssociation()) {
                 final Optional<UpdateChangeRecord> change = resolveAssociationChange(originalValue, updateValue, att,
-                        original.getUri());
+                                                                                     original.getUri());
                 change.ifPresent(records::add);
 
-            } else if (!Objects.equals(originalValue, updateValue)) {
+            } else if (!areEqual(att, originalValue, updateValue)) {
                 final UpdateChangeRecord record = createChangeRecord(original.getUri(), att.getIRI().toURI());
                 recordValues(record, att, originalValue, updateValue);
                 records.add(record);
@@ -78,6 +78,11 @@ private boolean shouldIgnoreChanges(Attribute<?, ?> att) {
         return att.getJavaField().isAnnotationPresent(IgnoreChanges.class);
     }
 
+    private boolean areEqual(Attribute<?, ?> att, Object originalValue, Object newValue) {
+        return att.isCollection() ? areCollectionsEqual((Collection<?>) originalValue, (Collection<?>) newValue) :
+               Objects.equals(originalValue, newValue);
+    }
+
     private void recordValues(UpdateChangeRecord record, Attribute<?, ?> att, Object originalValue, Object newValue) {
         if (!att.isCollection()) {
             if (originalValue != null) {
@@ -120,7 +125,7 @@ private Optional<UpdateChangeRecord> resolveAssociationChange(Object originalVal
             updateToCompare = updateValue != null ? getIdentifier(updateValue, metamodel) : null;
         }
 
-        if (Objects.equals(originalToCompare, updateToCompare)) {
+        if (areEqual(att, originalToCompare, updateToCompare)) {
             return Optional.empty();
         } else {
             final UpdateChangeRecord record = createChangeRecord(assetId, att.getIRI().toURI());

diff --git a/src/main/java/cz/cvut/kbss/termit/service/repository/BaseRepositoryService.java b/src/main/java/cz/cvut/kbss/termit/service/repository/BaseRepositoryService.java
@@ -152,7 +152,7 @@ private Class<T> resolveGenericType() {
         // Adapted from https://gist.github.com/yunspace/930d4d40a787a1f6a7d1
         final List<ResolvedType> typeParameters =
                 new TypeResolver().resolve(this.getClass()).typeParametersFor(BaseRepositoryService.class);
-        assert typeParameters.size() >= 1;
+        assert !typeParameters.isEmpty();
         return (Class<T>) typeParameters.get(0).getErasedType();
     }
 
@@ -230,10 +230,9 @@ protected void preUpdate(@NonNull T instance) {
     }
 
     /**
-     * Override this method to plug custom behavior into the transactional cycle of {@link #update(HasIdentifier)} )}.
+     * Override this method to plug custom behavior into the transactional cycle of {@link #update(HasIdentifier)}.
      *
-     * @param instance The updated instance which will be returned by {@link #update(HasIdentifier)} )}, not {@code
-     *                 null}
+     * @param instance The updated instance which will be returned by {@link #update(HasIdentifier)}, not {@code null}
      */
     protected void postUpdate(@NonNull T instance) {
         // Do nothing

diff --git a/src/main/java/cz/cvut/kbss/termit/service/repository/ResourceRepositoryService.java b/src/main/java/cz/cvut/kbss/termit/service/repository/ResourceRepositoryService.java
@@ -27,6 +27,7 @@
 import cz.cvut.kbss.termit.persistence.dao.TermOccurrenceDao;
 import cz.cvut.kbss.termit.service.IdentifierResolver;
 import cz.cvut.kbss.termit.util.Configuration;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -72,7 +73,7 @@ protected Resource mapToDto(Resource entity) {
     }
 
     @Override
-    protected void prePersist(Resource instance) {
+    protected void prePersist(@NotNull Resource instance) {
         super.prePersist(instance);
         if (instance.getUri() == null) {
             instance.setUri(idResolver.generateIdentifier(cfgNamespace.getResource(), instance.getLabel()));
@@ -97,17 +98,16 @@ public void persist(Resource resource, Vocabulary vocabulary) {
     }
 
     @Override
-    protected void preRemove(Resource instance) {
+    protected void preRemove(@NotNull Resource instance) {
         LOG.trace("Removing term occurrences in resource {} which is about to be removed.", instance);
         termOccurrenceDao.removeAll(instance);
         removeFromParentDocumentIfFile(instance);
     }
 
     private void removeFromParentDocumentIfFile(Resource instance) {
-        if (!(instance instanceof File)) {
+        if (!(instance instanceof File file)) {
             return;
         }
-        final File file = (File) instance;
         final Document parent = file.getDocument();
         if (parent != null) {
             LOG.trace("Removing file {} from its parent document {}.", instance, parent);

diff --git a/src/main/java/cz/cvut/kbss/termit/service/repository/TermRepositoryService.java b/src/main/java/cz/cvut/kbss/termit/service/repository/TermRepositoryService.java
@@ -125,7 +125,7 @@ private void pruneEmptyTranslations(Term instance) {
     }
 
     @Override
-    protected void postUpdate(Term instance) {
+    protected void postUpdate(@NotNull Term instance) {
         final Vocabulary vocabulary = vocabularyService.getRequiredReference(instance.getVocabulary());
         if (instance.hasParentInSameVocabulary()) {
             vocabulary.getGlossary().removeRootTerm(instance);
@@ -427,7 +427,7 @@ protected void preRemove(@NotNull Term instance) {
     }
 
     @Override
-    protected void postRemove(Term instance) {
+    protected void postRemove(@NotNull Term instance) {
         super.postRemove(instance);
         if (!instance.hasParentInSameVocabulary()) {
             final Vocabulary v = vocabularyService.findRequired(instance.getVocabulary());

diff --git a/src/main/java/cz/cvut/kbss/termit/service/repository/UserRepositoryService.java b/src/main/java/cz/cvut/kbss/termit/service/repository/UserRepositoryService.java
@@ -23,6 +23,7 @@
 import cz.cvut.kbss.termit.persistence.dao.UserAccountDao;
 import cz.cvut.kbss.termit.service.IdentifierResolver;
 import cz.cvut.kbss.termit.util.Configuration;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.crypto.password.PasswordEncoder;
 import org.springframework.stereotype.Service;
@@ -72,13 +73,13 @@ protected UserAccount mapToDto(UserAccount entity) {
     }
 
     @Override
-    protected UserAccount postLoad(UserAccount instance) {
+    protected UserAccount postLoad(@NotNull UserAccount instance) {
         instance.erasePassword();
         return instance;
     }
 
     @Override
-    protected void prePersist(UserAccount instance) {
+    protected void prePersist(@NotNull UserAccount instance) {
         super.prePersist(instance);
         if (instance.getUri() == null) {
             instance.setUri(idResolver
@@ -90,7 +91,7 @@ protected void prePersist(UserAccount instance) {
     }
 
     @Override
-    protected void preUpdate(UserAccount instance) {
+    protected void preUpdate(@NotNull UserAccount instance) {
         final UserAccount original = userAccountDao.find(instance.getUri()).orElseThrow(
                 () -> new NotFoundException("User " + instance + " does not exist."));
         if (instance.getPassword() != null) {