Merge pull request #4627 from inception-project/refactoring/4550-Clea…

…n-up-code

#4550 - Clean up code

inception/inception-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/results/unitizing/FullUnitizingAgreementResult.java

@@ -28,8 +28,8 @@ public class FullUnitizingAgreementResult
 {
     private static final long serialVersionUID = 2092691057728349705L;
 
-    public FullUnitizingAgreementResult(String aType, String aFeature, IUnitizingAnnotationStudy aStudy,
-            List<String> aCasGroupIds, boolean aExcludeIncomplete)
+    public FullUnitizingAgreementResult(String aType, String aFeature,
+            IUnitizingAnnotationStudy aStudy, List<String> aCasGroupIds, boolean aExcludeIncomplete)
     {
         super(aType, aFeature, aStudy, aCasGroupIds, aExcludeIncomplete);
     }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/preferences/AnnotationPreferencesDialogContent.java

@@ -105,7 +105,8 @@ public AnnotationPreferencesDialogContent(String aId, IModel<AnnotatorState> aMo
         editorChoices = getEditorChoices();
         onChangeAction = aOnChangeAction;
 
-        form = new Form<>("form", new CompoundPropertyModel<>(loadPreferences(stateModel.getObject())));
+        form = new Form<>("form",
+                new CompoundPropertyModel<>(loadPreferences(stateModel.getObject())));
 
         var windowSizeField = new NumberTextField<Integer>("windowSize");
         windowSizeField.setType(Integer.class);

inception/inception-build/src/main/resources/inception/eclipse/org.eclipse.jdt.core.prefs

@@ -12,10 +12,18 @@ org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=11
 org.eclipse.jdt.core.formatter.align_assignment_statements_on_columns=false
 org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647
+org.eclipse.jdt.core.formatter.align_selector_in_method_invocation_on_expression_first_line=false
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.align_variable_declarations_on_columns=false
 org.eclipse.jdt.core.formatter.align_with_spaces=false
 org.eclipse.jdt.core.formatter.alignment_for_additive_operator=16
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_enum_constant=49
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_field=49
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_local_variable=49
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_method=49
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_package=49
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_parameter=0
+org.eclipse.jdt.core.formatter.alignment_for_annotations_on_type=49
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16
@@ -32,6 +40,8 @@ org.eclipse.jdt.core.formatter.alignment_for_conditional_expression_chain=0
 org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16
 org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16
 org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header=0
+org.eclipse.jdt.core.formatter.alignment_for_expressions_in_switch_case_with_arrow=0
+org.eclipse.jdt.core.formatter.alignment_for_expressions_in_switch_case_with_colon=0
 org.eclipse.jdt.core.formatter.alignment_for_logical_operator=16
 org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
 org.eclipse.jdt.core.formatter.alignment_for_module_statements=16
@@ -40,6 +50,7 @@ org.eclipse.jdt.core.formatter.alignment_for_multiplicative_operator=16
 org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0
 org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_permitted_types_in_type_declaration=37
 org.eclipse.jdt.core.formatter.alignment_for_record_components=16
 org.eclipse.jdt.core.formatter.alignment_for_relational_operator=0
 org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
@@ -50,8 +61,10 @@ org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=37
 org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=37
 org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_record_declaration=37
 org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=37
+org.eclipse.jdt.core.formatter.alignment_for_switch_case_with_arrow=0
 org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=36
 org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=36
+org.eclipse.jdt.core.formatter.alignment_for_type_annotations=0
 org.eclipse.jdt.core.formatter.alignment_for_type_arguments=0
 org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0
 org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
@@ -80,7 +93,7 @@ org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=next_line
 org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line
 org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=next_line
 org.eclipse.jdt.core.formatter.brace_position_for_record_constructor=next_line
-org.eclipse.jdt.core.formatter.brace_position_for_record_declaration=next_line
+org.eclipse.jdt.core.formatter.brace_position_for_record_declaration=next_line_on_wrap
 org.eclipse.jdt.core.formatter.brace_position_for_switch=end_of_line
 org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line
 org.eclipse.jdt.core.formatter.comment.align_tags_descriptions_grouped=false
@@ -100,6 +113,7 @@ org.eclipse.jdt.core.formatter.comment.indent_tag_description=false
 org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
 org.eclipse.jdt.core.formatter.comment.insert_new_line_between_different_tags=do not insert
 org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
+org.eclipse.jdt.core.formatter.comment.javadoc_do_not_separate_block_tags=false
 org.eclipse.jdt.core.formatter.comment.line_length=100
 org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
 org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
@@ -172,6 +186,7 @@ org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arg
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_permitted_types=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_record_components=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_switch_case_expressions=insert
@@ -263,6 +278,7 @@ org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_ar
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_permitted_types=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_record_components=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_switch_case_expressions=do not insert
@@ -341,11 +357,13 @@ org.eclipse.jdt.core.formatter.keep_lambda_body_block_on_one_line=one_line_never
 org.eclipse.jdt.core.formatter.keep_loop_body_block_on_one_line=one_line_never
 org.eclipse.jdt.core.formatter.keep_method_body_on_one_line=one_line_never
 org.eclipse.jdt.core.formatter.keep_record_constructor_on_one_line=one_line_never
-org.eclipse.jdt.core.formatter.keep_record_declaration_on_one_line=one_line_never
+org.eclipse.jdt.core.formatter.keep_record_declaration_on_one_line=one_line_if_empty
 org.eclipse.jdt.core.formatter.keep_simple_do_while_body_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_simple_for_body_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_simple_getter_setter_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_simple_while_body_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_switch_body_block_on_one_line=one_line_never
+org.eclipse.jdt.core.formatter.keep_switch_case_with_arrow_on_one_line=one_line_never
 org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_type_declaration_on_one_line=one_line_never
 org.eclipse.jdt.core.formatter.lineSplit=100
@@ -386,5 +404,6 @@ org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
 org.eclipse.jdt.core.formatter.wrap_before_relational_operator=true
 org.eclipse.jdt.core.formatter.wrap_before_shift_operator=true
 org.eclipse.jdt.core.formatter.wrap_before_string_concatenation=true
+org.eclipse.jdt.core.formatter.wrap_before_switch_case_arrow_operator=false
 org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
 org.eclipse.jdt.core.javaFormatter=org.eclipse.jdt.core.defaultJavaFormatter

inception/inception-build/src/main/resources/inception/eclipse/org.eclipse.jdt.ui.prefs

@@ -1,7 +1,7 @@
 eclipse.preferences.version=1
 editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
 formatter_profile=_DKPro Style
-formatter_settings_version=20
+formatter_settings_version=23
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
 sp_cleanup.add_missing_annotations=true

inception/inception-curation-legacy/src/main/java/de/tudarmstadt/ukp/clarin/webanno/curation/casdiff/span/SpanDiffAdapter.java

@@ -49,8 +49,8 @@ public class SpanDiffAdapter
     public static final SpanDiffAdapter SENTENCE_DIFF_ADAPTER = new SpanDiffAdapter(
             Sentence.class.getName());
 
-    public static final SpanDiffAdapter POS_DIFF_ADAPTER = new SpanDiffAdapter(
-            POS.class.getName(), "PosValue", "coarseValue");
+    public static final SpanDiffAdapter POS_DIFF_ADAPTER = new SpanDiffAdapter(POS.class.getName(),
+            "PosValue", "coarseValue");
 
     public static final SpanDiffAdapter NER_DIFF_ADAPTER = new SpanDiffAdapter(
             NamedEntity.class.getName(), "value", "identifier");

inception/inception-diam-compactv2/src/main/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactAnnotationAttributes.java

@@ -60,7 +60,7 @@ public boolean isHideScore()
     {
         return hideScore;
     }
-    
+
     public void setHideScore(boolean aHideScore)
     {
         hideScore = aHideScore;

inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/service/DiamWebsocketController.java

@@ -229,7 +229,8 @@ public JsonNode onSubscribeToAnnotationDocument(SimpMessageHeaderAccessor aHeade
             vps.addSubscription(aHeaderAccessor.getSessionId(),
                     aHeaderAccessor.getSubscriptionId());
 
-            var json = render(project, aDocumentId, aDataOwner, aViewportBegin, aViewportEnd, aFormat);
+            var json = render(project, aDocumentId, aDataOwner, aViewportBegin, aViewportEnd,
+                    aFormat);
             vps.setJson(json);
             return json;
         }
@@ -270,8 +271,8 @@ public JsonNode onSubscribeToAnnotationDocument(SimpMessageHeaderAccessor aHeade
     // }
     // }
 
-    private JsonNode render(Project aProject, long aDocumentId, String aDataOwner, int aViewportBegin,
-            int aViewportEnd, String aFormat)
+    private JsonNode render(Project aProject, long aDocumentId, String aDataOwner,
+            int aViewportBegin, int aViewportEnd, String aFormat)
         throws IOException
     {
         var doc = documentService.getSourceDocument(aProject.getId(), aDocumentId);

inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide.adoc

@@ -284,7 +284,7 @@ include::{include-dir}formats-uimajson.adoc[leveloffset=+2]
 
 include::{include-dir}formats-uimajson-legacy.adoc[leveloffset=+2]
 
-include::{include-dir}formats-rdfcas.adoc.adoc[leveloffset=+2]
+include::{include-dir}formats-rdfcas.adoc[leveloffset=+2]
 
 include::{include-dir}formats-uimaxmi.adoc[leveloffset=+2]
 

inception/inception-documents-api/src/main/java/de/tudarmstadt/ukp/inception/documents/api/DocumentAccess.java

@@ -35,8 +35,8 @@ boolean canViewAnnotationDocument(String aUser, String aProjectId, long aDocumen
     boolean canEditAnnotationDocument(String aUser, String aProjectId, long aDocumentId,
             String aAnnotator);
 
-    void assertCanEditAnnotationDocument(User aSessionOwner,
-            SourceDocument aDocument, String aDataOwner)
+    void assertCanEditAnnotationDocument(User aSessionOwner, SourceDocument aDocument,
+            String aDataOwner)
         throws AccessDeniedException;
 
     boolean canExportAnnotationDocument(User aUser, Project aProject);

inception/inception-documents-api/src/main/java/de/tudarmstadt/ukp/inception/documents/api/RepositoryPropertiesImpl.java

@@ -33,7 +33,8 @@
  */
 @ConfigurationProperties("repository")
 @ManagedResource
-public class RepositoryPropertiesImpl implements RepositoryProperties
+public class RepositoryPropertiesImpl
+    implements RepositoryProperties
 {
     private File path;
 

inception/inception-imls-azureai-openai/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/azureaiopenai/config/AzureAiOpenAiRecommenderAutoConfiguration.java

@@ -27,7 +27,7 @@
 
 @Configuration
 @ConditionalOnProperty(prefix = "recommender.azureai-openai", name = "enabled", //
-    havingValue = "true", matchIfMissing = false)
+        havingValue = "true", matchIfMissing = false)
 public class AzureAiOpenAiRecommenderAutoConfiguration
 {
     @Bean

inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/MHtmlFormatSupport.java

@@ -109,7 +109,8 @@ public InputStream openResourceStream(File aDocFile, String aResourcePath) throw
         }
     }
 
-    private static SingleBody getResourcePartBody(Message message, String aResourcePath) throws IOException
+    private static SingleBody getResourcePartBody(Message message, String aResourcePath)
+        throws IOException
     {
         if (message.getBody() instanceof Multipart body) {
             var documentPart = body.getBodyParts().stream() //

inception/inception-processing/src/main/java/de/tudarmstadt/ukp/inception/processing/recommender/BulkPredictionTask.java

@@ -167,7 +167,8 @@ public void execute()
         }
     }
 
-    private void addProcessingMetadataAnnotation(SourceDocument doc, CAS cas) throws AnnotationException
+    private void addProcessingMetadataAnnotation(SourceDocument doc, CAS cas)
+        throws AnnotationException
     {
         var metadataAnnotationCache = new HashMap<AnnotationLayer, AnnotationBaseFS>();
         for (var metadataEntry : processingMetadata.entrySet()) {

inception/inception-processing/src/main/java/de/tudarmstadt/ukp/inception/processing/recommender/BulkRecommenderPanel.java

@@ -89,7 +89,7 @@ public BulkRecommenderPanel(String aId, IModel<Project> aModel)
                 .setRequired(true));
 
         processingMetadata = new FeatureEditorPanel("processingMetadata");
-                processingMetadata.setOutputMarkupPlaceholderTag(true);
+        processingMetadata.setOutputMarkupPlaceholderTag(true);
         queue(processingMetadata);
 
         var docMetaLayers = LoadableDetachableModel.of(this::listDocumentMetadataLayers);
@@ -112,7 +112,7 @@ private void actionStartProcessing(AjaxRequestTarget aTarget, Form<FormData> aFo
         for (var state : processingMetadata.getModelObject()) {
             metadata.put(state.getFeature(), state.getValue());
         }
-        
+
         var formData = aForm.getModelObject();
         schedulingService.enqueue(BulkPredictionTask.builder() //
                 .withSessionOwner(userService.getCurrentUser()) //

inception/inception-processing/src/main/java/de/tudarmstadt/ukp/inception/processing/recommender/FeatureEditorPanel.java

@@ -60,7 +60,8 @@ public FeatureEditorPanel(String aId, IModel<List<FeatureState>> aFeatureStates)
         queue(createFeaturesList(CID_FEATURE_EDITORS, aFeatureStates));
     }
 
-    private ListView<FeatureState> createFeaturesList(String aId, IModel<List<FeatureState>> aFeatureStates)
+    private ListView<FeatureState> createFeaturesList(String aId,
+            IModel<List<FeatureState>> aFeatureStates)
     {
         return new ListView<FeatureState>(aId, aFeatureStates)
         {

inception/installEclipseSettings.sh

@@ -15,14 +15,14 @@ function installPrefs {
 installPrefs inception-active-learning
 installPrefs inception-agreement
 installPrefs inception-annotation-storage
+installPrefs inception-annotation-storage-api
 installPrefs inception-api-annotation
 installPrefs inception-api-dao
 installPrefs inception-api-editor
 installPrefs inception-api-formats
 installPrefs inception-api-render
 installPrefs inception-api-schema
 installPrefs inception-app-webapp
-installPrefs inception-app.iml
 installPrefs inception-boot-loader
 installPrefs inception-bootstrap
 installPrefs inception-brat-editor
@@ -33,6 +33,7 @@ installPrefs inception-curation
 installPrefs inception-curation-legacy
 installPrefs inception-diag
 installPrefs inception-diam
+installPrefs inception-diam-compactv2
 installPrefs inception-diam-editor
 installPrefs inception-diam-word-alignment-editor
 installPrefs inception-doc
@@ -43,10 +44,12 @@ installPrefs inception-editor-api
 installPrefs inception-example-imls-data-majority
 installPrefs inception-experimental-editor
 installPrefs inception-export
+installPrefs inception-export-api
 installPrefs inception-external-editor
 installPrefs inception-external-search-core
 installPrefs inception-external-search-elastic
 installPrefs inception-external-search-mtas-embedded
+installPrefs inception-external-search-opensearch
 installPrefs inception-external-search-pubannotation
 installPrefs inception-external-search-pubmed
 installPrefs inception-external-search-solr
@@ -55,12 +58,13 @@ installPrefs inception-html-apache-annotator-editor
 installPrefs inception-html-editor
 installPrefs inception-html-recogito-editor
 installPrefs inception-image
+installPrefs inception-imls-azureai-openai
 installPrefs inception-imls-dl4j
 installPrefs inception-imls-elg
 installPrefs inception-imls-external
 installPrefs inception-imls-hf
 installPrefs inception-imls-lapps
-installPrefs inception-imls-openai
+installPrefs inception-imls-ollama
 installPrefs inception-imls-opennlp
 installPrefs inception-imls-stringmatch
 installPrefs inception-imls-weblicht
@@ -74,6 +78,7 @@ installPrefs inception-io-json
 installPrefs inception-io-lif
 installPrefs inception-io-nif
 installPrefs inception-io-perseus
+installPrefs inception-io-rdf
 installPrefs inception-io-tcf
 installPrefs inception-io-tei
 installPrefs inception-io-text
@@ -88,6 +93,7 @@ installPrefs inception-log
 installPrefs inception-log-ui
 installPrefs inception-model
 installPrefs inception-model-export
+installPrefs inception-model-vdoc
 installPrefs inception-pdf-editor
 installPrefs inception-pdf-editor2
 installPrefs inception-plugin-api
@@ -100,13 +106,15 @@ installPrefs inception-project-initializers
 installPrefs inception-project-initializers-basic
 installPrefs inception-project-initializers-doclabeling
 installPrefs inception-project-initializers-sentencelabeling
+installPrefs inception-project-initializers-ud
 installPrefs inception-project-initializers-wikidatalinking
 installPrefs inception-recommendation
 installPrefs inception-recommendation-api
 installPrefs inception-remote
 installPrefs inception-review-editor
 installPrefs inception-scheduling
 installPrefs inception-schema
+installPrefs inception-schema-api
 installPrefs inception-search-core
 installPrefs inception-search-mtas
 installPrefs inception-security
@@ -126,8 +134,8 @@ installPrefs inception-ui-external-search
 installPrefs inception-ui-kb
 installPrefs inception-ui-monitoring
 installPrefs inception-ui-project
-installPrefs inception-ui-search
 installPrefs inception-ui-scheduling
+installPrefs inception-ui-search
 installPrefs inception-ui-tagsets
 installPrefs inception-versioning
 installPrefs inception-websocket