Merge pull request #4811 from inception-project/feature/1319-Cross-La…

…yer-Relations

#1319 - Cross-Layer Relations

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/page/AnnotationPageBase.java

@@ -17,6 +17,7 @@
  */
 package de.tudarmstadt.ukp.clarin.webanno.api.annotation.page;
 
+import static de.tudarmstadt.ukp.clarin.webanno.model.ValidationMode.NEVER;
 import static de.tudarmstadt.ukp.inception.rendering.selection.FocusPosition.CENTERED;
 import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.CURATION_USER;
 import static java.lang.String.format;
@@ -56,7 +57,6 @@
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.preferences.UserPreferencesService;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
-import de.tudarmstadt.ukp.clarin.webanno.model.ValidationMode;
 import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
 import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
 import de.tudarmstadt.ukp.clarin.webanno.ui.core.page.ProjectPageBase;
@@ -410,7 +410,7 @@ public void actionValidateDocument(AjaxRequestTarget aTarget, CAS aCas)
                 continue;
             }
 
-            if (ValidationMode.NEVER.equals(layer.getValidationMode())) {
+            if (layer.getValidationMode() == NEVER) {
                 // If validation is disabled, then skip it
                 continue;
             }

inception/inception-diam-editor/pom.xml

@@ -83,11 +83,6 @@
       <artifactId>inception-support</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>org.apache.uima</groupId>
-      <artifactId>uimaj-core</artifactId>
-    </dependency>
-
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>

inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/DiamAnnotationBrowser.java

@@ -34,10 +34,8 @@
 import org.apache.wicket.spring.injection.annot.SpringBean;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
-import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.AnnotationPage;
 import de.tudarmstadt.ukp.inception.diam.editor.DiamAjaxBehavior;
 import de.tudarmstadt.ukp.inception.diam.editor.DiamJavaScriptReference;
-import de.tudarmstadt.ukp.inception.diam.editor.actions.ShowContextMenuHandler;
 import de.tudarmstadt.ukp.inception.diam.model.compactv2.CompactSerializerV2Impl;
 import de.tudarmstadt.ukp.inception.diam.model.websocket.ViewportDefinition;
 import de.tudarmstadt.ukp.inception.editor.AnnotationEditorExtensionRegistry;
@@ -71,11 +69,7 @@ protected void onInitialize()
     {
         super.onInitialize();
 
-        var page = findParent(AnnotationPage.class);
-
         add(diamBehavior = createDiamBehavior());
-        diamBehavior.addPriorityHandler(new ShowContextMenuHandler(extensionRegistry,
-                page.getModel(), page.getAnnotationActionHandler(), page::getEditorCas));
         add(new SvelteBehavior());
     }
 

inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/CreateRelationAnnotationHandler.java

@@ -28,6 +28,7 @@
 import org.springframework.core.annotation.Order;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.IllegalPlacementException;
+import de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.NotEditableException;
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
 import de.tudarmstadt.ukp.inception.annotation.layer.chain.ChainAdapter;
@@ -91,13 +92,23 @@ private void actionArc(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget,
             IRequestParameters aParams)
         throws IOException, AnnotationException
     {
-        var page = getPage();
-
-        page.ensureIsEditable();
-
         var originSpan = VID.parse(aParams.getParameterValue(PARAM_ORIGIN_SPAN_ID).toString());
         var targetSpan = VID.parse(aParams.getParameterValue(PARAM_TARGET_SPAN_ID).toString());
 
+        var cm = aBehavior.getContextMenu();
+        var clientX = cm.getClientX().getAsInt();
+        var clientY = cm.getClientY().getAsInt();
+
+        actionArc(aBehavior, aTarget, originSpan, targetSpan, clientX, clientY);
+    }
+
+    public void actionArc(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget, VID originSpan,
+            VID targetSpan, int aClientX, int aClientY)
+        throws NotEditableException, IOException, AnnotationException, IllegalPlacementException
+    {
+        var page = getPage();
+        page.ensureIsEditable();
+
         if (originSpan.isSynthetic() || targetSpan.isSynthetic()) {
             page.error("Relations cannot be created from/to synthetic annotations");
             aTarget.addChildren(page, IFeedback.class);
@@ -114,7 +125,8 @@ private void actionArc(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget,
             createChainLink(chainAdapter, aTarget, originSpan, targetSpan);
         }
         else {
-            createRelationAnnotation(aBehavior, aTarget, originLayer, originSpan, targetSpan);
+            createRelationAnnotation(aBehavior, aTarget, originLayer, originSpan, targetSpan,
+                    aClientX, aClientY);
         }
     }
 
@@ -144,7 +156,8 @@ private void createChainLink(ChainAdapter chainAdapter, AjaxRequestTarget aTarge
     }
 
     private void createRelationAnnotation(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget,
-            AnnotationLayer originLayer, VID aOriginSpan, VID aTargetSpan)
+            AnnotationLayer originLayer, VID aOriginSpan, VID aTargetSpan, int aClientX,
+            int aClientY)
         throws AnnotationException, IllegalPlacementException, IOException
     {
         var candidateLayers = schemaService.getRelationLayersFor(originLayer);
@@ -173,7 +186,7 @@ private void createRelationAnnotation(DiamAjaxBehavior aBehavior, AjaxRequestTar
             }));
         }
 
-        cm.onOpen(aTarget);
+        cm.onOpen(aTarget, aClientX, aClientY);
     }
 
     private void createRelationAnnotation(AjaxRequestTarget aTarget, AnnotationLayer relationLayer,

inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/CreateSpanAnnotationHandler.java

@@ -27,12 +27,20 @@
 import org.apache.wicket.request.Request;
 import org.springframework.core.annotation.Order;
 
+import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
+import de.tudarmstadt.ukp.inception.annotation.layer.chain.ChainAdapter;
+import de.tudarmstadt.ukp.inception.annotation.layer.span.CreateSpanAnnotationRequest;
+import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanAdapter;
 import de.tudarmstadt.ukp.inception.diam.editor.DiamAjaxBehavior;
 import de.tudarmstadt.ukp.inception.diam.editor.config.DiamAutoConfig;
 import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
 import de.tudarmstadt.ukp.inception.diam.model.compact.CompactRangeList;
 import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.rendering.selection.Selection;
+import de.tudarmstadt.ukp.inception.rendering.vmodel.VID;
+import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
+import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;
 import de.tudarmstadt.ukp.inception.support.json.JSONUtil;
 
 /**
@@ -47,26 +55,52 @@ public class CreateSpanAnnotationHandler
 {
     public static final String COMMAND = "spanOpenDialog";
 
+    private final AnnotationSchemaService schemaService;
+
+    public CreateSpanAnnotationHandler(AnnotationSchemaService aSchemaService)
+    {
+        schemaService = aSchemaService;
+    }
+
     @Override
     public String getCommand()
     {
         return COMMAND;
     }
 
     @Override
-    public DefaultAjaxResponse handle(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget, Request aRequest)
+    public DefaultAjaxResponse handle(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget,
+            Request aRequest)
     {
         try {
             var page = getPage();
-
             page.ensureIsEditable();
 
             var cas = page.getEditorCas();
             var state = getAnnotatorState();
             var range = getRangeFromRequest(state, aRequest.getRequestParameters(), cas);
 
-            state.getSelection().selectSpan(cas, range.getBegin(), range.getEnd());
-            page.getAnnotationActionHandler().actionCreateOrUpdate(aTarget, cas);
+            var adapter = schemaService.getAdapter(state.getDefaultAnnotationLayer());
+
+            var request = new CreateSpanAnnotationRequest(state.getDocument(),
+                    state.getUser().getUsername(), cas, range.getBegin(), range.getEnd());
+
+            Selection selection;
+            if (adapter instanceof SpanAdapter spanAdapter) {
+                var ann = spanAdapter.handle(request);
+                selection = adapter.select(VID.of(ann), ann);
+            }
+            else if (adapter instanceof ChainAdapter chainAdapter) {
+                var ann = chainAdapter.handle(request);
+                selection = adapter.select(VID.of(ann), ann);
+            }
+            else {
+                throw new AnnotationException("Cannot create span annotation on ["
+                        + state.getDefaultAnnotationLayer().getUiName() + "] of type ["
+                        + state.getDefaultAnnotationLayer().getType() + "]");
+            }
+
+            commitAnnotation(aTarget, page, state, selection);
 
             return new DefaultAjaxResponse(getAction(aRequest));
         }
@@ -85,12 +119,20 @@ static Range getRangeFromRequest(AnnotatorState aState, IRequestParameters reque
     {
         var offsets = request.getParameterValue(PARAM_OFFSETS).toString();
 
-        var offsetLists = JSONUtil.getObjectMapper().readValue(offsets, CompactRangeList.class);
+        var offsetLists = JSONUtil.fromJsonString(CompactRangeList.class, offsets);
 
-        int annotationBegin = aState.getWindowBeginOffset() + offsetLists.get(0).getBegin();
-        int annotationEnd = aState.getWindowBeginOffset()
-                + offsetLists.get(offsetLists.size() - 1).getEnd();
+        var begin = aState.getWindowBeginOffset() + offsetLists.get(0).getBegin();
+        var end = aState.getWindowBeginOffset() + offsetLists.get(offsetLists.size() - 1).getEnd();
 
-        return rangeClippedToDocument(aCas, annotationBegin, annotationEnd);
+        return rangeClippedToDocument(aCas, begin, end);
+    }
+
+    private void commitAnnotation(AjaxRequestTarget aTarget, AnnotationPageBase page,
+            AnnotatorState state, Selection selection)
+        throws IOException, AnnotationException
+    {
+        state.getSelection().set(selection);
+        page.getAnnotationActionHandler().actionSelect(aTarget);
+        page.getAnnotationActionHandler().writeEditorCas();
     }
 }

inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/EditorAjaxRequestHandler.java

@@ -29,6 +29,7 @@
 public interface EditorAjaxRequestHandler
     extends Extension<Request>
 {
+    int PRIO_CONTEXT_MENU = -10;
     int PRIO_RENDER_HANDLER = 0;
     int PRIO_SLOT_FILLER_HANDLER = 100;
     int PRIO_UNARM_SLOT_HANDLER = 180;

inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/ShowContextMenuHandler.java

@@ -17,49 +17,30 @@
  */
 package de.tudarmstadt.ukp.inception.diam.editor.actions;
 
-import static de.tudarmstadt.ukp.inception.support.uima.ICasUtil.selectAnnotationByAddr;
+import static de.tudarmstadt.ukp.inception.support.spring.ApplicationContextProvider.getApplicationContext;
 
 import java.io.IOException;
 import java.io.Serializable;
 
-import org.apache.uima.cas.CAS;
 import org.apache.wicket.ajax.AjaxRequestTarget;
-import org.apache.wicket.model.IModel;
 import org.apache.wicket.request.Request;
+import org.springframework.core.annotation.Order;
 
-import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasProvider;
 import de.tudarmstadt.ukp.inception.diam.editor.DiamAjaxBehavior;
 import de.tudarmstadt.ukp.inception.diam.model.ajax.AjaxResponse;
 import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
 import de.tudarmstadt.ukp.inception.editor.AnnotationEditorExtensionRegistry;
-import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
-import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
 import de.tudarmstadt.ukp.inception.rendering.vmodel.VID;
 import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;
 import de.tudarmstadt.ukp.inception.support.lambda.LambdaMenuItem;
 
+@Order(EditorAjaxRequestHandler.PRIO_CONTEXT_MENU)
 public class ShowContextMenuHandler
     extends EditorAjaxRequestHandlerBase
     implements Serializable
 {
     private static final long serialVersionUID = 2566256640285857435L;
 
-    private final AnnotationEditorExtensionRegistry extensionRegistry;
-    private final IModel<AnnotatorState> model;
-    private final AnnotationActionHandler actionHandler;
-    private final CasProvider casProvider;
-
-    public ShowContextMenuHandler(
-            AnnotationEditorExtensionRegistry aAnnotationEditorExtensionRegistry,
-            IModel<AnnotatorState> aState, AnnotationActionHandler aActionHandler,
-            CasProvider aCasProvider)
-    {
-        extensionRegistry = aAnnotationEditorExtensionRegistry;
-        model = aState;
-        actionHandler = aActionHandler;
-        casProvider = aCasProvider;
-    }
-
     @Override
     public String getCommand()
     {
@@ -83,14 +64,24 @@ public AjaxResponse handle(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget
             return new DefaultAjaxResponse(getAction(aRequest));
         }
 
+        var clientX = cm.getClientX().getAsInt();
+        var clientY = cm.getClientY().getAsInt();
+
+        // Need to fetch this here since the handler is not serializable
+        var extensionRegistry = getApplicationContext()
+                .getBean(AnnotationEditorExtensionRegistry.class);
+
         try {
 
             var items = cm.getItemList();
             items.clear();
 
-            if (model.getObject().getSelection().isSpan()) {
+            var state = getAnnotatorState();
+
+            if (state.getSelection().isSpan()) {
                 var vid = getVid(aRequest);
-                items.add(new LambdaMenuItem("Link to ...", $ -> actionLinkTo($, vid)));
+                items.add(new LambdaMenuItem("Link to ...",
+                        $ -> actionLinkTo(aBehavior, $, vid, clientX, clientY)));
             }
 
             extensionRegistry.generateContextMenuItems(items);
@@ -106,37 +97,24 @@ public AjaxResponse handle(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget
         return new DefaultAjaxResponse(getAction(aRequest));
     }
 
-    private void actionLinkTo(AjaxRequestTarget aTarget, VID paramId)
+    private void actionLinkTo(DiamAjaxBehavior aBehavior, AjaxRequestTarget aTarget, VID paramId,
+            int aClientX, int aClientY)
         throws IOException, AnnotationException
     {
         var page = getPage();
         page.ensureIsEditable();
 
-        var state = model.getObject();
+        var state = getAnnotatorState();
 
         if (!state.getSelection().isSpan()) {
             return;
         }
 
-        CAS cas;
-        try {
-            cas = casProvider.get();
-        }
-        catch (Exception e) {
-            handleError("Unable to load data", e);
-            return;
-        }
-
-        // Currently selected span
-        var originFs = selectAnnotationByAddr(cas, state.getSelection().getAnnotation().getId());
-
-        // Target span of the relation
-        var targetFs = selectAnnotationByAddr(cas, paramId.getId());
-
-        var selection = state.getSelection();
-        selection.selectArc(VID.NONE_ID, originFs, targetFs);
+        // Need to fetch this here since the handler is not serializable
+        var createRelationAnnotationHandler = getApplicationContext()
+                .getBean(CreateRelationAnnotationHandler.class);
 
-        // Create new annotation
-        actionHandler.actionCreateOrUpdate(aTarget, cas);
+        createRelationAnnotationHandler.actionArc(aBehavior, aTarget,
+                state.getSelection().getAnnotation(), paramId, aClientX, aClientY);
     }
 }

inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/config/DiamAutoConfig.java

@@ -42,6 +42,7 @@
 import de.tudarmstadt.ukp.inception.diam.editor.actions.SavePreferences;
 import de.tudarmstadt.ukp.inception.diam.editor.actions.ScrollToHandler;
 import de.tudarmstadt.ukp.inception.diam.editor.actions.SelectAnnotationHandler;
+import de.tudarmstadt.ukp.inception.diam.editor.actions.ShowContextMenuHandler;
 import de.tudarmstadt.ukp.inception.diam.editor.lazydetails.LazyDetailsLookupService;
 import de.tudarmstadt.ukp.inception.diam.editor.lazydetails.LazyDetailsLookupServiceImpl;
 import de.tudarmstadt.ukp.inception.diam.model.compact.CompactSerializer;
@@ -86,9 +87,10 @@ public ExtensionActionHandler extensionActionHandler(
     }
 
     @Bean
-    public CreateSpanAnnotationHandler createSpanAnnotationHandler()
+    public CreateSpanAnnotationHandler createSpanAnnotationHandler(
+            AnnotationSchemaService aSchemaService)
     {
-        return new CreateSpanAnnotationHandler();
+        return new CreateSpanAnnotationHandler(aSchemaService);
     }
 
     @Bean
@@ -106,6 +108,12 @@ public CreateRelationAnnotationHandler createRelationAnnotationHandler(
         return new CreateRelationAnnotationHandler(aSchemaService, aAnnotationSchemaProperties);
     }
 
+    @Bean
+    public ShowContextMenuHandler ShowContextMenuHandler()
+    {
+        return new ShowContextMenuHandler();
+    }
+
     @Bean
     public DeleteAnnotationHandler deleteAnnotationHandler(
             AnnotationSchemaService aAnnotationService)