Merge pull request #4619 from inception-project/bugfix/4618-Resizing-…

…a-span-does-not-update-annotations-on-disk #4618 - Resizing a span does not update annotations on disk
inception-project · Mar 11, 2024 · c2a7980 · c2a7980
2 parents 7f36c44 + 3d6d4cd
commit c2a7980
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Showing 17 changed files with 166 additions and 158 deletions.
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,24 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+#   means that files that GIT determines to be text files, will be 
+#     converted from CRLF -> LF upon being added to the repo, and
+#     converted from LF -> LF or CRLF when checked out (depending on the platform, I think)
+# * text=auto
+
+# We force LF for all text files because we have Checkstyle set up in such a way
+# The "text" by itself says these files must be line-ending-conversion controlled on check-in / out
+#   The internal repo form for these is always lf, 
+#   The eol=lf means on check-out do nothing, and on check-in, if the file has crlf, convert to lf
+* text eol=lf
+# *.sh text eol=lf
+
+# Make sure that these files are treated as binary so that newlines are preserved.
+#   overrides GIT's determination if a file is text or not
+*.bin binary
+*.dump binary
+*.xcas binary
+*.xmi binary
+#  next is probably the default
+*.pdf binary
+*.ser binary
+*.png binary
+*.jpg binary
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -16,15 +16,19 @@ on:
 
 jobs:
   build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        jdk: [17]
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 17
-      uses: actions/setup-java@v3
+    - uses: actions/checkout@v4
+    - name: Set up JDK ${{ matrix.jdk }}
+      uses: actions/setup-java@v4
       with:
-        java-version: '17'
+        java-version: ${{ matrix.jdk }}
         distribution: 'temurin'
         cache: maven
     - name: Build with Maven

diff --git a/inception/inception-app-webapp/pom.xml b/inception/inception-app-webapp/pom.xml
@@ -883,6 +883,7 @@
                uber-JAR and we get ClassNotFoundExceptions at runtime.
                -->
               <ignoredDependency>com.nimbusds:nimbus-jose-jwt</ignoredDependency>
+              <ignoredDependency>org.apache.logging.log4j:log4j-api</ignoredDependency>
               <!-- 
                 - Detection of this dependency is flickering. We need it for a menu-item. So
                 - for the moment, completely ignore it in the dependency checking.

diff --git a/...bapp/src/test/java/de/tudarmstadt/ukp/inception/InceptionRemoteApiJwtIntegrationTest.java b/...bapp/src/test/java/de/tudarmstadt/ukp/inception/InceptionRemoteApiJwtIntegrationTest.java
@@ -35,6 +35,7 @@
 import java.util.Map;
 import java.util.UUID;
 
+import org.apache.logging.log4j.LogManager;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Tag;
@@ -77,6 +78,7 @@ static void setup()
         var issuerUrl = oauth2Server.url(ISSUER_ID).toString();
 
         setProperty("java.awt.headless", "true");
+        setProperty("database.url", "jdbc:hsqldb:mem:testdb");
         setProperty("inception.home", appHome.toString());
         setProperty("remote-api.enabled", "true");
         setProperty("remote-api.oauth2.enabled", "true");
@@ -110,6 +112,7 @@ static void teardown()
         }
         context.close();
         oauth2Server.shutdown();
+        LogManager.shutdown();
     }
 
     @Test

diff --git a/inception/inception-curation/pom.xml b/inception/inception-curation/pom.xml
@@ -114,10 +114,6 @@
       <groupId>org.springframework</groupId>
       <artifactId>spring-core</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.springframework.security</groupId>
-      <artifactId>spring-security-core</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-autoconfigure</artifactId>

diff --git a/.../src/main/java/de/tudarmstadt/ukp/inception/curation/service/CurationDocumentService.java b/.../src/main/java/de/tudarmstadt/ukp/inception/curation/service/CurationDocumentService.java
@@ -23,7 +23,6 @@
 
 import org.apache.uima.UIMAException;
 import org.apache.uima.cas.CAS;
-import org.springframework.security.access.prepost.PreAuthorize;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.ConcurentCasModificationException;
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
@@ -50,7 +49,6 @@ public interface CurationDocumentService
      * @throws IOException
      *             if an I/O error occurs.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER')")
     void writeCurationCas(CAS aCas, SourceDocument document, boolean aUpdateTimestamp)
         throws IOException;
 

diff --git a/...main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/MoveSpanAnnotationHandler.java b/...main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/MoveSpanAnnotationHandler.java
@@ -22,16 +22,13 @@
 import java.io.IOException;
 
 import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.wicket.ajax.AjaxRequestTarget;
 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.span.SpanAdapter;
 import de.tudarmstadt.ukp.inception.diam.editor.config.DiamAutoConfig;
 import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
-import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
 import de.tudarmstadt.ukp.inception.rendering.vmodel.VID;
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
@@ -66,12 +63,13 @@ public String getCommand()
     public DefaultAjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
     {
         try {
-            AnnotationPageBase page = getPage();
-            CAS cas = page.getEditorCas();
+            var page = getPage();
+            var cas = page.getEditorCas();
             var vid = getVid(aRequest);
-            AnnotatorState state = getAnnotatorState();
+            var state = getAnnotatorState();
             var range = getRangeFromRequest(state, aRequest.getRequestParameters(), cas);
             moveSpan(aTarget, cas, vid, range);
+            page.writeEditorCas(cas);
             return new DefaultAjaxResponse(getAction(aRequest));
         }
         catch (Exception e) {
@@ -82,12 +80,11 @@ public DefaultAjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
     private void moveSpan(AjaxRequestTarget aTarget, CAS aCas, VID aVid, Range aRange)
         throws IOException, AnnotationException
     {
-        AnnotatorState state = getAnnotatorState();
+        var state = getAnnotatorState();
 
-        AnnotationFS annoFs = ICasUtil.selectAnnotationByAddr(aCas, aVid.getId());
+        var annoFs = ICasUtil.selectAnnotationByAddr(aCas, aVid.getId());
 
-        SpanAdapter adapter = (SpanAdapter) annotationService.findAdapter(state.getProject(),
-                annoFs);
+        var adapter = (SpanAdapter) annotationService.findAdapter(state.getProject(), annoFs);
 
         adapter.move(state.getDocument(), state.getUser().getUsername(), aCas, annoFs,
                 aRange.getBegin(), aRange.getEnd());

diff --git a/...e/tudarmstadt/ukp/inception/diam/service/DiamWebsocketController_ViewportRoutingTest.java b/...e/tudarmstadt/ukp/inception/diam/service/DiamWebsocketController_ViewportRoutingTest.java
@@ -219,22 +219,18 @@ public void tearDown()
     @Test
     public void thatViewportBasedMessageRoutingWorks() throws Exception
     {
-        CountDownLatch subscriptionDone = new CountDownLatch(2);
-        CountDownLatch initDone = new CountDownLatch(2);
+        var subscriptionDone = new CountDownLatch(2);
+        var initDone = new CountDownLatch(2);
 
-        ViewportDefinition vpd1 = new ViewportDefinition(testAnnotationDocument, 10, 20,
-                FORMAT_LEGACY);
-        ViewportDefinition vpd2 = new ViewportDefinition(testAnnotationDocument, 30, 40,
-                FORMAT_LEGACY);
+        var vpd1 = new ViewportDefinition(testAnnotationDocument, 10, 20, FORMAT_LEGACY);
+        var vpd2 = new ViewportDefinition(testAnnotationDocument, 30, 40, FORMAT_LEGACY);
 
         var sessionHandler1 = new SessionHandler(subscriptionDone, initDone, vpd1);
         var sessionHandler2 = new SessionHandler(subscriptionDone, initDone, vpd2);
 
         // try {
-        StompSession session1 = stompClient.connect(websocketUrl, sessionHandler1).get(1000,
-                SECONDS);
-        StompSession session2 = stompClient.connect(websocketUrl, sessionHandler2).get(1000,
-                SECONDS);
+        var session1 = stompClient.connect(websocketUrl, sessionHandler1).get(1000, SECONDS);
+        var session2 = stompClient.connect(websocketUrl, sessionHandler2).get(1000, SECONDS);
         // }
         // catch (Exception e) {
         // Thread.sleep(Duration.of(3, ChronoUnit.HOURS).toMillis());
@@ -341,7 +337,7 @@ public ApplicationContextProvider applicationContextProvider()
         public DaoAuthenticationProvider internalAuthenticationProvider(PasswordEncoder aEncoder,
                 @Lazy UserDetailsManager aUserDetailsManager)
         {
-            DaoAuthenticationProvider authProvider = new InceptionDaoAuthenticationProvider();
+            var authProvider = new InceptionDaoAuthenticationProvider();
             authProvider.setUserDetailsService(aUserDetailsManager);
             authProvider.setPasswordEncoder(aEncoder);
             return authProvider;
@@ -362,7 +358,7 @@ public String getId()
                 @Override
                 public void render(VDocument aResponse, RenderRequest aRequest)
                 {
-                    AnnotationLayer layer = new AnnotationLayer();
+                    var layer = new AnnotationLayer();
                     layer.setId(1l);
                     aResponse.add(
                             new VSpan(layer, new VID(1), new VRange(aRequest.getWindowBeginOffset(),

diff --git a/...cuments-api/src/main/java/de/tudarmstadt/ukp/inception/documents/api/DocumentService.java b/...cuments-api/src/main/java/de/tudarmstadt/ukp/inception/documents/api/DocumentService.java
@@ -32,7 +32,6 @@
 import org.apache.uima.cas.CAS;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.wicket.validation.ValidationError;
-import org.springframework.security.access.prepost.PreAuthorize;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasAccessMode;
 import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode;
@@ -71,7 +70,6 @@ public interface DocumentService
      *            {@link SourceDocument} to be created
      * @return the source document
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER','ROLE_REMOTE')")
     SourceDocument createSourceDocument(SourceDocument document);
 
     /**
@@ -152,7 +150,6 @@ List<SourceDocument> listSourceDocumentsInState(Project aProject,
      * @throws IOException
      *             If the source document searched for deletion is not available
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER', 'ROLE_REMOTE')")
     void removeSourceDocument(SourceDocument document) throws IOException;
 
     /**
@@ -168,7 +165,6 @@ List<SourceDocument> listSourceDocumentsInState(Project aProject,
      * @throws UIMAException
      *             if a conversion error occurs.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER','ROLE_REMOTE')")
     void uploadSourceDocument(InputStream file, SourceDocument document)
         throws IOException, UIMAException;
 
@@ -188,7 +184,6 @@ void uploadSourceDocument(InputStream file, SourceDocument document)
      * @throws UIMAException
      *             if a conversion error occurs.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER','ROLE_REMOTE')")
     void uploadSourceDocument(InputStream file, SourceDocument document,
             TypeSystemDescription aFullProjectTypeSystem)
         throws IOException, UIMAException;
@@ -221,7 +216,6 @@ SourceDocumentState setSourceDocumentState(SourceDocument aDocument,
      *            and id of {@link User}
      * @return the annotation document.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER')")
     AnnotationDocument createAnnotationDocument(AnnotationDocument annotationDocument);
 
     /**
@@ -237,7 +231,6 @@ SourceDocumentState setSourceDocumentState(SourceDocument aDocument,
      * @throws IOException
      *             if an I/O error occurs.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER')")
     void writeAnnotationCas(CAS aCas, AnnotationDocument aAnnotationDocument,
             boolean aExplicitAnnotatorUserAction)
         throws IOException;
@@ -257,7 +250,6 @@ void writeAnnotationCas(CAS aCas, AnnotationDocument aAnnotationDocument,
      * @throws IOException
      *             if an I/O error occurs.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER')")
     void writeAnnotationCas(CAS aCas, SourceDocument aDocument, User aUser,
             boolean aExplicitAnnotatorUserAction)
         throws IOException;
@@ -295,7 +287,6 @@ void writeAnnotationCas(CAS aCas, SourceDocument aDocument, String aUser,
      * @throws IOException
      *             if an I/O error occurs.
      */
-    @PreAuthorize("hasAnyRole('ROLE_ADMIN','ROLE_USER')")
     void resetAnnotationCas(SourceDocument aDocument, User aUser,
             AnnotationDocumentStateChangeFlag... aFlags)
         throws UIMAException, IOException;