#3611 - Upgrade to Spring 6, Boot 3, Wicket 10, etc.

- Remove some deprecated and unused APIs - Move a DB query to the criteria API as the string-based query no longer worked with Hibernate 6 - Fixed bug in hibernate integer enum type - Use SnakeYAML 1.33 for some tests because DKPro Core Dataset doesn't work with SnakeYAML 2.0 atm
inception-project · Jun 13, 2023 · 1a3d43a · 1a3d43a
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diff --git a/...ion/inception-api/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/ProjectService.java b/...ion/inception-api/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/ProjectService.java
@@ -381,29 +381,6 @@ List<Project> listProjectsWithUserHavingRole(User aUser, PermissionLevel aRole,
      */
     List<Project> listManageableProjects(User aUser);
 
-    /**
-     * List projects in which the given user is curator or manager
-     *
-     * @return list of projects manageable by the user.
-     * @deprecated Use
-     *             {{@link #listProjectsWithUserHavingRole(User, PermissionLevel, PermissionLevel...)}}
-     *             instead.
-     */
-    @SuppressWarnings("javadoc")
-    @Deprecated
-    List<Project> listManageableCuratableProjects(User aUser);
-
-    /**
-     * @return list of projects that allow calculation of pairwise agreement. That means it lists
-     *         all projects where there are at least two annotators.
-     * 
-     * @deprecated To be removed without replacement
-     */
-    @Deprecated
-    List<Project> listProjectsForAgreement();
-
-    File getProjectFolder(Project aProject);
-
     /**
      * Export the associated project log for this {@link Project} while copying a project
      *
@@ -444,45 +421,6 @@ void savePropertiesFile(Project aProject, InputStream aInputStream, String aFile
      */
     public boolean managesAnyProject(User aUser);
 
-    /**
-     * Determine if the user is allowed to update a project.
-     *
-     * @param aProject
-     *            the project
-     * @param aUser
-     *            the user.
-     * @return if the user may update a project.
-     * @deprecated Use {@link #hasRole(User, Project, PermissionLevel, PermissionLevel...)}
-     */
-    @Deprecated
-    boolean isManager(Project aProject, User aUser);
-
-    /**
-     * Determine if the user is a curator or not.
-     *
-     * @param aProject
-     *            the project.
-     * @param aUser
-     *            the user.
-     * @return if the user is a curator.
-     * @deprecated Use {@link #hasRole(User, Project, PermissionLevel, PermissionLevel...)}
-     */
-    @Deprecated
-    boolean isCurator(Project aProject, User aUser);
-
-    /**
-     * Determine if the User is member of a project
-     *
-     * @param aProject
-     *            the project.
-     * @param aUser
-     *            the user.
-     * @return if the user is a member.
-     * @deprecated Use {@link #hasRole(User, Project, PermissionLevel, PermissionLevel...)}
-     */
-    @Deprecated
-    boolean isAnnotator(Project aProject, User aUser);
-
     /**
      * Check whether the given user has any role at all in the given project.
      * 

diff --git a/inception/inception-concept-linking/pom.xml b/inception/inception-concept-linking/pom.xml
@@ -233,6 +233,14 @@
       <artifactId>dkpro-core-io-conll-asl</artifactId>
       <scope>test</scope>
     </dependency>
+
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+      <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+      <version>1.33</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
   <build>
     <pluginManagement>
@@ -242,6 +250,8 @@
           <artifactId>maven-dependency-plugin</artifactId>
           <configuration>
             <ignoredDependencies>
+              <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+              <ignoredDependency>org.yaml:snakeyaml</ignoredDependency>
               <!-- Dependency analysis does not get it... -->
               <ignoredDependency>org.danekja:jdk-serializable-functional</ignoredDependency>
               <ignoredDependency>javax.persistence:javax.persistence-api</ignoredDependency>

diff --git a/inception/inception-example-imls-data-majority/pom.xml b/inception/inception-example-imls-data-majority/pom.xml
@@ -129,5 +129,31 @@
       <artifactId>dkpro-core-io-conll-asl</artifactId>
       <scope>test</scope>
     </dependency>
+
+
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+      <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+      <version>1.33</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
+
+  <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-dependency-plugin</artifactId>
+          <configuration>
+            <ignoredDependencies>
+              <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+              <ignoredDependency>org.yaml:snakeyaml</ignoredDependency>
+            </ignoredDependencies>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>
 </project>
diff --git a/inception/inception-imls-external/pom.xml b/inception/inception-imls-external/pom.xml
@@ -150,6 +150,14 @@
       <artifactId>dkpro-core-api-ner-asl</artifactId>
       <scope>test</scope>
     </dependency>
+
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+      <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+      <version>1.33</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
 
   <build>
@@ -160,6 +168,8 @@
           <artifactId>maven-dependency-plugin</artifactId>
           <configuration>
             <ignoredDependencies>
+              <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+              <ignoredDependency>org.yaml:snakeyaml</ignoredDependency>
               <!-- Plugin does not get it -->
               <ignoredDependency>com.fasterxml.jackson.core:jackson-core</ignoredDependency>
             </ignoredDependencies>

diff --git a/inception/inception-imls-opennlp/pom.xml b/inception/inception-imls-opennlp/pom.xml
@@ -160,5 +160,29 @@
       <artifactId>dkpro-core-api-io-asl</artifactId>
       <scope>test</scope>
     </dependency>
+
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+      <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+      <version>1.33</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
+  <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-dependency-plugin</artifactId>
+          <configuration>
+            <ignoredDependencies>
+              <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+              <ignored>org.yaml:snakeyaml</ignored>
+            </ignoredDependencies>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>
 </project>
diff --git a/inception/inception-imls-stringmatch/pom.xml b/inception/inception-imls-stringmatch/pom.xml
@@ -210,18 +210,26 @@
       <artifactId>hsqldb</artifactId>
       <scope>test</scope>
     </dependency>
+
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+      <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+      <version>1.33</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
   <build>
     <pluginManagement>
       <plugins>
-        <plugin>
-          <groupId>org.apache.maven.plugins</groupId>
-          <artifactId>maven-surefire-plugin</artifactId>
-        </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-dependency-plugin</artifactId>
           <configuration>
+            <ignoredDependencies>
+              <!-- DKPro Core Datasets isn't compatible with SnakeYAML 2.0 atm -->
+              <ignored>org.yaml:snakeyaml</ignored>
+            </ignoredDependencies>
             <usedDependencies>
               <!-- Testing - used via reflection -->
               <usedDependency>org.hsqldb:hsqldb</usedDependency>

diff --git a/...n-project/src/main/java/de/tudarmstadt/ukp/clarin/webanno/project/ProjectServiceImpl.java b/...n-project/src/main/java/de/tudarmstadt/ukp/clarin/webanno/project/ProjectServiceImpl.java
@@ -18,8 +18,6 @@
 package de.tudarmstadt.ukp.clarin.webanno.project;
 
 import static de.tudarmstadt.ukp.clarin.webanno.api.ProjectService.withProjectLogger;
-import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.ANNOTATOR;
-import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.CURATOR;
 import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.MANAGER;
 import static de.tudarmstadt.ukp.clarin.webanno.model.Project.MAX_PROJECT_SLUG_LENGTH;
 import static de.tudarmstadt.ukp.clarin.webanno.model.Project.MIN_PROJECT_SLUG_LENGTH;
@@ -91,8 +89,10 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.clarin.webanno.model.ProjectPermission;
+import de.tudarmstadt.ukp.clarin.webanno.model.ProjectPermission_;
 import de.tudarmstadt.ukp.clarin.webanno.model.ProjectState;
 import de.tudarmstadt.ukp.clarin.webanno.model.ProjectUserPermissions;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project_;
 import de.tudarmstadt.ukp.clarin.webanno.project.config.ProjectServiceAutoConfiguration;
 import de.tudarmstadt.ukp.clarin.webanno.security.Realm;
 import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
@@ -231,13 +231,6 @@ public boolean existsProjectPermissionLevel(User aUser, Project aProject,
         return hasRole(aUser, aProject, aLevel);
     }
 
-    @Override
-    public File getProjectFolder(Project aProject)
-    {
-        return new File(repositoryProperties.getPath().getAbsolutePath() + "/" + PROJECT_FOLDER
-                + "/" + aProject.getId());
-    }
-
     @Override
     public File getProjectLogFile(Project aProject)
     {
@@ -751,30 +744,6 @@ public boolean managesAnyProject(User user)
         return false;
     }
 
-    @Deprecated
-    @Transactional
-    @Override
-    public boolean isManager(Project aProject, User aUser)
-    {
-        return hasRole(aUser, aProject, MANAGER);
-    }
-
-    @Deprecated
-    @Transactional
-    @Override
-    public boolean isCurator(Project aProject, User aUser)
-    {
-        return hasRole(aUser, aProject, CURATOR);
-    }
-
-    @Deprecated
-    @Transactional
-    @Override
-    public boolean isAnnotator(Project aProject, User aUser)
-    {
-        return hasRole(aUser, aProject, ANNOTATOR);
-    }
-
     @EventListener
     @Transactional
     public void onContextRefreshedEvent(ContextRefreshedEvent aEvent)
@@ -936,31 +905,6 @@ public void initializeProject(Project aProject, List<ProjectInitializer> aInitia
         }
     }
 
-    @Override
-    @Transactional
-    @Deprecated
-    public List<Project> listProjectsForAgreement()
-    {
-        String query = String.join("\n", //
-                "SELECT DISTINCT p FROM Project p, ProjectPermission pp ", //
-                "WHERE pp.project = p.id ", //
-                "AND pp.level = :annotator ", //
-                "GROUP BY p.id HAVING count(*) > 1 ", //
-                "ORDER BY p.name ASC");
-        List<Project> projects = entityManager.createQuery(query, Project.class)
-                .setParameter("annotator", ANNOTATOR) //
-                .getResultList();
-        return projects;
-    }
-
-    @Override
-    @Transactional
-    @Deprecated
-    public List<Project> listManageableCuratableProjects(User aUser)
-    {
-        return listProjectsWithUserHavingRole(aUser, CURATOR, MANAGER);
-    }
-
     @Override
     @Transactional
     public List<Project> listProjectsWithUserHavingRole(User aUser, PermissionLevel aRole,
@@ -975,17 +919,28 @@ public List<Project> listProjectsWithUserHavingRole(User aUser, PermissionLevel
             roles.addAll(asList(aMoreRoles));
         }
 
-        String query = String.join("\n", //
-                "SELECT DISTINCT p FROM Project p, ProjectPermission pp ", //
-                "WHERE pp.project = p.id ", //
-                "AND pp.user = :username ", //
-                "AND pp.level IN (:roles) ", //
-                "ORDER BY p.name ASC");
-        List<Project> projects = entityManager.createQuery(query, Project.class)
-                .setParameter("username", aUser.getUsername()) //
-                .setParameter("roles", roles) //
-                .getResultList();
-        return projects;
+        var cb = entityManager.getCriteriaBuilder();
+        var cq = cb.createQuery(Project.class);
+        var permission = cq.from(ProjectPermission.class);
+        var project = permission.join(ProjectPermission_.project);
+        cq.select(project).distinct(true);
+        cq.where(cb.and( //
+                cb.equal(permission.get(ProjectPermission_.user), aUser.getUsername()), //
+                permission.get(ProjectPermission_.level).in(roles)));
+        cq.orderBy(cb.asc(project.get(Project_.name)));
+        return entityManager.createQuery(cq).getResultList();
+
+        // String query = String.join("\n", //
+        // "SELECT DISTINCT p FROM Project p, ProjectPermission pp ", //
+        // "WHERE pp.project = p.id ", //
+        // "AND pp.user = :username ", //
+        // "AND pp.level IN (:roles) ", //
+        // "ORDER BY p.name ASC");
+        // List<Project> projects = entityManager.createQuery(query, Project.class)
+        // .setParameter("username", aUser.getUsername()) //
+        // .setParameter("roles", roles) //
+        // .getResultList();
+        // return projects;
     }
 
     @Override

diff --git a/...oject/src/test/java/de/tudarmstadt/ukp/clarin/webanno/project/ProjectServiceImplTest.java b/...oject/src/test/java/de/tudarmstadt/ukp/clarin/webanno/project/ProjectServiceImplTest.java
@@ -139,29 +139,6 @@ public void tearDown()
         testEntityManager.clear();
     }
 
-    @Deprecated
-    @Test
-    public void listProjectsForAgreement_ShouldReturnOneProject()
-    {
-        List<Project> foundProjects = sut.listProjectsForAgreement();
-
-        assertThat(foundProjects).containsExactly(testProject);
-    }
-
-    @Deprecated
-    @Test
-    public void thatListManageableCuratableProjectsReturnsOnlyProjectsWhereUserIsCuratorOrManager()
-    {
-        assertThat(sut.listManageableCuratableProjects(beate)) //
-                .containsExactlyInAnyOrder(testProject, testProject2, testProjectManagedByBeate);
-
-        assertThat(sut.listManageableCuratableProjects(kevin)) //
-                .containsExactlyInAnyOrder(testProjectManagedByKevin);
-
-        assertThat(sut.listManageableCuratableProjects(noPermissionUser)) //
-                .isEmpty();
-    }
-
     @Test
     public void thatListAccessibleProjectsWorks()
     {