Merge branch 'main' into refactoring/4843-Promote-sidebar-curation-mo…

…de-to-proper-curation-page

* main: (24 commits)
  #4919 - Unable to import project with knowledge-based exported by INCEpTION 33.0 (again)
  #4921 - Constraints do not work properly when rules are distributed over multiple rulesets
  #4915 - Support for MySQL 8
  #4051 - Postgres support
  #3407 - Remove old database migrations that seem to get always executed
  #3407 - Remove old database migrations that seem to get always executed
  #4909 - Upgrade dependencies
  #4911 - No results when searching as curator after re-indexing project
  #4909 - Upgrade dependencies
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-33.1
  #4901 - Consider document structure when splitting sentences in custom XML formats
  #4880 - Upgrade dependencies
  #4898 - Unable to import project with knowledge-based exported by INCEpTION 33.0
  #4896 - Ability to search for additional languages in knowledge-base
  No issue: Trim LLM responses
  #4892 - Curation sidebar state not cleared when logging out
  #4891 - Exception in sidebar curation mode when document-level annotations exist
  #4727 - Switching between editors can cause the old and the new editors to be loaded and initialized
  #4889 - Document sometimes not rendered in by-line brat render modes
  ...

% Conflicts:
%	inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/AnnotationPage.java

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/paging/SentenceOrientedPagingStrategy.java

@@ -86,8 +86,8 @@ private Unit toUnit(int aIndex, AnnotationFS aSentence)
     @Override
     public Component createPositionLabel(String aId, IModel<AnnotatorState> aModel)
     {
-        Label label = new Label(aId, () -> {
-            AnnotatorState state = aModel.getObject();
+        var label = new Label(aId, () -> {
+            var state = aModel.getObject();
             return String.format("%d-%d / %d sentences [doc %d / %d]",
                     state.getFirstVisibleUnitIndex(), state.getLastVisibleUnitIndex(),
                     state.getUnitCount(), state.getDocumentIndex() + 1,

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/paging/TokenWrappingPagingStrategy.java

@@ -52,7 +52,7 @@ public List<Unit> units(CAS aCas, int aFirstIndex, int aLastIndex)
     {
         Iterator<AnnotationFS> tokenIterator = WebAnnoCasUtil.selectTokens(aCas).iterator();
 
-        List<Unit> units = new ArrayList<>();
+        var units = new ArrayList<Unit>();
 
         int currentUnitStart = 0;
         int currentUnitEnd = 0;
@@ -65,7 +65,7 @@ public List<Unit> units(CAS aCas, int aFirstIndex, int aLastIndex)
                         currentToken.getBegin(), currentToken.getEnd(), currentUnitEnd));
             }
 
-            String gap = aCas.getDocumentText().substring(currentUnitEnd, currentToken.getBegin());
+            var gap = aCas.getDocumentText().substring(currentUnitEnd, currentToken.getBegin());
             int gapStart = currentUnitEnd;
             int lineBreakIndex = gap.indexOf("\n");
             while (lineBreakIndex > -1) {
@@ -75,8 +75,8 @@ public List<Unit> units(CAS aCas, int aFirstIndex, int aLastIndex)
                 lineBreakIndex = gap.indexOf("\n", lineBreakIndex + 1);
             }
 
-            boolean unitNonEmpty = (currentUnitEnd - currentUnitStart) > 0;
-            boolean unitFull = unitNonEmpty
+            var unitNonEmpty = (currentUnitEnd - currentUnitStart) > 0;
+            var unitFull = unitNonEmpty
                     && ((currentToken.getEnd() - currentUnitStart) > maxLineLength);
 
             // If the unit is full, finish the unit and start a new one

inception/inception-app-webapp/pom.xml

@@ -36,6 +36,10 @@
     </dependency>
 
     <!-- INCEPTION - CORE DEPENDENCIES -->
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-model</artifactId>
+    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-documents</artifactId>
@@ -64,10 +68,6 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-ui-scheduling</artifactId>
     </dependency>
-    <dependency>
-      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
-      <artifactId>inception-project</artifactId>
-    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-doc</artifactId>
@@ -112,6 +112,10 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-processing</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-project-api</artifactId>
+    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-project-initializers</artifactId>
@@ -531,10 +535,6 @@
       <groupId>org.slf4j</groupId>
       <artifactId>jul-to-slf4j</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.slf4j</groupId>
-      <artifactId>jcl-over-slf4j</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>log4j-over-slf4j</artifactId>
@@ -570,6 +570,11 @@
       <groupId>org.liquibase</groupId>
       <artifactId>liquibase-core</artifactId>
     </dependency>
+    <dependency>
+      <groupId>com.mattbertolini</groupId>
+      <artifactId>liquibase-slf4j</artifactId>
+      <version>5.0.0</version>
+    </dependency>
 
     <dependency>
       <groupId>org.hibernate.orm</groupId>
@@ -686,6 +691,31 @@
       <artifactId>mock-oauth2-server</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>junit-jupiter</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>mariadb</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>mysql</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>postgresql</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>mysql</groupId>
+      <artifactId>mysql-connector-java</artifactId>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
   <build>
     <plugins>
@@ -909,12 +939,17 @@
             <ignoredUsedUndeclaredDependencies>
               <ignoredUsedUndeclaredDependency>org.apache.tomcat.embed:tomcat-embed-core</ignoredUsedUndeclaredDependency>
             </ignoredUsedUndeclaredDependencies>
+            <ignoredNonTestScopedDependencies>
+              <dependency>de.tudarmstadt.ukp.inception.app:inception-model</dependency>
+              <dependency>de.tudarmstadt.ukp.inception.app:inception-project</dependency>
+              <dependency>de.tudarmstadt.ukp.inception.app:inception-project-api</dependency>
+              <dependency>de.tudarmstadt.ukp.inception.app:inception-project-initializers</dependency>
+            </ignoredNonTestScopedDependencies>
             <usedDependencies>
               <!-- INCEpTION backend modules - used via Spring -->
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-guidelines</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-documents</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-image</usedDependency>
-              <usedDependency>de.tudarmstadt.ukp.inception.app:inception-project</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-plugin-manager</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-concept-linking</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-recommendation</usedDependency>
@@ -955,7 +990,6 @@
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-layer-docmetadata</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-feature-lookup</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-processing</usedDependency>
-              <usedDependency>de.tudarmstadt.ukp.inception.app:inception-project-initializers</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-project-initializers-basic</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-project-initializers-doclabeling</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-project-initializers-sentencelabeling</usedDependency>
@@ -993,10 +1027,12 @@
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-telemetry</usedDependency>
               <!-- JDBC drivers and database stuff - used via reflection -->
               <usedDependency>org.hibernate.orm:hibernate-core</usedDependency>
+              <usedDependency>org.hsqldb:hsqldb</usedDependency>
               <usedDependency>org.mariadb.jdbc:mariadb-java-client</usedDependency>
+              <usedDependency>mysql:mysql-connector-java</usedDependency>
               <usedDependency>org.postgresql:postgresql</usedDependency>
-              <usedDependency>org.hsqldb:hsqldb</usedDependency>
               <!-- Logging - used via reflection / optional -->
+              <usedDependency>com.mattbertolini:liquibase-slf4j</usedDependency>
               <usedDependency>org.slf4j:log4j-over-slf4j</usedDependency>
               <usedDependency>org.apache.logging.log4j:log4j-slf4j2-impl</usedDependency>
               <usedDependency>org.apache.logging.log4j:log4j-core</usedDependency>

inception/inception-app-webapp/src/main/java/de/tudarmstadt/ukp/inception/app/config/InceptionApplicationContextInitializer.java

@@ -18,20 +18,24 @@
 package de.tudarmstadt.ukp.inception.app.config;
 
 import static de.tudarmstadt.ukp.inception.support.SettingsUtil.CFG_AUTH_MODE;
+import static de.tudarmstadt.ukp.inception.support.deployment.DeploymentModeService.PROFILE_AUTH_MODE_DATABASE;
+import static de.tudarmstadt.ukp.inception.support.deployment.DeploymentModeService.PROFILE_AUTH_MODE_EXTERNAL_PREAUTH;
 import static de.tudarmstadt.ukp.inception.support.logging.BaseLoggers.BOOT_LOG;
 
-import java.io.File;
 import java.io.IOException;
+import java.util.HashMap;
 
 import org.springframework.context.ApplicationContextInitializer;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.env.MapPropertySource;
 import org.springframework.core.io.FileSystemResource;
 import org.springframework.core.io.support.ResourcePropertySource;
 import org.springframework.util.unit.DataSize;
 
 import de.tudarmstadt.ukp.inception.support.SettingsUtil;
-import de.tudarmstadt.ukp.inception.support.deployment.DeploymentModeService;
+import de.tudarmstadt.ukp.inception.support.db.InceptionHSQLDialect;
+import de.tudarmstadt.ukp.inception.support.db.InceptionMySQLDialect;
 import de.tudarmstadt.ukp.inception.support.logging.BaseLoggers;
 import de.tudarmstadt.ukp.inception.support.logging.LoggingFilter;
 
@@ -45,9 +49,22 @@ public void initialize(ConfigurableApplicationContext aApplicationContext)
     {
         LoggingFilter.setLoggingUsername("SYSTEM");
 
-        ConfigurableEnvironment aEnvironment = aApplicationContext.getEnvironment();
+        var aEnvironment = aApplicationContext.getEnvironment();
 
-        File settings = SettingsUtil.getSettingsFileLocation();
+        loadSettings(aEnvironment);
+
+        applyDatabaseSpecificOverrides(aEnvironment);
+
+        activateAuthenticationProfiles(aEnvironment);
+
+        Runtime rt = Runtime.getRuntime();
+        BOOT_LOG.info("Max. application memory: {}MB",
+                DataSize.ofBytes(rt.maxMemory()).toMegabytes());
+    }
+
+    private void loadSettings(ConfigurableEnvironment aEnvironment)
+    {
+        var settings = SettingsUtil.getSettingsFileLocation();
 
         BaseLoggers.BOOT_LOG.info("Settings: {} {}", settings,
                 settings.exists() ? "(file exists)" : "(file does not exist)");
@@ -62,19 +79,56 @@ public void initialize(ConfigurableApplicationContext aApplicationContext)
                 throw new IllegalStateException(e);
             }
         }
+    }
+
+    private void applyDatabaseSpecificOverrides(ConfigurableEnvironment aEnvironment)
+    {
+        var datasourceUrl = aEnvironment.getProperty("spring.datasource.url");
+        if (datasourceUrl == null) {
+            return;
+        }
 
+        if (datasourceUrl.startsWith("jdbc:hsqldb:")) {
+            var overrides = new HashMap<String, Object>();
+            overrides.put("spring.jpa.properties.hibernate.dialect",
+                    InceptionHSQLDialect.class.getName());
+            // Existing HSQLDBs will have all-caps table and column names - if we quote, it will
+            // break loading these.
+            overrides.put("spring.jpa.properties.hibernate.globally_quoted_identifiers", false);
+            aEnvironment.getPropertySources()
+                    .addFirst(new MapPropertySource("HSQLDB-Overrides", overrides));
+        }
+
+        if (datasourceUrl.startsWith("jdbc:postgresql:")) {
+            var overrides = new HashMap<String, Object>();
+            // PostgreSQL does not like unquoted mixed-case columns - but we have those, e.g.
+            // the `curationSettings_users` table.
+            overrides.put("spring.jpa.properties.hibernate.globally_quoted_identifiers", true);
+            aEnvironment.getPropertySources()
+                    .addFirst(new MapPropertySource("PostgreSQL-Overrides", overrides));
+        }
+
+        if (datasourceUrl.startsWith("jdbc:mysql:")) {
+            var overrides = new HashMap<String, Object>();
+            // We use certain column names like `rank` that are reserved words in MySQL
+            overrides.put("spring.jpa.properties.hibernate.globally_quoted_identifiers", true);
+            overrides.put("spring.jpa.properties.hibernate.dialect",
+                    InceptionMySQLDialect.class.getName());
+            aEnvironment.getPropertySources()
+                    .addFirst(new MapPropertySource("MySQL-Overrides", overrides));
+        }
+    }
+
+    private void activateAuthenticationProfiles(ConfigurableEnvironment aEnvironment)
+    {
         // Activate bean profile depending on authentication mode
         if (AUTH_MODE_PREAUTH.equals(aEnvironment.getProperty(CFG_AUTH_MODE))) {
-            aEnvironment.addActiveProfile(DeploymentModeService.PROFILE_AUTH_MODE_EXTERNAL_PREAUTH);
+            aEnvironment.addActiveProfile(PROFILE_AUTH_MODE_EXTERNAL_PREAUTH);
             BOOT_LOG.info("Authentication: pre-auth");
         }
         else {
-            aEnvironment.addActiveProfile(DeploymentModeService.PROFILE_AUTH_MODE_DATABASE);
+            aEnvironment.addActiveProfile(PROFILE_AUTH_MODE_DATABASE);
             BOOT_LOG.info("Authentication: database");
         }
-
-        Runtime rt = Runtime.getRuntime();
-        BOOT_LOG.info("Max. application memory: {}MB",
-                DataSize.ofBytes(rt.maxMemory()).toMegabytes());
     }
 }