[Snyk] Upgrade org.springframework.boot:spring-boot-starter from 3.4.10 to 3.5.7

.github/workflows/CI.yml

@@ -37,7 +37,7 @@ jobs:
         ports:
           - 1025:1025
       openldap:
-        image: docker.io/bitnami/openldap:2.6
+        image: docker.io/bitnamilegacy/openldap:2.6
         ports:
           - 1389:1389
           - 1636:1636

.github/workflows/development.yml

@@ -36,7 +36,7 @@ jobs:
           POSTGRES_PASSWORD: roda
           POSTGRES_DB: roda_core_db
       openldap:
-        image: docker.io/bitnami/openldap:2.6
+        image: docker.io/bitnamilegacy/openldap:2.6
         ports:
           - 1389:1389
           - 1636:1636

.github/workflows/latest.yml

@@ -36,7 +36,7 @@ jobs:
         ports:
           - 1025:1025
       openldap:
-        image: docker.io/bitnami/openldap:2.6
+        image: docker.io/bitnamilegacy/openldap:2.6
         ports:
           - 1389:1389
           - 1636:1636

.github/workflows/release.yml

@@ -38,7 +38,7 @@ jobs:
         ports:
           - 1025:1025
       openldap:
-        image: docker.io/bitnami/openldap:2.6
+        image: docker.io/bitnamilegacy/openldap:2.6
         ports:
           - 1389:1389
           - 1636:1636
@@ -142,8 +142,8 @@ jobs:
         uses: svenstaro/upload-release-action@v2
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
-          file: roda-ui/roda-wui/target/roda-wui-${{ env.release_version }}.war
-          asset_name: roda-wui-${{ env.release_version }}.war
+          file: roda-ui/roda-wui/target/roda-wui-${{ env.release_version }}.jar
+          asset_name: roda-wui-${{ env.release_version }}.jar
           tag: ${{ github.ref }}
           release_name: ${{ github.ref_name }}
           draft: true

.github/workflows/staging.yml

@@ -36,7 +36,7 @@ jobs:
         ports:
           - 1025:1025
       openldap:
-        image: docker.io/bitnami/openldap:2.6
+        image: docker.io/bitnamilegacy/openldap:2.6
         ports:
           - 1389:1389
           - 1636:1636

deploys/standalone/docker-compose-dev.yaml

@@ -79,7 +79,7 @@ services:
       - "8025:8025" # web ui
 
   openldap:
-    image: docker.io/bitnami/openldap:2.6
+    image: docker.io/bitnamilegacy/openldap:2.6
     container_name: openldap
     restart: unless-stopped
     user: 1001:root

pom.xml

@@ -123,16 +123,16 @@
         <gwt.version>2.12.2</gwt.version>
         <cas.client.version>4.0.4</cas.client.version>
         <swagger.version>2.2.34</swagger.version>
-        <jackson.version>2.19.1</jackson.version>
+        <jackson.version>2.20.1</jackson.version>
         <spring.version>6.2.11</spring.version>
-        <solr.version>9.8.1</solr.version>
+        <solr.version>9.10.0</solr.version>
         <pekko.version>1.1.4</pekko.version>
         <httpcomponents.version>5.5</httpcomponents.version>
         <commons_ip2.version>2.10.0</commons_ip2.version>
         <metrics.version>3.2.6</metrics.version>
         <roda_community_url>https://roda-community.org</roda_community_url>
         <testng.groups>all</testng.groups>
-        <springboot.version>3.4.10</springboot.version>
+        <springboot.version>3.5.7</springboot.version>
         <scope.gwt-dev>provided</scope.gwt-dev>
         <logback.version>1.5.19</logback.version>
     </properties>
@@ -478,6 +478,13 @@
                 <artifactId>jaxb-runtime</artifactId>
                 <version>4.0.5</version>
             </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson</groupId>
+                <artifactId>jackson-bom</artifactId>
+                <version>2.20.0</version>
+                <scope>import</scope>
+                <type>pom</type>
+            </dependency>
             <dependency>
                 <!-- Import dependency management from Spring Boot -->
                 <groupId>org.springframework.boot</groupId>
@@ -486,36 +493,6 @@
                 <type>pom</type>
                 <scope>import</scope>
             </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-core</artifactId>
-                <version>${jackson.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-databind</artifactId>
-                <version>${jackson.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-annotations</artifactId>
-                <version>${jackson.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.dataformat</groupId>
-                <artifactId>jackson-dataformat-xml</artifactId>
-                <version>${jackson.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.dataformat</groupId>
-                <artifactId>jackson-dataformat-yaml</artifactId>
-                <version>${jackson.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.datatype</groupId>
-                <artifactId>jackson-datatype-jsr310</artifactId>
-                <version>${jackson.version}</version>
-            </dependency>
             <dependency>
                 <groupId>org.gwtproject</groupId>
                 <artifactId>gwt-dev</artifactId>
@@ -560,7 +537,7 @@
             <dependency>
                 <groupId>commons-io</groupId>
                 <artifactId>commons-io</artifactId>
-                <version>2.19.0</version>
+                <version>2.20.0</version>
             </dependency>
             <dependency>
                 <groupId>commons-logging</groupId>
@@ -960,19 +937,11 @@
                 <artifactId>icu4j</artifactId>
                 <version>63.2</version>
             </dependency>
-
             <dependency>
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-starter-tomcat</artifactId>
                 <scope>provided</scope>
             </dependency>
-
-            <!-- https://mvnrepository.com/artifact/com.google.code.gson/gson -->
-            <dependency>
-                <groupId>com.google.code.gson</groupId>
-                <artifactId>gson</artifactId>
-                <version>2.11.0</version>
-            </dependency>
         </dependencies>
     </dependencyManagement>
     <reporting>

roda-common/roda-common-data/src/main/java/org/roda/core/data/common/RodaConstants.java

@@ -401,6 +401,9 @@ public enum DateGranularity {
   // dips
   public static final String API_REST_V2_DIPS = "api/v2/dips/";
 
+  // dipfiles
+  public static final String API_REST_V2_DIPFILES = "api/v2/dip-files/";
+
   // representation-information
   public static final String API_REST_V2_REPRESENTATION_INFORMATION = "api/v2/representation-information/";
 

roda-common/roda-common-data/src/main/java/org/roda/core/data/utils/URNUtils.java

@@ -51,7 +51,7 @@ public static String createRodaPreservationURN(PreservationMetadataType preserva
   }
 
   public static String createRodaTechnicalMetadataURN(String id, String instanceId, String technicalMetadataType) {
-    return getTechnicalMetadataPrefix(technicalMetadataType, instanceId) + id;
+    return getTechnicalMetadataPrefix(technicalMetadataType, instanceId) + id + RodaConstants.REPRESENTATION_INFORMATION_FILE_EXTENSION;
   }
 
   public static String getTechnicalMetadataPrefix(String technicalMetadataType, String instanceId) {

roda-common/roda-common-utils/src/main/java/org/roda/core/util/HTTPUtility.java

@@ -32,39 +32,41 @@ private HTTPUtility() {
     // do nothing
   }
 
+  public static String doMethodBearer(String url, String method, Optional<String> token) throws GenericException {
+    try {
+      URL obj = new URL(url);
+      HttpURLConnection con = (HttpURLConnection) obj.openConnection();
+      con.setRequestProperty("Accept", "application/json");
+      con.setRequestProperty("Content-Type", "application/json");
+      con.setRequestMethod(method);
+      addBearerAuthToConnection(con, token);
+      return executeRequest(con);
+    } catch (IOException e) {
+      throw new GenericException("Unable to connect to server", e);
+    }
+  }
+
   public static String doMethod(String url, String method, Optional<Pair<String, String>> basicAuth)
     throws GenericException {
-    String res = null;
     try {
       URL obj = new URL(url);
       HttpURLConnection con = (HttpURLConnection) obj.openConnection();
       con.setRequestMethod(method);
       addBasicAuthToConnection(con, basicAuth);
-      int responseCode = con.getResponseCode();
-      if (responseCode == 200) {
-        InputStream is = con.getInputStream();
-        BufferedReader in = new BufferedReader(new InputStreamReader(is));
-        String inputLine;
-        StringBuilder response = new StringBuilder();
-        while ((inputLine = in.readLine()) != null) {
-          response.append(inputLine);
-        }
-        in.close();
-        is.close();
-        res = response.toString();
-      } else {
-        throw new GenericException("Unable to connect to server, response code: " + responseCode);
-      }
+      return executeRequest(con);
     } catch (IOException e) {
       throw new GenericException("Unable to connect to server", e);
     }
-    return res;
   }
 
   public static String doGet(String url) throws GenericException {
     return doMethod(url, METHOD_GET, Optional.empty());
   }
 
+  public static String doGetBearer(String url, Optional<String> token) throws GenericException {
+    return doMethodBearer(url, METHOD_GET, token);
+  }
+
   public static String doGet(String url, Optional<Pair<String, String>> basicAuth) throws GenericException {
     return doMethod(url, METHOD_GET, basicAuth);
   }
@@ -77,6 +79,10 @@ public static String doDelete(String url, Optional<Pair<String, String>> basicAu
     return doMethod(url, METHOD_DELETE, basicAuth);
   }
 
+  public static String doDeleteBearer(String url, Optional<String> token) throws GenericException {
+    return doMethodBearer(url, METHOD_DELETE, token);
+  }
+
   private static void addBasicAuthToConnection(HttpURLConnection connection,
     Optional<Pair<String, String>> credentials) {
     if (credentials.isPresent()) {
@@ -85,4 +91,28 @@ private static void addBasicAuthToConnection(HttpURLConnection connection,
       connection.setRequestProperty("Authorization", "Basic " + encoded);
     }
   }
+
+  private static void addBearerAuthToConnection(HttpURLConnection connection, Optional<String> token) {
+    token.ifPresent(s -> connection.setRequestProperty("Authorization", "Bearer " + s));
+  }
+
+  private static String executeRequest(HttpURLConnection con) throws IOException, GenericException {
+    int resCode = con.getResponseCode();
+
+    if (resCode == 200) {
+      InputStream is = con.getInputStream();
+      try (BufferedReader in = new BufferedReader(new InputStreamReader(is))) {
+        String inputLine;
+        StringBuilder response = new StringBuilder();
+        while ((inputLine = in.readLine()) != null) {
+          response.append(inputLine);
+        }
+        return response.toString();
+      } finally {
+        is.close();
+      }
+    } else {
+      throw new GenericException("Unable to connect to server, response code: " + resCode);
+    }
+  }
 }

roda-common/roda-common-utils/src/main/java/org/roda/core/util/IdUtils.java

@@ -191,6 +191,12 @@ public static String getTransferredResourceUUID(Path relativeToBase) {
     return getTransferredResourceUUID(relativeToBase.toString());
   }
 
+  public static String createTechnicalMetadataFileId(String fileId, List<String> fileDirectoryPath){
+    if(fileDirectoryPath.isEmpty()) return fileId;
+    String pathPrefix = String.join(ID_SEPARATOR, fileDirectoryPath);
+    return pathPrefix + ID_SEPARATOR + fileId;
+  }
+
   public static String getTransferredResourceUUID(String relativeToBase) {
     return IdUtils.createUUID(relativeToBase);
   }

roda-core/roda-core-tests/pom.xml

@@ -155,7 +155,7 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
-            <version>1.21.1</version>
+            <version>2.0.2</version>
         </dependency>
     </dependencies>
 </project>

roda-core/roda-core-tests/src/main/java/org/roda/core/security/LdapUtilityTestHelper.java

@@ -38,7 +38,7 @@ public LdapUtility getLdapUtility() {
 
   public LdapUtilityTestHelper() {
     final String ldapBaseDN = "dc=roda,dc=org";
-    DockerImageName OPENLDAP_IMAGE = DockerImageName.parse("docker.io/bitnami/openldap:2.6");
+    DockerImageName OPENLDAP_IMAGE = DockerImageName.parse("docker.io/bitnamilegacy/openldap:2.6");
 
     openldap = new GenericContainer<>(OPENLDAP_IMAGE);
     openldap.withExposedPorts(1389);

roda-core/roda-core/pom.xml

@@ -46,16 +46,12 @@
                                     <shadedClassifierName>jar-with-dependencies</shadedClassifierName>
                                     <createDependencyReducedPom>false</createDependencyReducedPom>
                                     <transformers>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.ComponentsXmlResourceTransformer"/>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.ComponentsXmlResourceTransformer"/>
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                             <mainClass>org.roda.core.RodaCoreFactory</mainClass>
                                         </transformer>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                             <!-- akka related conf appending -->
                                             <resource>reference.conf</resource>
                                         </transformer>
@@ -96,16 +92,12 @@
                                     <shadedClassifierName>jar-with-dependencies</shadedClassifierName>
                                     <createDependencyReducedPom>false</createDependencyReducedPom>
                                     <transformers>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.ComponentsXmlResourceTransformer"/>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.ComponentsXmlResourceTransformer"/>
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                             <mainClass>org.roda.core.RodaCoreFactory</mainClass>
                                         </transformer>
-                                        <transformer
-                                                implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                        <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                             <!-- akka related conf appending -->
                                             <resource>reference.conf</resource>
                                         </transformer>
@@ -164,7 +156,7 @@
         <dependency>
             <groupId>org.apache.zookeeper</groupId>
             <artifactId>zookeeper</artifactId>
-            <version>3.9.3</version>
+            <version>3.9.4</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/org.apache.solr/solr-solrj-zookeeper -->
         <dependency>

roda-core/roda-core/src/main/java/org/roda/core/index/schema/collections/FileCollection.java

@@ -195,8 +195,11 @@ public SolrInputDocument toSolrDocument(ModelService model, File file, IndexingA
 
     Long sizeInBytes = 0L;
 
-    SolrUtils.indexRepresentationTechnicalMetadata(model,
-      getRepresentationTechnicalMetadata(((Info) info).aip, file.getRepresentationId()), fileId, doc);
+    if (!file.isDirectory()) {
+      String techMdFileId = IdUtils.createTechnicalMetadataFileId(fileId, file.getPath());
+      SolrUtils.indexRepresentationTechnicalMetadata(model,
+        getRepresentationTechnicalMetadata(((Info) info).aip, file.getRepresentationId()), techMdFileId, doc);
+    }
 
     // Add information from PREMIS
     Binary premisFile = getFilePremisFile(model, file);

roda-core/roda-core/src/main/java/org/roda/core/index/utils/SolrUtils.java

@@ -1545,7 +1545,7 @@ public static void indexRepresentationTechnicalMetadata(ModelService model,
 
       StoragePath storagePath = ModelUtils.getTechnicalMetadataStoragePath(techMd.getAipId(),
         techMd.getRepresentationId(), Collections.singletonList(techMd.getType()),
-        urn + RodaConstants.REPRESENTATION_INFORMATION_FILE_EXTENSION);
+        urn);
 
       Binary binary = model.getStorage().getBinary(storagePath);