Next patch release (v2.1.2)

.github/workflows/codeql-analysis.yml

@@ -38,11 +38,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@8aad20d150bbac5944a9f9d289da16a4b0d87c1e # v4.36.2
+      uses: github/codeql-action/init@e4fba868fa4b1b91e1fdab776edc8cfbe6e9fb81 # v4.37.3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@8aad20d150bbac5944a9f9d289da16a4b0d87c1e # v4.36.2
+      uses: github/codeql-action/autobuild@e4fba868fa4b1b91e1fdab776edc8cfbe6e9fb81 # v4.37.3
 
     # Command-line programs to run using the OS shell.
     # See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@8aad20d150bbac5944a9f9d289da16a4b0d87c1e # v4.36.2
+      uses: github/codeql-action/analyze@e4fba868fa4b1b91e1fdab776edc8cfbe6e9fb81 # v4.37.3

.github/workflows/gradle.yml

@@ -22,9 +22,9 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - name: Set up openJDK version
-        uses: actions/setup-java@ad2b38190b15e4d6bdf0c97fb4fca8412226d287 # v5.3.0
+        uses: actions/setup-java@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 # v5.6.0
         with:
           java-version: ${{ matrix.jdk }}
           distribution: "zulu"
@@ -47,9 +47,9 @@ jobs:
       jdkversion: 25
     steps:
       - name: Checkout repo
-        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - name: Set up OpenJDK version ...
-        uses: actions/setup-java@ad2b38190b15e4d6bdf0c97fb4fca8412226d287 # v5.3.0
+        uses: actions/setup-java@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 # v5.6.0
         with:
           distribution: "zulu"
           java-version: ${{ env.jdkversion }}

.github/workflows/publishRelease.yml

@@ -8,9 +8,9 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - name: Set up Java
-        uses: actions/setup-java@ad2b38190b15e4d6bdf0c97fb4fca8412226d287 # v5.3.0
+        uses: actions/setup-java@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 # v5.6.0
         with:
           java-version: 21
           distribution: 'zulu' # openjdk

build.gradle

@@ -38,12 +38,12 @@ repositories {
 }
 
 ext {
-    jacksonVersion  = '2.22.0'
+    jacksonVersion  = '2.22.1'
 }
 
 dependencies {
     // JUnit setup for testing
-    testImplementation(platform("org.junit:junit-bom:6.1.0"))
+    testImplementation(platform("org.junit:junit-bom:6.1.2"))
     testImplementation('org.junit.jupiter:junit-jupiter')
     testRuntimeOnly('org.junit.platform:junit-platform-launcher')
     // JSON object mapping / (de-)serialization

src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java

@@ -48,6 +48,16 @@ public void addAuthorId(String id) {
         this.addIdProperty("author", id);
     }
 
+    /**
+     * Gets the path of this entity.
+     * <p>
+     * When reading a crate, this will point to the entity's file within the crate.
+     * When creating a new entity or crate, it might point to a file outside the crate,
+     * as set by {@link DataEntityBuilder#setLocation(Path)}.
+     * Such a file will be copied into the crate when writing.
+     *
+     * @return the path to the file this entity represents.
+     */
     @JsonIgnore
     public Path getPath() {
         return path;

src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java

@@ -22,6 +22,7 @@
 import java.nio.file.Path;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import java.util.stream.StreamSupport;
 
 /**
@@ -142,6 +143,7 @@ private RoCrate rebuildCrate(ObjectNode metadataJson, File files, HashSet<String
 
                         // Handle data entities with corresponding file
                         checkFolderHasFile(entityJson.get(PROP_ID).asText(), files).ifPresent(file -> {
+                            System.out.println("Found file for: " + file.toString());
                             usedFiles.add(file.getPath());
                             builder.setLocationWithExceptions(file.toPath())
                                     .setId(file.getName());
@@ -237,15 +239,24 @@ protected String unpackId(JsonNode node) {
     }
 
     protected Optional<File> checkFolderHasFile(String filepathOrId, File folder) {
+        System.out.println("DEBUG: " + Arrays.toString(folder.listFiles()));
         if (IdentifierUtils.isUrl(filepathOrId)) {
             return Optional.empty();
         }
-        return IdentifierUtils.decode(filepathOrId)
-                .map(decoded -> folder.toPath().resolve(decoded).normalize())
+        System.out.println( "DEBUG: " +
+                IdentifierUtils.decode(filepathOrId)
+                    .map(decoded -> folder.toPath().resolve(decoded).normalize())
+                    .filter(resolved -> resolved.startsWith(folder.toPath()))
+                    .map(Path::toFile)
+                    .map(File::exists)
+        );
+        return Stream.of(IdentifierUtils.decode(filepathOrId).orElse(filepathOrId), filepathOrId)
+                .map(filename -> folder.toPath().resolve(filename).normalize().toAbsolutePath())
                 // defence-in-depth: ensure we are still inside the crate folder
                 .filter(resolved -> resolved.startsWith(folder.toPath()))
                 .map(Path::toFile)
-                .filter(File::exists);
+                .filter(File::exists)
+                .findFirst();
     }
 
     /**

src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java

@@ -5,6 +5,7 @@
 import edu.kit.datamanager.ro_crate.Crate;
 import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
 import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
+import edu.kit.datamanager.ro_crate.special.IdentifierUtils;
 import org.apache.commons.io.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -54,7 +55,7 @@
         inputStream.close();
         // save also the preview files to the crate destination
         if (crate.getPreview() != null && this.writePreview) {
             crate.getPreview().saveAllToFolder(file);
         }
         for (var e : crate.getUntrackedFiles()) {
             if (e.isDirectory()) {
@@ -64,16 +65,18 @@
             }
         }
         for (DataEntity dataEntity : crate.getAllDataEntities()) {
-            savetoFile(dataEntity, file);
+            saveToFile(dataEntity, file);
         }
     }
 
-    private void savetoFile(DataEntity entity, File file) throws IOException {
+    private void saveToFile(DataEntity entity, File file) throws IOException {
         if (entity.getPath() != null) {
+            String id = entity.getId();
+            String filename = IdentifierUtils.decode(id).orElse(id);
             if (entity.getPath().toFile().isDirectory()) {
-                FileUtils.copyDirectory(entity.getPath().toFile(), file.toPath().resolve(entity.getId()).toFile());
+                FileUtils.copyDirectory(entity.getPath().toFile(), file.toPath().resolve(filename).toFile());
             } else {
-                FileUtils.copyFile(entity.getPath().toFile(), file.toPath().resolve(entity.getId()).toFile());
+                FileUtils.copyFile(entity.getPath().toFile(), file.toPath().resolve(filename).toFile());
             }
         }
     }

src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java

@@ -15,6 +15,7 @@
 import java.util.UUID;
 
 import edu.kit.datamanager.ro_crate.preview.CratePreview;
+import edu.kit.datamanager.ro_crate.special.IdentifierUtils;
 import edu.kit.datamanager.ro_crate.util.FileSystemUtil;
 import edu.kit.datamanager.ro_crate.util.ZipStreamUtil;
 import net.lingala.zip4j.io.outputstream.ZipOutputStream;
@@ -154,16 +155,18 @@ private void saveToStream(DataEntity entity, ZipOutputStream zipStream, String p
         }
 
         boolean isDirectory = entity.getPath().toFile().isDirectory();
+        String id = entity.getId();
+        String filename = IdentifierUtils.decode(id).orElse(id);
         if (isDirectory) {
             ZipStreamUtil.addFolderToZipStream(
                     zipStream,
                     entity.getPath().toFile(),
-                    prefix + entity.getId());
+                    prefix + filename);
         } else {
             ZipStreamUtil.addFileToZipStream(
                     zipStream,
                     entity.getPath().toFile(),
-                    prefix + entity.getId());
+                    prefix + filename);
         }
     }
 }