Investigation in renaming directories in zip writers

.github/workflows/gradle.yml

@@ -11,7 +11,6 @@ on:
   push:
     branches: [ main, development ]
   pull_request:
-    branches: [ main, development ]
   workflow_dispatch:
 
 env:

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

@@ -65,6 +65,7 @@ public void addAuthorId(String id) {
      * @throws ZipException when something goes wrong with the writing to the
      * zip file.
      */
+    @Deprecated(since = "2.1.0", forRemoval = true)
     public void saveToZip(ZipFile zipFile) throws ZipException {
         if (this.path != null) {
             ZipParameters zipParameters = new ZipParameters();
@@ -82,6 +83,7 @@ public void saveToZip(ZipFile zipFile) throws ZipException {
      * zip file.
      * @throws IOException If opening the file input stream fails.
      */
+    @Deprecated(since = "2.1.0", forRemoval = true)
     public void saveToStream(ZipOutputStream zipStream) throws ZipException, IOException {
         if (this.path != null) {
             ZipUtil.addFileToZipStream(zipStream, this.path.toFile(), this.getId());
@@ -95,6 +97,7 @@ public void saveToStream(ZipOutputStream zipStream) throws ZipException, IOExcep
      * @param file the folder location where the entity should be written.
      * @throws IOException if something goes wrong with the writing.
      */
+    @Deprecated(since = "2.1.0", forRemoval = true)
     public void savetoFile(File file) throws IOException {
         if (this.getPath() != null) {
             if (this.getPath().toFile().isDirectory()) {

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

@@ -25,6 +25,16 @@ public class FolderStrategy implements GenericWriterStrategy<String> {
 
     private static final Logger logger = LoggerFactory.getLogger(FolderStrategy.class);
 
+    protected void saveDataEntity(DataEntity dataEntity, File file) throws IOException {
+        if (dataEntity.getPath() != null) {
+            if (dataEntity.getPath().toFile().isDirectory()) {
+                FileUtils.copyDirectory(dataEntity.getPath().toFile(), file.toPath().resolve(dataEntity.getId()).toFile());
+            } else {
+                FileUtils.copyFile(dataEntity.getPath().toFile(), file.toPath().resolve(dataEntity.getId()).toFile());
+            }
+        }
+    }
+
     @Override
     public void save(Crate crate, String destination) {
         File file = new File(destination);
@@ -54,7 +64,7 @@ public void save(Crate crate, String destination) {
         }
         for (DataEntity dataEntity : crate.getAllDataEntities()) {
             try {
-                dataEntity.savetoFile(file);
+                this.saveDataEntity(dataEntity, file);
             } catch (IOException e) {
                 logger.error("Cannot save " + dataEntity.getId() + " to destination folder!", e);
             }

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

@@ -35,17 +35,25 @@ public void save(Crate crate, String destination) {
         }
     }
 
-    private void saveDataEntities(Crate crate, ZipFile zipFile) {
+    protected void saveDataEntities(Crate crate, ZipFile zipFile) {
         for (DataEntity dataEntity : crate.getAllDataEntities()) {
             try {
-                dataEntity.saveToZip(zipFile);
+                this.saveDataEntity(dataEntity, zipFile);
             } catch (ZipException e) {
                 logger.error("Could not save " + dataEntity.getId() + " to zip file!", e);
             }
         }
     }
 
-    private void saveMetadataJson(Crate crate, ZipFile zipFile) {
+    protected void saveDataEntity(DataEntity dataEntity, ZipFile zipFile) throws ZipException {
+        if (dataEntity.getPath() != null) {
+            ZipParameters zipParameters = new ZipParameters();
+            zipParameters.setFileNameInZip(dataEntity.getId());
+            zipFile.addFile(dataEntity.getPath().toFile(), zipParameters);
+        }
+    }
+
+    protected void saveMetadataJson(Crate crate, ZipFile zipFile) {
         try {
             // write the metadata.json file
             ZipParameters zipParameters = new ZipParameters();

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

@@ -12,6 +12,10 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
+
+import edu.kit.datamanager.ro_crate.util.ZipUtil;
+import net.lingala.zip4j.exception.ZipException;
 import net.lingala.zip4j.io.outputstream.ZipOutputStream;
 import net.lingala.zip4j.model.ZipParameters;
 import org.slf4j.Logger;
@@ -36,17 +40,24 @@ public void save(Crate crate, OutputStream destination) {
         }
     }
 
-    private void saveDataEntities(Crate crate, ZipOutputStream zipStream) {
+    protected void saveDataEntities(Crate crate, ZipOutputStream zipStream) {
         for (DataEntity dataEntity : crate.getAllDataEntities()) {
             try {
-                dataEntity.saveToStream(zipStream);
+                this.saveDataEntity(dataEntity, zipStream);
             } catch (IOException e) {
                 logger.error("Could not save {} to zip stream!", dataEntity.getId(), e);
             }
         }
     }
 
-    private void saveMetadataJson(Crate crate, ZipOutputStream zipStream) {
+    protected void saveDataEntity(DataEntity dataEntity, ZipOutputStream zipStream) throws ZipException, IOException {
+        Path path = dataEntity.getPath();
+        if (path != null) {
+            ZipUtil.addFileToZipStream(zipStream, path.toFile(), dataEntity.getId());
+        }
+    }
+
+    protected void saveMetadataJson(Crate crate, ZipOutputStream zipStream) {
         try {
             // write the metadata.json file
             ZipParameters zipParameters = new ZipParameters();

src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java

@@ -11,6 +11,7 @@
 import org.apache.commons.io.FileUtils;
 import io.json.compare.JSONCompare;
 import io.json.compare.JsonComparator;
+import org.opentest4j.AssertionFailedError;
 
 import java.io.File;
 import java.io.IOException;
@@ -19,6 +20,7 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class HelpFunctions {
 
@@ -89,6 +91,16 @@ public static void compareCrateJsonToFileInResources(Crate crate1, String jsonFi
         compare(node1, node2, true);
     }
 
+    /**
+     * Compare two directories. The method will compare the content of the two and return true if they are equal.
+     * 
+     * @param dir1 the first directory
+     * @param dir2 the second directory
+     * @return true if the two directories are equal, false otherwise.
+     * @throws IOException If something goes wrong with the file system.
+     * 
+     */
+    //@Deprecated(since = "2.1.0", forRemoval = true)
     public static boolean compareTwoDir(File dir1, File dir2) throws IOException {
         // compare the content of the two directories
         Map<String, File> result_map = FileUtils.listFiles(dir1, null, true)
@@ -117,4 +129,53 @@ public static boolean compareTwoDir(File dir1, File dir2) throws IOException {
         }
         return true;
     }
+
+    /**
+     * Asserts that the two directories are equal. Throws an exception otherwise.
+     *
+     * @param originalDirectory the original directory to compare to
+     * @param testingDirectory the testing directory to test
+     * @throws IOException If something goes wrong with the file system.
+     */
+    public static void assertEqualDirectories(File originalDirectory, File testingDirectory) throws IOException, AssertionFailedError {
+        assertTrue(originalDirectory.isDirectory(), "The original directory is not a directory.");
+        assertTrue(testingDirectory.isDirectory(), "The testing directory is not a directory.");
+        // compare the content of the two directories
+        Map<String, File> referenceFiles = FileUtils.listFiles(originalDirectory, null, true)
+                .stream()
+                .collect(Collectors.toMap(java.io.File::getName, Function.identity()));
+
+        Map<String, java.io.File> compareThoseFiles = FileUtils.listFiles(testingDirectory, null, true)
+                .stream()
+                .collect(Collectors.toMap(java.io.File::getName, Function.identity()));;
+
+        for (String filename : compareThoseFiles.keySet()) {
+            // we do that because the ro-crate-metadata.json can be differently formatted,
+            // or the order of the entities may be different
+            // the same holds for the html file
+            if (filename.equals("ro-crate-preview.html") || filename.equals("ro-crate-metadata.json")) {
+                if (!referenceFiles.containsKey(filename)) {
+                    throw new AssertionFailedError("The file %s is not present in the reference directory.".formatted(filename));
+                }
+            } else if (!FileUtils.contentEqualsIgnoreEOL(compareThoseFiles.get(filename), referenceFiles.get(filename), null)) {
+                throw new AssertionFailedError("The content of the file %s is not equal.".formatted(filename));
+            }
+        }
+
+        referenceFiles.keySet().forEach(filename -> {
+                    if (!compareThoseFiles.containsKey(filename)) {
+                        throw new AssertionFailedError("The file %s is not present in the testing directory.".formatted(filename));
+                    }
+                });
+
+        compareThoseFiles.keySet().forEach(filename -> {
+                    if (!referenceFiles.containsKey(filename)) {
+                        throw new AssertionFailedError("The file %s is not present in the reference directory.".formatted(filename));
+                    }
+                });
+
+        if (referenceFiles.size() != compareThoseFiles.size()) {
+            throw new AssertionFailedError("The number of files in the two directories is not equal.");
+        }
+    }
 }

src/test/java/edu/kit/datamanager/ro_crate/writer/CrateWriterTest.java

@@ -123,9 +123,9 @@ void testWriting(@TempDir Path tempDir) throws IOException {
         Path extractionPath = tempDir.resolve("extracted_for_testing");
         this.ensureCrateIsExtractedIn(pathToZip, extractionPath);
         // compare the extracted directory with the correct one
-        assertTrue(HelpFunctions.compareTwoDir(
+        HelpFunctions.assertEqualDirectories(
                 correctCrate.toFile(),
-                extractionPath.toFile()));
+                extractionPath.toFile());
         HelpFunctions.compareCrateJsonToFileInResources(
                 builtCrate,
                 "/json/crate/fileAndDir.json");