fix: detect files matching the decoded or encoded id of an entity

Author: Pfeil

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();
     }
 
     /**