Merge pull request #164 from craquet/fix/crate-reader

Fix issues with crate reader

Author: sabrineChe

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

@@ -118,7 +118,7 @@ public T addContent(Path path, String id) {
         public T addContent(URI uri) {
             if (isUrl(uri.toString())) {
                 this.setId(uri.toString());
-            }
+            } else throw new IllegalArgumentException("This Data Entity remote ID does not resolve to a valid URL.");
             return self();
         }
 

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

@@ -12,6 +12,8 @@
 import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity;
 import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions;
 import static edu.kit.datamanager.ro_crate.special.UriUtil.decode;
+import static edu.kit.datamanager.ro_crate.special.UriUtil.isUrl;
+
 import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation;
 import edu.kit.datamanager.ro_crate.validation.Validator;
 
@@ -92,17 +94,18 @@ public RoCrate readCrate(String location) {
         // if the id is in the root hasPart list, we know this entity is a data entity
         RootDataEntity root = crate.getRootDataEntity();
         if (root != null && root.hasInHasPart(node.get(PROP_ID).asText())) {
+          // data entity
+          DataEntity.DataEntityBuilder dataEntity = new DataEntity.DataEntityBuilder()
+                  .setAll(node.deepCopy());
+
+          // Handle data entities with corresponding file
           File loc = checkFolderHasFile(node.get(PROP_ID).asText(), files);
           if (loc != null) {
             usedFiles.add(loc.getPath());
-            
-          // data entity
-          DataEntity dataEntity = new DataEntity.DataEntityBuilder()
-              .setAll(node.deepCopy())
-              .addContent(loc.toPath(), loc.getName())
-              .build();
-          crate.addDataEntity(dataEntity, false);
+            dataEntity.addContent(loc.toPath(), loc.getName());
           }
+
+          crate.addDataEntity(dataEntity.build(), false);
         } else {
           // contextual entity
           crate.addContextualEntity(
@@ -124,6 +127,7 @@ public RoCrate readCrate(String location) {
   }
 
   protected File checkFolderHasFile(String id, File file) {
+    if (isUrl(id)) return null;
     Path path = file.toPath().resolve(decode(id).get());
     if (path.toFile().exists()) {
       return path.toFile();

src/main/java/edu/kit/datamanager/ro_crate/special/UriUtil.java

@@ -56,7 +56,11 @@ public static boolean isValidUri(String uri) {
      * @return true if it is a url, false otherwise.
      */
     public static boolean isUrl(String uri) {
-        return asUrl(uri).isPresent();
+        try {
+            return asUrl(uri).isPresent();
+        } catch (Exception e) {
+            return false;
+        }
     }
 
     /**