From 7d5a99717b094e68a499089581c991dac3556260 Mon Sep 17 00:00:00 2001
From: Christopher Raquet <uitxy@student.kit.edu>
Date: Tue, 9 Jul 2024 14:53:57 +0200
Subject: [PATCH 1/3] Prevent crate reader from removing data entities without
 corresponding file

---
 .../ro_crate/reader/RoCrateReader.java          | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java
index cf5cc4e..ae7c6aa 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java
+++ b/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(

From 6998c9868157361d1dee9ce4a54a5bcbcdcc88e0 Mon Sep 17 00:00:00 2001
From: Christopher Raquet <uitxy@student.kit.edu>
Date: Tue, 9 Jul 2024 14:54:24 +0200
Subject: [PATCH 2/3] Fix path exceptions for windows in crate reader

---
 .../java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java
index ae7c6aa..0355962 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java
+++ b/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java
@@ -127,6 +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();

From da44684c832d3fc20a1d2dd0f20f08900c9f6825 Mon Sep 17 00:00:00 2001
From: Christopher Raquet <uitxy@student.kit.edu>
Date: Wed, 10 Jul 2024 13:20:37 +0200
Subject: [PATCH 3/3] Fix exception when checking URL validity

---
 .../kit/datamanager/ro_crate/entities/data/DataEntity.java  | 2 +-
 .../java/edu/kit/datamanager/ro_crate/special/UriUtil.java  | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java
index 388d3db..cc4b9ac 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java
+++ b/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();
         }
 
diff --git a/src/main/java/edu/kit/datamanager/ro_crate/special/UriUtil.java b/src/main/java/edu/kit/datamanager/ro_crate/special/UriUtil.java
index 135db6b..63eaa13 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/special/UriUtil.java
+++ b/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;
+        }
     }
 
     /**