From a68cd0c269edf455b19247b38a2c23267e45a6af Mon Sep 17 00:00:00 2001
From: systemoperator <3658393+systemoperator@users.noreply.github.com>
Date: Wed, 29 Jan 2020 13:18:21 +0100
Subject: [PATCH] Fixes making paths of linked files relative (web urls will
 not be touched anymore) (#5879)

* Fixes #5861
Description:
- Cleanup entries: "Make paths of linked files relative (if possible)" broke web URLs and resulted in various other issues subsequently. This PR fixes this issue.
It has been tested for local files and web urls.

* changelog updated

* refactoring: use existing method isOnlineLink() for checking whether a file link is an online link; improving isOnlineLink()
---
 CHANGELOG.md                                     |  1 +
 .../logic/cleanup/RelativePathsCleanup.java      | 16 +++++++++++-----
 .../java/org/jabref/model/entry/LinkedFile.java  |  5 +++--
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aacb7819b24..6ffa4e88747 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the ampersand character wasn't rendering correctly on previews. [#3840](https://github.com/JabRef/jabref/issues/3840)
 - We fixed an issue where an erroneous "The library has been modified by another program" message was shown when saving. [#4877](https://github.com/JabRef/jabref/issues/4877)
 - We fixed an issue where the file extension was missing after downloading a file (we now fall-back to pdf). [#5816](https://github.com/JabRef/jabref/issues/5816)
+- We fixed an issue where cleaning up entries broke web URLs, if "Make paths of linked files relative (if possible)" was enabled, which resulted in various other issues subsequently. [#5861](https://github.com/JabRef/jabref/issues/5861)
 
 ### Removed
 - Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action.
diff --git a/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java b/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java
index 9b18e939782..1bbecb2f41c 100644
--- a/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java
+++ b/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java
@@ -33,10 +33,17 @@ public List<FieldChange> cleanup(BibEntry entry) {
 
         for (LinkedFile fileEntry : fileList) {
             String oldFileName = fileEntry.getLink();
-            String newFileName = FileUtil
-                    .relativize(Paths.get(oldFileName), databaseContext.getFileDirectoriesAsPaths(filePreferences))
-                    .toString();
-
+            String newFileName = null;
+            if (fileEntry.isOnlineLink()) {
+                // keep online link untouched
+                newFileName = oldFileName;
+            }
+            else {
+                // only try to transform local file path to relative one
+                newFileName = FileUtil
+                        .relativize(Paths.get(oldFileName), databaseContext.getFileDirectoriesAsPaths(filePreferences))
+                        .toString();
+            }
             LinkedFile newFileEntry = fileEntry;
             if (!oldFileName.equals(newFileName)) {
                 newFileEntry = new LinkedFile(fileEntry.getDescription(), newFileName, fileEntry.getFileType());
@@ -56,5 +63,4 @@ public List<FieldChange> cleanup(BibEntry entry) {
 
         return Collections.emptyList();
     }
-
 }
diff --git a/src/main/java/org/jabref/model/entry/LinkedFile.java b/src/main/java/org/jabref/model/entry/LinkedFile.java
index 62a71dac417..3c79ffd6812 100644
--- a/src/main/java/org/jabref/model/entry/LinkedFile.java
+++ b/src/main/java/org/jabref/model/entry/LinkedFile.java
@@ -135,10 +135,11 @@ private void readObject(ObjectInputStream in) throws IOException {
     /**
      * Checks if the given String is an online link
      * @param toCheck The String to check
-     * @return True if it starts with http://, https:// or contains www; false otherwise
+     * @return <code>true</code>, if it starts with "http://", "https://" or contains "www."; <code>false</code> otherwise
      */
     private boolean isOnlineLink(String toCheck) {
-        return toCheck.startsWith("http://") || toCheck.startsWith("https://") || toCheck.contains("www.");
+        String normalizedFilePath = toCheck.trim().toLowerCase();
+        return normalizedFilePath.startsWith("http://") || normalizedFilePath.startsWith("https://") || normalizedFilePath.contains("www.");
     }
 
     @Override