Merge branch 'master' into jacoco-toolversion

CHANGELOG.md

@@ -23,13 +23,16 @@ For more details refer to the [field mapping help page](http://help.jabref.org/e
 - We added Facebook and Twitter icons in the toolbar to link to our [Facebook](https://www.facebook.com/JabRef/) and [Twitter](https://twitter.com/jabref_org) pages.
 - We no longer print empty lines when exporting an entry in RIS format [#3634](https://github.com/JabRef/jabref/issues/3634)
 - We improved file saving so that hard links are now preserved when a save is performed [#2633](https://github.com/JabRef/jabref/issues/2633)
+- We changed the default dialog option when removing a [file link](http://help.jabref.org/en/FileLinks#adding-external-links-to-an-entry) from an entry.
+The new default removes the linked file from the entry instead of deleting the file from disk. [#3679](https://github.com/JabRef/jabref/issues/3679)
 
 ### Fixed
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
 - Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
 - We fixed and extended the RIS import functionality to cover more fields. [#3634](https://github.com/JabRef/jabref/issues/3634) [#2607](https://github.com/JabRef/jabref/issues/2607)
 - Chaining modifiers in BibTeX key pattern now works as described in the documentation. [#3648](https://github.com/JabRef/jabref/issues/3648)
 - We fixed an issue where not all bibtex/biblatex fields would be exported as latex-free to MS-Office XML [koppor#284](https://github.com/koppor/jabref/issues/284)
+- We fixed an issue where linked files would be deleted from bibliography entries despite choosing the "Cancel" option in the dialog menu.
 
 ### Removed
 - We removed the [Look and Feels from JGoodies](http://www.jgoodies.com/freeware/libraries/looks/), because the open source version is not compatible with Java 9.

CONTRIBUTING.md

@@ -66,7 +66,7 @@ You can see the result in `build\resources\main\help\en\About.html` or when clic
 
 
 ### When making an architectural decision
-In case you add a library or do mayor code rewrites, we ask you to document your decision.
+In case you add a library or do major code rewrites, we ask you to document your decision.
 Recommended reading: <https://adr.github.io/>.
 
 We simply ask to create a new markdown file in `docs/adr` following the template presented at <https://adr.github.io/madr/>.

DEVELOPERS

@@ -1,9 +1,7 @@
 Oliver Kopp (since 2011)
-Simon Harrer (since 2014)
 Jörg Lenhard (since 2015)
 Stefan Kolb (since 2015)
 Matthias Geiger (since 2015)
-Oscar Gustafsson (since 2015)
 Tobias Diez (since 2015)
 Christoph Schwentker (since 2016)
 Linus Dietz (since 2017)

README.md

@@ -12,7 +12,7 @@ Stay on top of your literature: JabRef helps you to collect and organize sources
 ## Features
 
 JabRef is a cross-platform application that works on Windows, Linux and Mac OS X. It is available free of charge and is actively developed.
-JabRef supports you every step of your research work.
+JabRef supports you in every step of your research work.
 
 #### Collect
 
@@ -21,7 +21,7 @@ JabRef supports you every step of your research work.
 - Easily retrieve and link full-text articles
 - Fetch complete bibliographic information based on ISBN, DOI, PubMed-ID and arXiv-ID
 - Extract metadata from PDFs
-- [Firefox Add-on](https://addons.mozilla.org/en-US/firefox/addon/jabfox/) that lets you import new references directly from the browser with one click
+- [JabFox Firefox Add-on](https://addons.mozilla.org/en-US/firefox/addon/jabfox/) lets you import new references directly from the browser with one click
 
 #### Organize
 
@@ -32,21 +32,21 @@ JabRef supports you every step of your research work.
 - Customize and add new metadata fields or reference types
 - Find and merge duplicates
 - Attach related documents: 20 different kinds of documents supported out of the box, completely customizable and extendable
-- Automatically rename and moves associated documents according to customizable rules
+- Automatically rename and move associated documents according to customizable rules
 - Keep track of what you read: ranking, priority, printed, quality-assured 
 
 #### Cite
 
 - Native [BibTeX] and [Biblatex] support
 - Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt.
 - Format references in one of the many thousand built-in citation styles or create your own style
-- Support for Word and LibreOffice/OpenOffice to insert and format citations
+- Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
 
 #### Share
 
 - Many built-in export options or create your own export format
-- Library is saved as a simple text file and thus easy to share with others via Dropbox and is version-control friendly
-- Work in a team: sync the contents of your library with a SQL database
+- Library is saved as a simple text file and thus it is easy to share with others via Dropbox and is version-control friendly
+- Work in a team: sync the contents of your library via a SQL database
 
 ## Installation
 
@@ -70,9 +70,9 @@ Try to double click the `jar` file or execute the following command:
 We are thankful for any bug reports or other feedback.
 If you have ideas for new features you want to be included in JabRef, [tell us in our forum](http://discourse.jabref.org/c/features)!
 If you need support in using JabRef, please read [the documentation](https://help.jabref.org/) first and have a look at our [community forum](http://discourse.jabref.org/c/help).
-You can use our [GitHub issue tracker](https://github.com/JabRef/jabref/issues) to send in bug reports.
+You can use our [GitHub issue tracker](https://github.com/JabRef/jabref/issues) to file bug reports.
 
-Explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).
+An explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).
 
 ## Contributing
 

build.gradle

@@ -121,7 +121,7 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:23.6-jre'
+    compile 'com.google.guava:guava:24.0-jre'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'

src/main/java/org/jabref/gui/BasePanel.java

@@ -1510,7 +1510,7 @@ public void showAndEdit(BibEntry entry) {
             entryEditor.setEntry(entry);
             newEntryShowing(entry);
         }
-        entryEditor.requestFocus();
+        DefaultTaskExecutor.runInJavaFXThread(() -> entryEditor.requestFocus());
         adjustSplitter();
     }
 

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -44,6 +44,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static javafx.scene.control.ButtonBar.ButtonData;
+
 public class LinkedFileViewModel extends AbstractViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(LinkedFileViewModel.class);
@@ -54,15 +56,21 @@ public class LinkedFileViewModel extends AbstractViewModel {
     private final BooleanProperty downloadOngoing = new SimpleBooleanProperty(false);
     private final BooleanProperty isAutomaticallyFound = new SimpleBooleanProperty(false);
     private final BooleanProperty canWriteXMPMetadata = new SimpleBooleanProperty(false);
-    private final DialogService dialogService = new FXDialogService();
+    private final DialogService dialogService;
     private final BibEntry entry;
     private final TaskExecutor taskExecutor;
 
     public LinkedFileViewModel(LinkedFile linkedFile, BibEntry entry, BibDatabaseContext databaseContext, TaskExecutor taskExecutor) {
+        this(linkedFile, entry, databaseContext, taskExecutor, new FXDialogService());
+    }
+
+    protected LinkedFileViewModel(LinkedFile linkedFile, BibEntry entry, BibDatabaseContext databaseContext,
+                                  TaskExecutor taskExecutor, DialogService dialogService) {
         this.linkedFile = linkedFile;
         this.databaseContext = databaseContext;
         this.entry = entry;
         this.taskExecutor = taskExecutor;
+        this.dialogService = dialogService;
 
         downloadOngoing.bind(downloadProgress.greaterThanOrEqualTo(0).and(downloadProgress.lessThan(100)));
         canWriteXMPMetadata.setValue(!linkedFile.isOnlineLink() && linkedFile.getFileType().equalsIgnoreCase("pdf"));
@@ -274,14 +282,14 @@ public void moveToDefaultDirectory() {
 
     public boolean delete() {
         Optional<Path> file = linkedFile.findIn(databaseContext, Globals.prefs.getFileDirectoryPreferences());
-        ButtonType removeFromEntry = new ButtonType(Localization.lang("Remove from entry"));
+        ButtonType removeFromEntry = new ButtonType(Localization.lang("Remove from entry"), ButtonData.YES);
 
         if (file.isPresent()) {
             ButtonType deleteFromEntry = new ButtonType(Localization.lang("Delete from disk"));
             Optional<ButtonType> buttonType = dialogService.showCustomButtonDialogAndWait(AlertType.INFORMATION,
                     Localization.lang("Delete '%0'", file.get().toString()),
                     Localization.lang("Delete the selected file permanently from disk, or just remove the file from the entry? Pressing Delete will delete the file permanently from disk."),
-                    deleteFromEntry, removeFromEntry, ButtonType.CANCEL);
+                    removeFromEntry, deleteFromEntry, ButtonType.CANCEL);
 
             if (buttonType.isPresent()) {
                 if (buttonType.get().equals(removeFromEntry)) {
@@ -304,7 +312,7 @@ public boolean delete() {
         } else {
             LOGGER.warn("Could not find file " + linkedFile.getLink());
         }
-        return true;
+        return false;
     }
 
     public void edit() {