Merge remote-tracking branch 'upstream/master' into convertSearchWorker

* upstream/master:
  Fix downloading pdf produces html as extension (#4965)
  Too big error message #4827 (#4966)
  Reformat Understanding the basics section of CONTRIBUTING.md (#4978)
  Revised README.md (#4974)
  Switch Jsoup's StringUtil for JabRef's StringUtil (#4970)

CHANGELOG.md

@@ -114,8 +114,7 @@ We refer to [GitHub issues](/~https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](/~https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](/~https://github.com/JabRef/jabref/issues/4816)
 - We fixed an issue where an NullPointer exception was thrown when a referenced entry in an Open/Libre Office document was no longer present in the library. Now an error message with the reference marker of the missing entry is shown. [#4932](/~https://github.com/JabRef/jabref/issues/4932)
-
-
+- We fixed an issue where a database exception related to a missing timezone was too big. [#4827](/~https://github.com/JabRef/jabref/issues/4827)
 
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.

CONTRIBUTING.md

@@ -1,14 +1,15 @@
 After reading through this guide, check out some good first issues to contribute to by clicking here: [Good First Issues](/~https://github.com/JabRef/jabref/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22)
 
 ## Understanding the basics
-We welcome contributions to JabRef and encourage to create a fork, clone, **create a new branch** (such as `fix-for-issue-121`), **work on the new branch — not master**, and create a pull request.
-Be sure to create a **separate branch** for each improvement you implement.
-Take a look at GitHub's excellent overview on the [GitHub flow](https://guides.github.com/introduction/flow/index.html) and their [pull request help documentation](https://help.github.com/articles/about-pull-requests/) for a detailed explanation and the explanation of [Feature Branch Workflow](https://de.atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
-
-We also have [code howtos](/~https://github.com/JabRef/jabref/wiki/Code-Howtos) and [guidelines for setting up a local workspace](/~https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
-
-In case you have any question, do not hesitate to write one of our [JabRef developers](/~https://github.com/orgs/JabRef/teams/developers) an email.
-We should also be online at [gitter](https://gitter.im/JabRef/jabref).
+We welcome contributions to JabRef and encourage you to follow the GitHub workflow specified below. If you are not familiar with this type of workflow, take a look at GitHub's excellent overview on the [GitHub flow](https://guides.github.com/introduction/flow/index.html) and the explanation of [Feature Branch Workflow](https://atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
+1. Get the JabRef code on your local machine. Detailed instructions about this step can be found in our [guidelines for setting up a local workspace](/~https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
+    1. Fork the JabRef into your GitHub account.
+    2. Clone your forked repository on your local machine.
+3. **Create a new branch** (such as `fix-for-issue-121`). Be sure to create a **separate branch** for each improvement you implement.
+4. Do your work on the **new branch - not the master branch.** Refer to our [code howtos](/~https://github.com/JabRef/jabref/wiki/Code-Howtos) if you have questions about your implementation.
+5. Create a pull request. For an overview of pull requests, take a look at GitHub's [pull request help documentation](https://help.github.com/articles/about-pull-requests/).
+
+In case you have any questions, do not hesitate to write one of our [JabRef developers](/~https://github.com/orgs/JabRef/teams/developers) an email. We should also be online at [gitter](https://gitter.im/JabRef/jabref).
 
 
 ## Formal requirements for a pull request

README.md

@@ -82,11 +82,11 @@ An explanation of donation possibilities and usage of donations is available at
 
 > Not a programmer? [Learn how to help.](http://contribute.jabref.org)
 
-Want to be part of a free and open-source project that tens of thousands scientist use every day?
-Check out our [issue tracker](/~https://github.com/JabRef/jabref/issues) to find something to work on.
-You are also welcome to contribute new features.
-To get your code included into JabRef, just fork JabRef and create a pull request.
-For details have a look at our [guidelines for contributing](CONTRIBUTING.md).
+Want to be part of a free and open-source project that tens of thousands scientist use every day? Check out the ways you can contribute, below:
+- For details on how to contribute, have a look at our [guidelines for contributing](CONTRIBUTING.md).
+- You are welcome to contribute new features. To get your code included into JabRef, just [fork](https://help.github.com/en/articles/fork-a-repo) the JabRef repository, make your changes, and create a [pull request](https://help.github.com/en/articles/about-pull-requests).
+- To work on existing JabRef issues, check out our [issue tracker](/~https://github.com/JabRef/jabref/issues). New to open source contributing? Look for issues with the ["good first issue"](/~https://github.com/JabRef/jabref/labels/good%20first%20issue) label to get started.
+
 We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.
 We will discuss improvements with you and agree to merge them once the [developers](/~https://github.com/JabRef/jabref/blob/master/DEVELOPERS) approve.

build.gradle

@@ -136,9 +136,9 @@ dependencies {
     compile 'com.jfoenix:jfoenix:8.0.8'
 
     // Cannot be updated to 9.*.* until Jabref works with Java 9
-    compile 'org.controlsfx:controlsfx:8.40.15-SNAPSHOT'
+    compile 'org.controlsfx:controlsfx:8.40.16-SNAPSHOT'
 
-    compile 'org.jsoup:jsoup:1.11.3'
+    compile 'org.jsoup:jsoup:1.12.1'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility

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

@@ -165,6 +165,7 @@ public void showErrorDialogAndWait(String title, String content) {
     @Override
     public void showErrorDialogAndWait(String message, Throwable exception) {
         ExceptionDialog exceptionDialog = new ExceptionDialog(exception);
+        exceptionDialog.getDialogPane().setMaxWidth(mainWindow.getWidth() / 2);
         exceptionDialog.setHeaderText(message);
         exceptionDialog.showAndWait();
     }

src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java

@@ -13,6 +13,7 @@
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.fieldeditors.LinkedFileViewModel;
 import org.jabref.gui.fieldeditors.LinkedFilesEditorViewModel;
 import org.jabref.gui.util.BackgroundTask;
@@ -136,15 +137,15 @@ private void addLinkedFileFromURL(URL url, BibEntry entry, Path targetDirectory)
                     basePanel.getBibDatabaseContext(),
                     Globals.TASK_EXECUTOR,
                     dialogService,
-                    JabRefPreferences.getInstance());
+                    JabRefPreferences.getInstance(), ExternalFileTypes.getInstance());
 
             try {
                 URLDownload urlDownload = new URLDownload(newLinkedFile.getLink());
                 BackgroundTask<Path> downloadTask = onlineFile.prepareDownloadTask(targetDirectory, urlDownload);
                 downloadTask.onSuccess(destination -> {
                     LinkedFile downloadedFile = LinkedFilesEditorViewModel.fromFile(
                             destination,
-                            basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(JabRefPreferences.getInstance().getFilePreferences()));
+                            basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(JabRefPreferences.getInstance().getFilePreferences()), ExternalFileTypes.getInstance());
                     entry.addFile(downloadedFile);
                     dialogService.notify(Localization.lang("Finished downloading full text document for entry %0.",
                             entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));

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

@@ -66,13 +66,15 @@ public class LinkedFileViewModel extends AbstractViewModel {
     private final FilePreferences filePreferences;
     private final XmpPreferences xmpPreferences;
     private final LinkedFileHandler linkedFileHandler;
+    private final ExternalFileTypes externalFileTypes;
 
     public LinkedFileViewModel(LinkedFile linkedFile,
                                BibEntry entry,
                                BibDatabaseContext databaseContext,
                                TaskExecutor taskExecutor,
                                DialogService dialogService,
-                               JabRefPreferences preferences) {
+                               JabRefPreferences preferences,
+                               ExternalFileTypes externalFileTypes) {
 
         this.linkedFile = linkedFile;
         this.filePreferences = preferences.getFilePreferences();
@@ -81,6 +83,7 @@ public LinkedFileViewModel(LinkedFile linkedFile,
         this.entry = entry;
         this.dialogService = dialogService;
         this.taskExecutor = taskExecutor;
+        this.externalFileTypes = externalFileTypes;
 
         xmpPreferences = preferences.getXMPPreferences();
         downloadOngoing.bind(downloadProgress.greaterThanOrEqualTo(0).and(downloadProgress.lessThan(1)));
@@ -402,7 +405,7 @@ public void download() {
             URLDownload urlDownload = new URLDownload(linkedFile.getLink());
             BackgroundTask<Path> downloadTask = prepareDownloadTask(targetDirectory.get(), urlDownload);
             downloadTask.onSuccess(destination -> {
-                LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences));
+                LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences), externalFileTypes);
                 linkedFile.setLink(newLinkedFile.getLink());
                 linkedFile.setFileType(newLinkedFile.getFileType());
             });
@@ -420,7 +423,7 @@ public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownloa
                     String suggestedTypeName = suggestedType.map(ExternalFileType::getName).orElse("");
                     linkedFile.setFileType(suggestedTypeName);
 
-                    String suggestedName = linkedFileHandler.getSuggestedFileName();
+                    String suggestedName = linkedFileHandler.getSuggestedFileName(suggestedTypeName);
                     return targetDirectory.resolve(suggestedName);
                 })
                 .then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))
@@ -443,15 +446,15 @@ private Optional<ExternalFileType> inferFileTypeFromMimeType(URLDownload urlDown
 
         if (mimeType != null) {
             LOGGER.debug("MIME Type suggested: " + mimeType);
-            return ExternalFileTypes.getInstance().getExternalFileTypeByMimeType(mimeType);
+            return externalFileTypes.getExternalFileTypeByMimeType(mimeType);
         } else {
             return Optional.empty();
         }
     }
 
     private Optional<ExternalFileType> inferFileTypeFromURL(String url) {
         return URLUtil.getSuffix(url)
-                      .flatMap(extension -> ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension));
+                      .flatMap(extension -> externalFileTypes.getExternalFileTypeByExt(extension));
     }
 
     public LinkedFile getFile() {

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

@@ -48,21 +48,22 @@ public class LinkedFilesEditorViewModel extends AbstractEditorViewModel {
     private final BibDatabaseContext databaseContext;
     private final TaskExecutor taskExecutor;
     private final JabRefPreferences preferences;
+    private final ExternalFileTypes externalFileTypes = ExternalFileTypes.getInstance();
 
     public LinkedFilesEditorViewModel(String fieldName, AutoCompleteSuggestionProvider<?> suggestionProvider,
                                       DialogService dialogService,
                                       BibDatabaseContext databaseContext,
                                       TaskExecutor taskExecutor,
                                       FieldCheckers fieldCheckers,
                                       JabRefPreferences preferences) {
+
         super(fieldName, suggestionProvider, fieldCheckers);
 
         this.dialogService = dialogService;
         this.databaseContext = databaseContext;
         this.taskExecutor = taskExecutor;
         this.preferences = preferences;
 
-
         BindingsHelper.bindContentBidirectional(
                 files,
                 text,
@@ -86,9 +87,9 @@ private static String getStringRepresentation(List<LinkedFileViewModel> files) {
      *
      * TODO: Move this method to {@link LinkedFile} as soon as {@link CustomExternalFileType} lives in model.
      */
-    public static LinkedFile fromFile(Path file, List<Path> fileDirectories) {
+    public static LinkedFile fromFile(Path file, List<Path> fileDirectories, ExternalFileTypes externalFileTypesFile) {
         String fileExtension = FileHelper.getFileExtension(file).orElse("");
-        ExternalFileType suggestedFileType = ExternalFileTypes.getInstance()
+        ExternalFileType suggestedFileType = externalFileTypesFile
                 .getExternalFileTypeByExt(fileExtension)
                 .orElse(new UnknownExternalFileType(fileExtension));
         Path relativePath = FileUtil.relativize(file, fileDirectories);
@@ -98,8 +99,8 @@ public static LinkedFile fromFile(Path file, List<Path> fileDirectories) {
     public LinkedFileViewModel fromFile(Path file) {
         List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
 
-        LinkedFile linkedFile = fromFile(file, fileDirectories);
-        return new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences);
+        LinkedFile linkedFile = fromFile(file, fileDirectories, externalFileTypes);
+        return new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes);
 
     }
 
@@ -113,7 +114,7 @@ public BooleanProperty fulltextLookupInProgressProperty() {
 
     private List<LinkedFileViewModel> parseToFileViewModel(String stringValue) {
         return FileFieldParser.parse(stringValue).stream()
-                              .map(linkedFile -> new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences))
+                              .map(linkedFile -> new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes))
                               .collect(Collectors.toList());
     }
 
@@ -135,8 +136,8 @@ public void addNewFile() {
 
         List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
-                LinkedFile newLinkedFile = fromFile(newFile, fileDirectories);
-            files.add(new LinkedFileViewModel(newLinkedFile, entry, databaseContext, taskExecutor, dialogService, preferences));
+                LinkedFile newLinkedFile = fromFile(newFile, fileDirectories, externalFileTypes);
+            files.add(new LinkedFileViewModel(newLinkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes));
                 });
     }
 
@@ -162,7 +163,7 @@ private List<LinkedFileViewModel> findAssociatedNotLinkedFiles(BibEntry entry) {
         try {
             List<LinkedFile> linkedFiles = util.findAssociatedNotLinkedFiles(entry);
             for (LinkedFile linkedFile : linkedFiles) {
-                LinkedFileViewModel newLinkedFile = new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences);
+                LinkedFileViewModel newLinkedFile = new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes);
                 newLinkedFile.markAsAutomaticallyFound();
                 result.add(newLinkedFile);
             }
@@ -205,7 +206,7 @@ public void addFromURL() {
     }
 
     private void addFromURL(URL url) {
-        LinkedFileViewModel onlineFile = new LinkedFileViewModel(new LinkedFile(url, ""), entry, databaseContext, taskExecutor, dialogService, preferences);
+        LinkedFileViewModel onlineFile = new LinkedFileViewModel(new LinkedFile(url, ""), entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes);
         files.add(onlineFile);
         onlineFile.download();
     }

src/main/java/org/jabref/gui/filelist/AttachFileAction.java

@@ -6,6 +6,7 @@
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.fieldeditors.LinkedFilesEditorViewModel;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.FileDialogConfiguration;
@@ -38,7 +39,7 @@ public void execute() {
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
 
-            LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile, panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()));
+            LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile, panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()), ExternalFileTypes.getInstance());
 
             LinkedFileEditDialogView dialog = new LinkedFileEditDialogView(linkedFile);
 

src/main/java/org/jabref/gui/filelist/LinkedFilesEditDialogViewModel.java

@@ -76,9 +76,9 @@ public void openBrowseDialog() {
         String fileName = Paths.get(fileText).getFileName().toString();
 
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .withInitialDirectory(workingDir)
-                .withInitialFileName(fileName)
-                .build();
+                                                                                               .withInitialDirectory(workingDir)
+                                                                                               .withInitialFileName(fileName)
+                                                                                               .build();
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(path -> {
             // Store the directory for next time:
@@ -92,8 +92,11 @@ public void openBrowseDialog() {
     public void setValues(LinkedFile linkedFile) {
         description.set(linkedFile.getDescription());
 
-        Path linkPath = Paths.get(linkedFile.getLink());
-        link.set(relativize(linkPath));
+        if (linkedFile.isOnlineLink()) {
+            link.setValue(linkedFile.getLink()); //Might be an URL
+        } else {
+            link.setValue(relativize(Paths.get(linkedFile.getLink())));
+        }
 
         selectedExternalFileType.setValue(null);