Merge pull request #1 from JabRef/master

dc

AUTHORS

@@ -56,7 +56,6 @@ Eduard Braun
 Eduardo Greco
 Egon Willighagen
 Ellen Reitmayr
-Erdem Derebasoglu
 Erdem Derebaşoğlu
 Erik Putrycz
 Ervin Kolenovic

CHANGELOG.md

@@ -16,6 +16,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added a short DOI field formatter which shortens DOI to more human-readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
 - We improved the display of group memberships by adding multiple colored bars if the entry belongs to more than one group. [#4574](https://github.com/JabRef/jabref/issues/4574)
 - We added an option to show the preview as an extra tab in the entry editor (instead of in a split view). [#5244](https://github.com/JabRef/jabref/issues/5244)
+- A custom Open/LibreOffice jstyle file now requires a layout line for the entry type `default` [#5452](https://github.com/JabRef/jabref/issues/5452)
 
 ### Fixed
 
@@ -32,9 +33,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where empty keywords lead to a strange display of automatic keyword groups. [#5333](https://github.com/JabRef/jabref/issues/5333)
 - We fixed an error where the default color of a new group was white instead of dark gray. [#4868](https://github.com/JabRef/jabref/issues/4868)
 - We fixed an issue where the first field in the entry editor got the focus while performing a different action (like searching). [#5084](https://github.com/JabRef/jabref/issues/5084)
+- We fixed an issue where multiple entries were highlighted in the web search result after scrolling. [#5035](https://github.com/JabRef/jabref/issues/5035)
+- We fixed an issue where the hover indication in the web search pane was not working. [#5277](https://github.com/JabRef/jabref/issues/5277)
 - We fixed an error mentioning "javafx.controls/com.sun.javafx.scene.control" that was thrown when interacting with the toolbar.
 - We fixed an error where a cleared search was restored after switching libraries. [#4846](https://github.com/JabRef/jabref/issues/4846) 
 - We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed an issues where the search highlight in the entry preview did not worked. [#5069](https://github.com/JabRef/jabref/issues/5069)
 - The context menu for fields in the entry editor is back. [#5254](https://github.com/JabRef/jabref/issues/5254)
 - We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - We fixed a problem where the "editor" information has been duplicated during saving a .bib-Database. [#5359](https://github.com/JabRef/jabref/issues/5359)
@@ -43,6 +47,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed some display errors in the preferences dialog and replaced some of the controls [#5033](https://github.com/JabRef/jabref/pull/5033) [#5047](https://github.com/JabRef/jabref/pull/5047) [#5062](https://github.com/JabRef/jabref/pull/5062) [#5141](https://github.com/JabRef/jabref/pull/5141) [#5185](https://github.com/JabRef/jabref/pull/5185) [#5265](https://github.com/JabRef/jabref/pull/5265) [#5315](https://github.com/JabRef/jabref/pull/5315) [#5360](https://github.com/JabRef/jabref/pull/5360)
 - We fixed an exception which occurred when trying to import entries without an open library. [#5447](https://github.com/JabRef/jabref/issues/5447) 
 - After successful import of one or multiple bib entries the main table scrolls to the first imported entry [#5383](https://github.com/JabRef/jabref/issues/5383)
+- We fixed an exception which occurred when an invalid jstyle was loaded. [#5452](https://github.com/JabRef/jabref/issues/5452)
 
 
 ### Removed

CONTRIBUTING.md

@@ -2,10 +2,10 @@
 
 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 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.
@@ -14,22 +14,20 @@ We welcome contributions to JabRef and encourage you to follow the GitHub workfl
 4. 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/).
 5. In case your pull request is not yet complete or not yet ready for review, consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) instead.
 
-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).
-
+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
 
 The main goal of the formal requirements is to provide credit to you and to be able to understand the patch.
 
-
 ### Add your change to CHANGELOG.md
 
 You should edit the [CHANGELOG.md](CHANGELOG.md) located in the root directory of the JabRef source.
 Add a line with your changes in the appropriate section.
 
 If you did internal refactorings or improvements not visible to the user (e.g., UI, .bib file), then you don't need to put an entry there.
 
-
 #### Key format
 
 Example: `<kbd>Ctrl</kbd> + <kbd>Enter</kbd>`
@@ -41,7 +39,6 @@ In case you add keys to the changelog, please follow these rules:
 - Combined keys separated by `+`
 - Spaces before and after separator `+`
 
-
 ### Author credits
 
 You will be given credit in the [`AUTHORS`](AUTHORS) file in the root of the repository and the 'About' pages inside the main application.
@@ -58,21 +55,18 @@ The contribution information is tracked via the version control system.
 
 Your contribution is considered being made under [MIT license](https://tldrlegal.com/license/mit-license).
 
-
 ### Write a good commit message
 
 See [good commit message] or [commit guidelines section of Pro Git].
 The first line of your commit message is automatically taken as the title for the pull-request.
 All other lines make up the body of the pull request. Add the words `fixes #xxx` to your PR to auto-close the corresponding issue.
 
-
 ### Test your code
 
 We know that writing test cases takes a lot of time.
 Nevertheless, we rely on our test cases to ensure that a bug fix or a feature implementation doesn't break anything.
 In case you do not have time to add a test case, we nevertheless ask you to at least run `gradlew check` to ensure that your change doesn't break anything else.
 
-
 ### When adding a library
 
 Please try to use a version available at jCenter and add it to `build.gradle`.
@@ -82,7 +76,6 @@ Also add a txt file stating the license in `libraries/`.
 It is used at `gradlew processResources` to generate the About.html files.
 You can see the result in `build\resources\main\help\en\About.html` or when clicking Help -> About.
 
-
 ### When making an architectural decision
 
 In case you add a library or do major code rewrites, we ask you to document your decision.
@@ -92,7 +85,7 @@ We simply ask to create a new markdown file in `docs/adr` following the template
 
 In case you want to directly add a comment to a class, simply use following template (based on [sustainable architectural decisions](https://www.infoq.com/articles/sustainable-architectural-design-decisions)):
 
-```
+```text
 In the context of <use case/user story u>,
 facing <concern c>
 we decided for <option o>
@@ -102,15 +95,14 @@ accepting <downside / undesired consequences>,
 because <additional rationale>.
 ```
 
-
 ### When adding a new Localization.lang entry
 
 Add new `Localization.lang("KEY")` to a Java file.
 The tests will fail. In the test output a snippet is generated, which must be added to the English translation file.
 
 Example:
 
-```
+```text
 java.lang.AssertionError: DETECTED LANGUAGE KEYS WHICH ARE NOT IN THE ENGLISH LANGUAGE FILE
 PASTE THESE INTO THE ENGLISH LANGUAGE FILE
 [
@@ -127,7 +119,6 @@ You can also directly run the specific test in your IDE.
 The test "LocalizationConsistencyTest" is placed under `src/test/java/net.sf.jabref.logic.l10n/LocalizationConsistencyTest.java`
 Find more information in the [JabRef Wiki](https://github.com/JabRef/jabref/wiki/Code-Howtos#using-localization-correctly).
 
-
 ### Create a pull request
 
 Create a pull request on GitHub.
@@ -136,6 +127,5 @@ For text inspirations, consider [How to write the perfect pull request](https://
 If you want to indicate that a pull request is not yet complete **before** creating the pull request, you may consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
 Alternatively, once the PR has been created, you can add the prefix `[WIP]` (which stands for "Work in Progress") to indicate that the pull request is not yet complete, but you want to discuss something or inform about the current state of affairs.
 
-
 [commit guidelines section of Pro Git]: http://git-scm.com/book/en/Distributed-Git-Contributing-to-a-Project#Commit-Guidelines
 [good commit message]: https://github.com/joelparkerhenderson/git_commit_message

README.md

@@ -34,7 +34,7 @@ JabRef supports you in every step of your research work.
 
 #### Organize
 
-- Group your research into hierarchical collections and organize research items based on keywords/tags, search terms or your own manual assignments
+- Group your research into hierarchical collections and organize research items based on keywords/tags, search terms or your manual assignments
 - Advanced search and filter features
 - Complete and fix bibliographic data by comparing with curated online catalogues such as Google Scholar, Springer or MathSciNet
 - Customizable citation key generator
@@ -48,12 +48,12 @@ JabRef supports you in every step of your research work.
 
 - 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
+- Format references in one of the many thousand built-in citation styles or create your style
 - Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
 
 #### Share
 
-- Many built-in export options or create your own export format
+- Many built-in export options or create your export format
 - 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
 
@@ -91,7 +91,7 @@ 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 the ways you can contribute, below:
+Want to be part of a free and open-source project that tens of thousands of scientists 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.

build.gradle

@@ -592,7 +592,6 @@ jlink {
                     '--linux-menu-group', 'Office;',
                     '--linux-rpm-license-type', 'MIT',
                     // '--license-file', "${projectDir}/LICENSE.md",
-                    '--file-associations', "${projectDir}/buildres/linux/desktop.properties",
                     '--description', 'JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.',
                     '--linux-shortcut'
             ]

buildres/linux/copyright

@@ -1,5 +1,5 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 
 Files: *
-Copyright: APPLICATION_COPYRIGHT
-License: APPLICATION_LICENSE_TEXT
+Copyright: Copyright (C) 2003-2019 JabRef Authors
+License: MIT

buildres/linux/jabref-JabRef.desktop

@@ -6,6 +6,7 @@ Exec=APPLICATION_LAUNCHER
 Icon=APPLICATION_ICON
 Terminal=false
 Type=Application
+MimeType=text/x-bibtex;
 Categories=DEPLOY_BUNDLE_CATEGORY
 Keywords=bibtex;biblatex;latex;bibliography
 StartupWMClass=org-jabref-JabRefMain

buildres/linux/prerm → buildres/linux/postrm

@@ -18,9 +18,10 @@ set -e
 # the debian-policy package
 case "$1" in
     purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
-    INSTALL_PATH="/usr/lib/mozilla/native-messaging-hosts/"
-    if grep --quiet '"path": "/opt' /usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json; then
-        rm -D -m0755 /opt/jabref/lib/org.jabref.jabref.json $INSTALL_PATH
+    INSTALL_PATH="/usr/lib/mozilla/native-messaging-hosts"
+    if grep --quiet '"path": "/opt' $INSTALL_PATH/org.jabref.jabref.json; then
+        rm $INSTALL_PATH/org.jabref.jabref.json
+    fi
     ;;
 
     *)

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -9,6 +9,7 @@
 import java.util.List;
 import java.util.Locale;
 import java.util.Optional;
+import java.util.Set;
 import java.util.prefs.BackingStoreException;
 
 import org.jabref.Globals;
@@ -533,7 +534,7 @@ private Optional<ParserResult> fetch(String fetchCommand) {
         String engine = split[0];
         String query = split[1];
 
-        List<SearchBasedFetcher> fetchers = WebFetchers.getSearchBasedFetchers(Globals.prefs.getImportFormatPreferences());
+        Set<SearchBasedFetcher> fetchers = WebFetchers.getSearchBasedFetchers(Globals.prefs.getImportFormatPreferences());
         Optional<SearchBasedFetcher> selectedFetcher = fetchers.stream()
                                                                .filter(fetcher -> fetcher.getName().equalsIgnoreCase(engine))
                                                                .findFirst();

src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java

@@ -27,7 +27,6 @@
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.BaseDialog;
-import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.NoSelectionModel;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.gui.util.TextFlowLimited;
@@ -110,7 +109,6 @@ private void initialize() {
                     HBox.setHgrow(entryNode, Priority.ALWAYS);
                     HBox container = new HBox(entryNode, separator, addToggle);
                     container.getStyleClass().add("entry-container");
-                    BindingsHelper.includePseudoClassWhen(container, entrySelected, addToggle.selectedProperty());
 
                     BackgroundTask.wrap(() -> viewModel.hasDuplicate(entry)).onSuccess(duplicateFound -> {
                         if (duplicateFound) {

src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java

@@ -1,7 +1,7 @@
 package org.jabref.gui.importer.fetcher;
 
-import java.util.Comparator;
 import java.util.List;
+import java.util.SortedSet;
 
 import javafx.beans.property.ListProperty;
 import javafx.beans.property.ObjectProperty;
@@ -18,7 +18,6 @@
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.SearchBasedFetcher;
-import org.jabref.logic.importer.WebFetcher;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
@@ -40,8 +39,7 @@ public WebSearchPaneViewModel(ImportFormatPreferences importPreferences, JabRefF
         this.frame = frame;
         this.dialogService = dialogService;
 
-        List<SearchBasedFetcher> allFetchers = WebFetchers.getSearchBasedFetchers(importPreferences);
-        allFetchers.sort(Comparator.comparing(WebFetcher::getName));
+        SortedSet<SearchBasedFetcher> allFetchers = WebFetchers.getSearchBasedFetchers(importPreferences);
         fetchers.setAll(allFetchers);
 
         // Choose last-selected fetcher as default
@@ -97,7 +95,7 @@ public void search() {
         BackgroundTask<List<BibEntry>> task = BackgroundTask.wrap(() -> activeFetcher.performSearch(getQuery().trim()))
                                                             .withInitialMessage(Localization.lang("Processing %0", getQuery()));
 
-        task.onFailure(ex -> dialogService.showErrorDialogAndWait(ex));
+        task.onFailure(dialogService::showErrorDialogAndWait);
 
         ImportEntriesDialog dialog = new ImportEntriesDialog(frame.getCurrentBasePanel().getBibDatabaseContext(), task);
         dialog.setTitle(activeFetcher.getName());

src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java

@@ -24,6 +24,7 @@
 import org.jabref.logic.openoffice.StyleLoader;
 import org.jabref.logic.util.TestEntry;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.views.ViewLoader;
@@ -118,8 +119,8 @@ private void initialize() {
 
         EasyBind.subscribe(viewModel.selectedItemProperty(), style -> {
             tvStyles.getSelectionModel().select(style);
-            previewArticle.setLayout(new TextBasedPreviewLayout(style.getStyle().getDefaultBibLayout()));
-            previewBook.setLayout(new TextBasedPreviewLayout(style.getStyle().getDefaultBibLayout()));
+            previewArticle.setLayout(new TextBasedPreviewLayout(style.getStyle().getReferenceFormat(StandardEntryType.Article)));
+            previewBook.setLayout(new TextBasedPreviewLayout(style.getStyle().getReferenceFormat(StandardEntryType.Book)));
         });
     }