Merged JabRef#5628 into JabRef#5614

Author: nikch

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,5 +9,4 @@
 - [ ] Tests created for changes
 - [ ] Manually tested changed features in running JabRef
 - [ ] Screenshots added in PR description (for bigger UI changes)
-- [ ] Ensured that [the git commit message is a good one](https://github.com/joelparkerhenderson/git_commit_message)
-- [ ] Check documentation status (Issue created for outdated help page at [help.jabref.org](https://github.com/JabRef/help.jabref.org/issues)?)
+- [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not: Issue created at <https://github.com/JabRef/user-documentation/issues>.

.github/workflows/deployment.yml

@@ -11,17 +11,17 @@ jobs:
         include:
          - os: ubuntu-latest
            displayName: linux
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-67_linux-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_linux-x64_bin.tar.gz
            jdk14Path: /jdk-14
            archivePortable: tar -czf build/distribution/JabRef-portable_linux.tar.gz -C build/distribution JabRef && rm -R build/distribution/JabRef
          - os: windows-latest
            displayName: windows
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-67_windows-x64_bin.zip
+           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_windows-x64_bin.zip
            jdk14Path: /jdk-14
            archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
          - os: macOS-latest
            displayName: macOS
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-67_osx-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_osx-x64_bin.tar.gz
            jdk14Path: /jdk-14.jdk/Contents/Home
            archivePortable: tar -czf build/distribution/JabRef-portable_macos.tar.gz -C build/distribution JabRef.app && rm -R build/distribution/JabRef.app
 

.travis.yml

@@ -30,6 +30,7 @@ env:
 matrix:
     fast_finish: true
     allow_failures:
+      - env: TEST_SUITE=codecov
       - env: TEST_SUITE=fetcherTest
       - env: TEST_SUITE=databaseTest
       - env: TEST_SUITE=guiTest

CHANGELOG.md

@@ -20,6 +20,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The entry editor is now open by default when JabRef starts up. [#5460](https://github.com/JabRef/jabref/issues/5460)
 - We added a new ADS fetcher to use the new ADS API [#4949](https://github.com/JabRef/jabref/issues/4949)
 - We added support of the [X11 primary selection](https://unix.stackexchange.com/a/139193/18033) [#2389](https://github.com/JabRef/jabref/issues/2389)
+- We added support to switch between biblatex and bibtex library types. [#5550](https://github.com/JabRef/jabref/issues/5550)
+- We changed the save action buttons to be easier to understand. [#5565](https://github.com/JabRef/jabref/issues/5565)
 - We made the columns for groups, files and uri in the main table reorderable and merged the clickable icon columns for uri, url, doi and eprint. [#5544](https://github.com/JabRef/jabref/pull/5544)
 
 ### Fixed
@@ -28,12 +30,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where it was no longer possible to connect to LibreOffice. [#5261](https://github.com/JabRef/jabref/issues/5261)
 - The "All entries group" is no longer shown when no library is open.
 - We fixed an exception which occurred when closing JabRef. [#5348](https://github.com/JabRef/jabref/issues/5348)
-- We fixed an issue where JabRef reports incorrectly about customized entry types. [#5332](https://github.com/JabRef/jabref/issues/5332) 
+- We fixed an issue where JabRef reports incorrectly about customized entry types. [#5332](https://github.com/JabRef/jabref/issues/5332)
 - We fixed a few problems that prevented JabFox to communicate with JabRef. [#4737](https://github.com/JabRef/jabref/issues/4737) [#4303](https://github.com/JabRef/jabref/issues/4303)
-- We fixed an error where the groups containing an entry loose their highlight color when scrolling. [#5022](https://github.com/JabRef/jabref/issues/5022) 
+- We fixed an error where the groups containing an entry loose their highlight color when scrolling. [#5022](https://github.com/JabRef/jabref/issues/5022)
 - We fixed an error where scrollbars were not shown. [#5374](https://github.com/JabRef/jabref/issues/5374)
 - We fixed an error where an exception was thrown when merging entries. [#5169](https://github.com/JabRef/jabref/issues/5169)
-- We fixed an error where certain metadata items were not serialized alphabetically. 
+- We fixed an error where certain metadata items were not serialized alphabetically.
 - After assigning an entry to a group, the item count is now properly colored to reflect the new membership of the entry. [#3112](https://github.com/JabRef/jabref/issues/3112)
 - The group panel is now properly updated when switching between libraries (or when closing/opening one). [#3142](https://github.com/JabRef/jabref/issues/3142)
 - We fixed an error where the number of matched entries shown in the group pane was not updated correctly. [#4441](https://github.com/JabRef/jabref/issues/4441)
@@ -44,7 +46,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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 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)
@@ -53,7 +55,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We re-introduced the feature to switch between different preview styles. [#5221](https://github.com/JabRef/jabref/issues/5221)
 - We fixed various issues (including [#5263](https://github.com/JabRef/jabref/issues/5263)) related to copying entries to the clipboard
 - 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) 
+- 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)
 - We fixed an error where the preview theme did not adapt to the "Dark" mode [#5463](https://github.com/JabRef/jabref/issues/5463)
@@ -143,7 +145,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Change default icon for groups to a circle because a colored version of the old icon was hard to distinguish from its black counterpart.
 - In the main table, the context menu appears now when you press the "context menu" button on the keyboard. [feature request in the forum](http://discourse.jabref.org/t/how-to-enable-keyboard-context-key-windows)
 - We added icons to the group side panel to quickly switch between `union` and `intersection` group view mode https://github.com/JabRef/jabref/issues/3269.
-- We use `https` for [fetching from most online bibliographic database](https://help.jabref.org/en/#-using-online-bibliographic-database).
+- We use `https` for [fetching from most online bibliographic database](https://docs.jabref.org/import-using-online-bibliographic-database).
 - We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀<kbd>alt</kbd> + <kbd>up/down</kbd>.
 - Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file.
 - Window state is saved on close and restored on start.
@@ -162,7 +164,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We optimized the code responsible for connecting to an external database, which should lead to huge improvements in performance.
 - For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
-- We added the ability to change the column widths directly in the main 
+- We added the ability to change the column widths directly in the main
 . [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added a description of how recommendations were chosen and better error handling to Related Articles tab
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)

README.md

@@ -64,9 +64,9 @@ The [latest stable release is available at FossHub](https://www.fosshub.com/JabR
 
 JabRef runs on any system equipped with the Java Virtual Machine (Java 11 or higher), which can be downloaded at no cost from [AdoptOpenDJK](https://adoptopenjdk.net/).
 From JabRef 4.0 onwards, [JavaFX] support has to be installed.
- - Windows: JabRef offers an installer, which also adds a shortcut to JabRef to your start menu. Please also see our [Windows FAQ](https://help.jabref.org/en/FAQwindows)
- - Linux: Please see our [Installation Guide](http://help.jabref.org/en/Installation).
- - Mac OS X: Please see our [Mac OS X FAQ](https://help.jabref.org/en/FAQosx).
+ - Windows: JabRef offers an installer, which also adds a shortcut to JabRef to your start menu. Please also see our [Windows FAQ](https://docs.jabref.org/faq/faqwindows)
+ - Linux: Please see our [Installation Guide](https://docs.jabref.org/general/installation).
+ - Mac OS X: Please see our [Mac OS X FAQ](https://docs.jabref.org/faq/faqosx).
 
 In addition, JabRef can be downloaded as an executable `.jar` file. 
 Try to double click the `jar` file or execute the following command:
@@ -78,7 +78,7 @@ 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).
+If you need support in using JabRef, please read [the documentation](https://docs.jabref.org/) first and have a look at our [community forum](https://discourse.jabref.org/c/help).
 You can use our [GitHub issue tracker](https://github.com/JabRef/jabref/issues) to file bug reports.
 
 An explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).

build.gradle

@@ -23,7 +23,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.27.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
-    id 'org.beryx.jlink' version '2.16.3'
+    id 'org.beryx.jlink' version '2.16.4'
 }
 
 gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.ALWAYS
@@ -449,7 +449,8 @@ test {
 
     testLogging {
         // set options for log level LIFECYCLE
-        events = ["FAILED", "STANDARD_OUT", "STANDARD_ERROR"]
+        // for debugging tests: add "STANDARD_OUT", "STANDARD_ERROR"
+        events = ["FAILED"]
         exceptionFormat "full"
     }
 }

buildres/linux/jabref.spec

@@ -0,0 +1,71 @@
+Summary: APPLICATION_SUMMARY
+Name: APPLICATION_PACKAGE
+Version: APPLICATION_VERSION
+Release: APPLICATION_RELEASE
+License: APPLICATION_LICENSE_TYPE
+Vendor: APPLICATION_VENDOR
+Prefix: %{dirname:APPLICATION_DIRECTORY}
+Provides: APPLICATION_PACKAGE
+%if "xAPPLICATION_GROUP" != x
+Group: APPLICATION_GROUP
+%endif
+
+Autoprov: 0
+Autoreq: 0
+%if "xPACKAGE_DEFAULT_DEPENDENCIES" != x || "xPACKAGE_CUSTOM_DEPENDENCIES" != x
+Requires: PACKAGE_DEFAULT_DEPENDENCIES PACKAGE_CUSTOM_DEPENDENCIES
+%endif
+
+#avoid ARCH subfolder
+%define _rpmfilename %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm
+
+#comment line below to enable effective jar compression
+#it could easily get your package size from 40 to 15Mb but
+#build time will substantially increase and it may require unpack200/system java to install
+%define __jar_repack %{nil}
+
+%description
+APPLICATION_DESCRIPTION
+
+%prep
+
+%build
+
+%install
+rm -rf %{buildroot}
+install -d -m 755 %{buildroot}APPLICATION_DIRECTORY
+cp -r %{_sourcedir}APPLICATION_DIRECTORY/* %{buildroot}APPLICATION_DIRECTORY
+%if "xAPPLICATION_LICENSE_FILE" != x
+  %define license_install_file %{_defaultlicensedir}/%{name}-%{version}/%{basename:APPLICATION_LICENSE_FILE}
+  install -d -m 755 %{buildroot}%{dirname:%{license_install_file}}
+  install -m 644 APPLICATION_LICENSE_FILE %{buildroot}%{license_install_file}
+%endif
+
+%files
+%if "xAPPLICATION_LICENSE_FILE" != x
+  %license %{license_install_file}
+  %{dirname:%{license_install_file}}
+%endif
+# If installation directory for the application is /a/b/c, we want only root
+# component of the path (/a) in the spec file to make sure all subdirectories
+# are owned by the package.
+%(echo APPLICATION_DIRECTORY | sed -e "s|\(^/[^/]\{1,\}\).*$|\1|")
+
+%post
+install -D -m0755 /opt/jabref/lib/native-messaging-host/firefox/org.jabref.jabref.json /usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
+install -D -m0755 /opt/jabref/lib/native-messaging-host/chromium/org.jabref.jabref.json /etc/chromium/native-messaging-hosts/org.jabref.jabref.json
+install -D -m0755 /opt/jabref/lib/native-messaging-host/chromium/org.jabref.jabref.json /etc/opt/chrome/native-messaging-hosts/org.jabref.jabref.json
+DESKTOP_COMMANDS_INSTALL
+
+%preun
+for NATIVE_MESSAGING_JSON in "/usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json"\
+                             "/etc/chromium/native-messaging-hosts/org.jabref.jabref.json"\
+                             "/etc/opt/chrome/native-messaging-hosts/org.jabref.jabref.json"; do
+    if [ -e $NATIVE_MESSAGING_JSON ] && grep --quiet '"path": "/opt' $NATIVE_MESSAGING_JSON; then
+        rm $NATIVE_MESSAGING_JSON
+    fi
+done
+UTILITY_SCRIPTS
+DESKTOP_COMMANDS_UNINSTALL
+
+%clean

buildres/linux/native-messaging-host/chromium/org.jabref.jabref.json

@@ -0,0 +1,9 @@
+{
+  "name": "org.jabref.jabref",
+  "description": "JabRef",
+  "path": "/opt/jabref/lib/jabrefHost.py",
+  "type": "stdio",
+  "allowed_origins": [
+    "chrome-extension://bifehkofibaamoeaopjglfkddgkijdlh/"
+  ]
+}

buildres/linux/org.jabref.jabref.json buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json

@@ -4,6 +4,7 @@
   "path": "/opt/jabref/lib/jabrefHost.py",
   "type": "stdio",
   "allowed_extensions": [
-    "browserextension@jabref.org"
+    "browserextension@jabref.org",
+    "@jabfox"
   ]
 }

buildres/linux/postinst

@@ -19,8 +19,9 @@ set -e
 
 case "$1" in
     configure)
-        INSTALL_PATH="/usr/lib/mozilla/native-messaging-hosts"
-        install -D -m0755 /opt/jabref/lib/org.jabref.jabref.json $INSTALL_PATH/org.jabref.jabref.json
+        install -D -m0755 /opt/jabref/lib/native-messaging-host/firefox/org.jabref.jabref.json /usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
+        install -D -m0755 /opt/jabref/lib/native-messaging-host/chromium/org.jabref.jabref.json /etc/chromium/native-messaging-hosts/org.jabref.jabref.json
+        install -D -m0755 /opt/jabref/lib/native-messaging-host/chromium/org.jabref.jabref.json /etc/opt/chrome/native-messaging-hosts/org.jabref.jabref.json
         DESKTOP_COMMANDS_INSTALL
     ;;
 

buildres/linux/postrm

@@ -16,12 +16,16 @@ set -e
 #          <overwriter-version>
 # for details, see http://www.debian.org/doc/debian-policy/ or
 # the debian-policy package
+
 case "$1" in
     purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
-    NATIVE_MESSAGING_JSON="/usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json"
-    if [ -e $NATIVE_MESSAGING_JSON ] && grep --quiet '"path": "/opt' $NATIVE_MESSAGING_JSON; then
-        rm $NATIVE_MESSAGING_JSON
-    fi
+		for NATIVE_MESSAGING_JSON in "/usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json"\
+                                     "/etc/chromium/native-messaging-hosts/org.jabref.jabref.json"\
+                                     "/etc/opt/chrome/native-messaging-hosts/org.jabref.jabref.json"; do
+		    if [ -e $NATIVE_MESSAGING_JSON ] && grep --quiet '"path": "/opt' $NATIVE_MESSAGING_JSON; then
+		        echo $NATIVE_MESSAGING_JSON
+		    fi
+		done
     ;;
 
     *)
@@ -30,4 +34,4 @@ case "$1" in
     ;;
 esac
 
-exit 0
+exit 0

buildres/windows/JabRef-post-image.wsf

@@ -16,8 +16,8 @@
         var contents = wxsFile.ReadAll();
         wxsFile.Close();
 
-        // Add registry values for JabFox
-        contents = contents.replace("</Product>", "<DirectoryRef Id=\"TARGETDIR\"><Component Id=\"RegistryJabFoxEntries\" Guid=\"b6bc55ad-905c-4258-89b1-8b37abbe559c\" Win64=\"yes\"><RegistryKey Root=\"HKMU\" Key=\"SOFTWARE\\Mozilla\\NativeMessagingHosts\\org.jabref.jabref\" Action=\"createAndRemoveOnUninstall\" ForceCreateOnInstall=\"yes\"><RegistryValue Type=\"string\" Value=\"[APPLICATIONFOLDER]jabref.json\"/></RegistryKey></Component></DirectoryRef><Feature Id=\"JabFox\" Level=\"1\"><ComponentRef Id=\"RegistryJabFoxEntries\" /></Feature></Product>");
+        // Add registry values for JabRef Browser Extension
+        contents = contents.replace("</Product>", "<DirectoryRef Id=\"TARGETDIR\"><Component Id=\"RegistryJabRefBrowserEntries\" Guid=\"b6bc55ad-905c-4258-89b1-8b37abbe559c\" Win64=\"yes\"><RegistryKey Root=\"HKMU\" Key=\"SOFTWARE\\Mozilla\\NativeMessagingHosts\\org.jabref.jabref\" Action=\"createAndRemoveOnUninstall\" ForceCreateOnInstall=\"yes\"><RegistryValue Type=\"string\" Value=\"[APPLICATIONFOLDER]jabref.json\"/></RegistryKey><RegistryKey Root=\"HKMU\" Key=\"Software\\Google\\Chrome\\NativeMessagingHosts\\org.jabref.jabref\" Action=\"createAndRemoveOnUninstall\" ForceCreateOnInstall=\"yes\"><RegistryValue Type=\"string\" Value=\"[APPLICATIONFOLDER]jabref-chrome.json\"/></RegistryKey></Component></DirectoryRef><Feature Id=\"JabFox\" Level=\"1\"><ComponentRef Id=\"RegistryJabFoxEntries\" /></Feature></Product>");
 
         // Specify correct icon in Add/Remove Programs
         contents = contents.replace("</Product>", "<Property Id=\"ARPPRODUCTICON\" Value=\"DesktopIcon.exe\" /></Product>");

buildres/windows/jabref.json

@@ -4,6 +4,7 @@
   "path": "JabRefHost.bat",
   "type": "stdio",
   "allowed_extensions": [
-    "browserextension@jabref.org"
+    "browserextension@jabref.org",
+    "@jabfox"
   ]
 }