Merge branch 'master' into switch-to-gradle-6

.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+1-49_linux-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-67_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+1-49_windows-x64_bin.zip
+           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-67_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+1-49_osx-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-67_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
 
@@ -46,6 +46,14 @@ jobs:
       uses: actions/setup-java@v1
       with:
         java-version: 12.0.2
+    - uses: actions/cache@v1
+      with:
+        path: ~/.gradle/caches
+        key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+        restore-keys: |
+          ${{ runner.OS }}-gradle-${{ env.cache-name }}-
+          ${{ runner.OS }}-gradle-
+          ${{ runner.OS }}-
     - name: Download jpackage
       # We need to download jpackage from https://jdk.java.net/jpackage/
       run: |

CHANGELOG.md

@@ -57,9 +57,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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)
 - We fixed an issue where the merge dialog showed the wrong text colour in "Dark" mode [#5516](https://github.com/JabRef/jabref/issues/5516)
+- We fixed an issue where the author field was not correctly parsed during bibtex key-generation. [#5551](https://github.com/JabRef/jabref/issues/5551)
+- We fixed an issue where notifications where shown during autosave. [#5555](https://github.com/JabRef/jabref/issues/5555)
 
 ### Removed
 
+- We removed some obsolete notifications. [#5555](https://github.com/JabRef/jabref/issues/5555)
 
 
 

README.md

@@ -1,4 +1,4 @@
-# JabRef Bibliography Management [![Hacktoberfest](https://img.shields.io/github/hacktoberfest/2019/JabRef/jabref?suggestion_label=hacktoberfest)](https://www.jabref.org/hacktoberfest/2019.html)
+# JabRef Bibliography Management
 
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)

build.gradle

@@ -26,6 +26,8 @@ plugins {
     id 'org.beryx.jlink' version '2.16.2'
 }
 
+gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.ALWAYS 
+
 apply plugin: 'java'
 apply plugin: 'application'
 apply plugin: 'project-report'
@@ -107,6 +109,8 @@ dependencies {
     compile 'org.apache.pdfbox:fontbox:2.0.17'
     compile 'org.apache.pdfbox:xmpbox:2.0.17'
 
+    compile group: 'org.apache.commons', name: 'commons-csv', version: '1.7'
+
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.22'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
@@ -135,6 +139,11 @@ dependencies {
 
     compile 'org.postgresql:postgresql:42.2.8'
 
+    compile ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
+        // causing module issues
+        exclude module: 'oraclepki'
+    }
+
     compile ('com.google.guava:guava:28.1-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
@@ -569,7 +578,8 @@ jlink {
                     '--vendor', 'JabRef',
                     '--app-version', "${project.version}",
                     '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
-                    '--win-dir-chooser',
+                    // temporarily disabled due to conflict with Jpackage update
+                    //'--win-dir-chooser',
                     '--win-shortcut',
                     '--temp', "$buildDir/installer",
                     '--resource-dir', "${projectDir}/buildres/windows"

buildres/linux/org.jabref.jabref.json

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

buildres/windows/JabRef-post-image.wsf

@@ -11,7 +11,7 @@
         // Copy additional installer resources
         fileSystem.CopyFile(jabRefRoot + "/buildres/windows/JabRefTopBanner.bmp", installerConfig);
 
-        var wxsFilePath = installerConfig + "JabRef.wxs";
+        var wxsFilePath = jabRefRoot + "/buildres/windows/JabRef.wxs";
         wxsFile = fileSystem.OpenTextFile(wxsFilePath, 1);
         var contents = wxsFile.ReadAll();
         wxsFile.Close();

buildres/windows/JabRef.wxs

@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi"
+     xmlns:util="http://schemas.microsoft.com/wix/UtilExtension">
+
+  <?ifdef JpIsSystemWide ?>
+    <?define JpInstallScope="perMachine"?>
+  <?else?>
+    <?define JpInstallScope="perUser"?>
+  <?endif?>
+
+  <Product  Id="$(var.JpProductCode)" Name="$(var.JpAppName)"
+            Language="1033" Version="$(var.JpAppVersion)"
+            Manufacturer="$(var.JpAppVendor)"
+            UpgradeCode="$(var.JpProductUpgradeCode)">
+    <Package  Description="$(var.JpAppDescription)"
+              Manufacturer="$(var.JpAppVendor)"
+              InstallerVersion="200" Compressed="yes"
+              InstallScope="$(var.JpInstallScope)" Platform="x64"/>
+    <Media Id="1" Cabinet="simple.cab" EmbedCab="yes" />
+
+    <?ifdef JpAllowDowngrades ?>
+    <MajorUpgrade AllowDowngrades="yes"/>
+    <?endif?>
+
+    <!-- Standard required root -->
+    <Directory Id="TARGETDIR" Name="SourceDir"/>
+
+    <Feature Id="DefaultFeature" Title="Main Feature" Level="1">
+      <ComponentGroupRef Id="Shortcuts"/>
+      <ComponentGroupRef Id="Files"/>
+      <ComponentGroupRef Id="FileAssociations"/>
+    </Feature>
+
+    <?ifdef JpInstallDirChooser ?>
+    <Binary Id="JpCaDll" SourceFile="wixhelper.dll"/>
+    <CustomAction Id="JpCheckInstallDir" BinaryKey="JpCaDll" DllEntry="CheckInstallDir" />
+    <?endif?>
+
+    <UI>
+      <?ifdef JpInstallDirChooser ?>
+      <Dialog Id="JpInvalidInstallDir" Width="300" Height="85" Title="[ProductName] Setup" NoMinimize="yes">
+        <Control Id="JpInvalidInstallDirYes" Type="PushButton" X="100" Y="55" Width="50" Height="15" Default="no" Cancel="no" Text="Yes">
+          <Publish Event="NewDialog" Value="VerifyReadyDlg">1</Publish>
+        </Control>
+        <Control Id="JpInvalidInstallDirNo" Type="PushButton" X="150" Y="55" Width="50" Height="15" Default="yes" Cancel="yes" Text="No">
+          <Publish Event="NewDialog" Value="InstallDirDlg">1</Publish>
+        </Control>
+        <Control Id="Text" Type="Text" X="25" Y="15" Width="250" Height="30" TabSkip="no">
+          <Text>!(loc.message.install.dir.exist)</Text>
+        </Control>
+      </Dialog>
+
+      <!--
+        Run WixUI_InstallDir dialog in the default install directory.
+      -->
+      <Property Id="WIXUI_INSTALLDIR" Value="APPLICATIONFOLDER"/>
+      <UIRef Id="WixUI_InstallDir" />
+
+      <Publish Dialog="InstallDirDlg" Control="Next" Event="DoAction" Value="JpCheckInstallDir" Order="3">1</Publish>
+      <Publish Dialog="InstallDirDlg" Control="Next" Event="NewDialog" Value="JpInvalidInstallDir" Order="5">INSTALLDIR_VALID="0"</Publish>
+      <Publish Dialog="InstallDirDlg" Control="Next" Event="NewDialog" Value="VerifyReadyDlg" Order="5">INSTALLDIR_VALID="1"</Publish>
+
+      <?ifndef JpLicenseRtf ?>
+      <!--
+        No license file provided.
+        Override the dialog sequence in built-in dialog set "WixUI_InstallDir"
+        to exclude license dialog.
+      -->
+      <Publish Dialog="WelcomeDlg" Control="Next" Event="NewDialog" Value="InstallDirDlg" Order="2">1</Publish>
+      <Publish Dialog="InstallDirDlg" Control="Back" Event="NewDialog" Value="WelcomeDlg" Order="2">1</Publish>
+      <?endif?>
+
+      <?else?>
+
+      <?ifdef JpLicenseRtf ?>
+      <UIRef Id="WixUI_Minimal" />
+      <?endif?>
+
+      <?endif?>
+    </UI>
+
+    <?ifdef JpLicenseRtf ?>
+    <WixVariable Id="WixUILicenseRtf" Value="$(var.JpLicenseRtf)"/>
+    <?endif?>
+
+  <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><Property Id="ARPPRODUCTICON" Value="DesktopIcon.exe" /><WixVariable Id="WixUIBannerBmp" Value="JabRefTopBanner.bmp" /><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><Property Id="ARPPRODUCTICON" Value="DesktopIcon.exe" /><WixVariable Id="WixUIBannerBmp" Value="JabRefTopBanner.bmp" /><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><Property Id="ARPPRODUCTICON" Value="DesktopIcon.exe" /><WixVariable Id="WixUIBannerBmp" Value="JabRefTopBanner.bmp" /></Product>
+</Wix>

buildres/windows/jabref.json

@@ -4,6 +4,6 @@
   "path": "JabRefHost.bat",
   "type": "stdio",
   "allowed_extensions": [
-    "@jabfox"
+    "[email protected]"
   ]
 }

docs/adr/0007-human-readable-changelog.md

@@ -0,0 +1,22 @@
+# Provide a human-readable changelog
+
+## Context and Problem Statement
+
+Changes of a release have to be communicated.
+How and which stile to use?
+
+## Considered Options
+
+* Keep-a-changelog format with freedom in the bullet points
+* Keep-a-changelog format and fixed terms
+
+## Decision Outcome
+
+Chosen option: "Keep-a-changelog format with freedom in the bullet points", because
+
+- [Keep-a-changelog](https://keepachangelog.com/) structures the changelog
+- Each entry can be structured to be understandable
+- Forcing to prefix each line with `We fixed`, `We changed`, ... seems to be read strange.
+  We nevertheless try to follow that style.
+
+Further discussion can be found at [#2277](https://github.com/JabRef/jabref/issues/2277).

docs/adr/README.md

@@ -12,6 +12,7 @@ This log lists the architectural decisions for JabRef.
 - [ADR-0004](0004-use-mariadb-connector.md) - Use MariaDB Connector
 - [ADR-0005](0005-fully-support-utf8-only-for-latex-files.md) - Fully Support UTF-8 Only For LaTeX Files
 - [ADR-0006](0006-only-translated-strings-in-language-file.md) - Only translated strings in language file
+- [ADR-0007](0007-human-readable-changelog.md) - Provide a human-readable changelog
 
 <!-- adrlogstop -->
 

external-libraries.txt

@@ -65,6 +65,11 @@ Project: Application Insights SDK for Java
 URL:     https://github.com/Microsoft/ApplicationInsights-Java
 License: MIT
 
+Id:      com.oracle.ojdbc:ojdbc10
+Project: Oracle's JDBC drivers
+URL:     https://medium.com/oracledevs/oracle-jdbc-drivers-on-maven-central-64fcf724d8b
+License: Proprietary
+
 Id:      com.sibvisions.external.jvxfx:DnDTabPane
 Project: Drag'n'Drop TabPane
 URL:     https://github.com/sibvisions/javafx.DndTabPane
@@ -125,6 +130,11 @@ Project: ANTLR 4
 URL:     http://www.antlr.org/
 License: BSD-3-Clause
 
+Id:      org.apache.commons:commons-csv
+Project: Apache Commons CSV
+URL:     https://commons.apache.org/proper/commons-csv/
+License: Apache-2.0
+
 Id:      org.apache.commons:commons-lang3
 Project: Apache Commons Lang
 URL:     https://commons.apache.org/proper/commons-lang/

src/main/java/module-info.java

@@ -66,4 +66,5 @@
     requires unirest.java;
     requires org.apache.httpcomponents.httpclient;
     requires org.jsoup;
+    requires commons.csv;
 }