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

* upstream/master: (47 commits) Make attached files relative to the file directory (#4212) execute set visible in swing thread to avoid blocking Fix isbn chimbori test (#4234) Rewrite web search pane in JavaFX (#4203) Update dependencies (#4231) Update to latest release of richtextfx (#4213) Fix fetcher tests (#4216) single line text fields (#4138) Make it easier to rename and move files (#4200) Fix that swing dialogs are hidden behind main window (#4205) Fixed: #4166 add move & rename file (#4217) update gradle plugins and gradlen to 4.9 Update dependencies Remove unnecessary look and feel migration (#4204) Revert threading fix since this sometimes lead to freezes... Update year Fix a few more threading exceptions Refactor Convert CiteSeerX fetcher to new infrastructure (#4185) Make global font size customizable (#4178) ... # Conflicts: # src/main/java/org/jabref/gui/BasePanel.java # src/main/java/org/jabref/gui/JabRefFrame.java # src/main/java/org/jabref/gui/mergeentries/MergeEntries.java # src/main/resources/l10n/JabRef_en.properties
JabRef · Jul 26, 2018 · 1d4db3d · 1d4db3d
2 parents 07272ac + 077fdac
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
@@ -24,6 +25,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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.
+- Files without a defined external file type are now directly opened with the default aplication of the operating system
+- We streamlined the process to rename and move files by removing the confirmation dialogs.
 
 
 
@@ -41,10 +44,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where in rare cases entries where overlayed in the main table. https://github.com/JabRef/jabref/issues/3281
 - We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
+- We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
 - We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
+- We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
 - We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
 - We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410
 - We fixed an issue where the default icon of a group was not colored correctly.
@@ -55,7 +60,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
 - We fixed an issue where the preview pane in entry preview in preferences wasn't showing the citation style selected [#3849](https://github.com/JabRef/jabref/issues/3849)
 - We fixed an issue where the default entry preview style still contained the field `review`. The field `review` in the style is now replaced with comment to be consistent with the entry editor [#4098](https://github.com/JabRef/jabref/issues/4098)
-
+- We fixed an issue where filles added via the "Attach file" contextmenu of an entry were not made relative. [#4201](https://github.com/JabRef/jabref/issues/4201)
 
 
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 ## 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 [help documentation] 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.
+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).
 
@@ -118,5 +118,4 @@ You can add the prefix `[WIP]` to indicate that the pull request is not yet comp
 
 
 [commit guidelines section of Pro Git]: http://git-scm.com/book/en/Distributed-Git-Contributing-to-a-Project#Commit-Guidelines
-[good commit message]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
-[help documentation]: https://help.github.com/articles/about-pull-requests/
+[good commit message]: https://github.com/joelparkerhenderson/git_commit_message
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright © 2003-2016 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS)
+Copyright © 2003-2018 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/build.gradle b/build.gradle
@@ -15,14 +15,14 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '1.11'
-    id 'com.install4j.gradle' version '7.0.4'
-    id 'com.github.johnrengelman.shadow' version '2.0.2'
+    id 'com.gradle.build-scan' version '1.15.1'
+    id 'com.install4j.gradle' version '7.0.6'
+    id 'com.github.johnrengelman.shadow' version '2.0.4'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.6.0-1'
-    id 'me.champeau.gradle.jmh' version '0.4.3'
-    id 'net.ltgt.errorprone' version '0.0.13'
-    id 'com.github.ben-manes.versions' version '0.17.0'
+    id 'me.champeau.gradle.jmh' version '0.4.7'
+    id 'net.ltgt.errorprone' version '0.0.15'
+    id 'com.github.ben-manes.versions' version '0.20.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -44,8 +44,8 @@ apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.4-dev"
-project.ext.threeDotVersion = "4.3.0.1"
+version = "5.0-dev"
+project.ext.threeDotVersion = "5.0.0.0"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j7' : 'install4j7')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
@@ -87,12 +87,12 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.9'
-    compile 'org.apache.pdfbox:fontbox:2.0.9'
-    compile 'org.apache.pdfbox:xmpbox:2.0.9'
+    compile 'org.apache.pdfbox:pdfbox:2.0.11'
+    compile 'org.apache.pdfbox:fontbox:2.0.11'
+    compile 'org.apache.pdfbox:xmpbox:2.0.11'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.59'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.60'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -101,7 +101,7 @@ dependencies {
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"
 
-    compile 'com.github.bkromhout:java-diff-utils:2.1.1'
+    compile 'io.github.java-diff-utils:java-diff-utils:2.2.0'
     compile 'info.debatty:java-string-similarity:1.1.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
@@ -113,7 +113,7 @@ dependencies {
     // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
     compile 'mysql:mysql-connector-java:5.1.46'
 
-    compile 'org.postgresql:postgresql:42.2.2'
+    compile 'org.postgresql:postgresql:42.2.4'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
@@ -125,7 +125,7 @@ dependencies {
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.0'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.1'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
 
@@ -157,20 +157,20 @@ dependencies {
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.2.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.2.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.2.0'
-    testCompile 'org.junit-pioneer:junit-pioneer:0.1-SNAPSHOT'
+    testCompile 'org.junit-pioneer:junit-pioneer:0.1.2'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
-    testCompile 'org.mockito:mockito-core:2.18.3'
-    testCompile 'com.github.tomakehurst:wiremock:2.17.0'
+    testCompile 'org.mockito:mockito-core:2.20.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.18.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.0'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
-    testCompile 'com.tngtech.archunit:archunit-junit:0.8.0'
+    testCompile 'com.tngtech.archunit:archunit-junit:0.8.3'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.10.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.11'
 }
 
 jacoco {
@@ -181,34 +181,38 @@ dependencyUpdates {
     outputFormatter = "json"
 }
 
+//We have to use this as long as junit-pioneer has no official release
+dependencyUpdates.revision = 'integration'
+
 // We have some dependencies which cannot be updated due to various reasons.
 dependencyUpdates.resolutionStrategy = {
-    componentSelection {
-        withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
+    componentSelection { rules ->
+        rules.all { ComponentSelection selection ->
+            if ( selection.candidate.module!="javax.inject"  && selection.candidate.version ==~ /[0-9].*SNAPSHOT/ ) {
+                selection.reject("Ignore SNAPSHOT releases")
+            }
+        }
+        rules.withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /9.*/) { // Reject version 9 or higher
-                selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
+                 selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
+            }
+        }
+		rules.withModule("com.github.tomtung:latex2unicode_2.12") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /0.2.2/) { // Reject version higher than 2.0.2
+                 selection.reject("Cannot be updated to 0.2.4 until JabRef is prepared for it")
             }
         }
-        withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
+        rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /2.*/) {
                 selection.reject("Cannot be upgraded to version 2")
             }
         }
-        withModule("mysql:mysql-connector-java") { ComponentSelection selection ->
+        rules.withModule("mysql:mysql-connector-java") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /[6-9].*/) {
                 selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
             }
         }
-        withModule("org.jacoco:org.jacoco.agent") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /0.8.*/) {
-                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
-            }
-        }
-        withModule("org.jacoco:org.jacoco.ant") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /0.8.*/) {
-                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
-            }
-        }
+
     }
 }
 

diff --git a/docs/adr/0003-use-gradle-as-build-tool.md b/docs/adr/0003-use-gradle-as-build-tool.md
@@ -0,0 +1,60 @@
+# Use Gradle as build tool
+
+## Context and Problem Statement
+
+Which build tool should be used?
+
+## Considered Options
+
+* [Maven](https://maven.apache.org/)
+* [Gradle](https://gradle.org/)
+* [Ant](https://ant.apache.org/)
+
+## Decision Outcome
+
+Chosen option: "Gradle", because it is lean and fits our development style.
+
+## Pros and Cons of the Options
+
+### Maven
+
+* Good, because [there is a plugin for almost everything](https://www.slant.co/versus/2107/11592/~apache-maven_vs_gradle)
+* Good, because [it has good integration with third party tools](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Good, because [it has robust performance](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Good, because [it has a high popularity](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Good, [if one favors declarative over imperative](https://www.slant.co/versus/2107/11592/~apache-maven_vs_gradle)
+* Bad, because [getting a dependency list is not straight forward](https://stackoverflow.com/q/1677473/873282)
+* Bad, because [it based on a fixed and linear model of phases](https://dzone.com/articles/gradle-vs-maven)
+* Bad, because [it is hard to customize](https://www.slant.co/versus/2107/11592/~apache-maven_vs_gradle)
+* Bad, because [it needs plugins for everything](https://www.slant.co/versus/2107/11592/~apache-maven_vs_gradle)
+* Bad, because [it is verbose leading to huge build files](https://technologyconversations.com/2014/06/18/build-tools/)
+
+### Gradle
+
+* Good, because [its build scripts are short](https://technologyconversations.com/2014/06/18/build-tools/)
+* Good, because [it follows the convention over configuration approach](https://www.safaribooksonline.com/library/view/building-and-testing/9781449306816/ch04.html)
+* Good, because [it offers a graph-based task dependencies](https://dzone.com/articles/gradle-vs-maven)
+* Good, because [it is easy to customize](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Good, because [it offers custom dependency scopes](https://gradle.org/maven-vs-gradle/)
+* Good, because [it has good community support](https://linuxhint.com/ant-vs-maven-vs-gradle/)
+* Good, because [its performance can be 100 times more than maven's performance](https://gradle.org/gradle-vs-maven-performance/).
+* Bad, because [not that many plugins are available/maintained yet](https://blog.philipphauer.de/moving-back-from-gradle-to-maven/)
+* Bad, because [it lacks a wide variety of application server integrations](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Bad, because [it has a medium popularity](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Bad, because [it allows custom build scripts which need to be debugged](https://www.softwareyoga.com/10-reasons-why-we-chose-maven-over-gradle/)
+
+### Ant
+
+* Good, because [it offers a lot of control over the build process](https://technologyconversations.com/2014/06/18/build-tools/)
+* Good, because [it has an agile dependency manager](https://blog.alejandrocelaya.com/2014/02/22/dependency-management-in-java-projects-with-ant-and-ivy/)
+* Good, because [it has a low learning curve](https://technologyconversations.com/2014/06/18/build-tools/)
+* Bad, because [build scripts can quickly become huge](https://technologyconversations.com/2014/06/18/build-tools/)
+* Bad, because [everything has to be written from scratch](http://www.baeldung.com/ant-maven-gradle)
+* Bad, because [no conventions are enforced which can make it hard to understand someone else's build script](http://www.baeldung.com/ant-maven-gradle)
+* Bad, because [it has nearly no community support](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Bad, because [it has a low popularity](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
+* Bad, because [it offers too much freedom](https://www.slant.co/versus/2106/2107/~apache-ant_vs_apache-maven)
+
+## Links
+
+* GADR: <https://github.com/adr/gadr-java/blob/master/gadr-java--build-tool.md>
diff --git a/docs/adr/index.md b/docs/adr/index.md
@@ -7,6 +7,7 @@ This log lists the architectural decisions for JabRef.
 - [ADR-0000](0000-use-markdown-architectural-decision-records.md) - Use Markdown Architectural Decision Records
 - [ADR-0001](0001-use-crowdin-for-translations.md) - Use Crowdin for translations
 - [ADR-0002](0002-use-slf4j-for-logging.md) - Use slf4j together with log4j2 for logging
+- [ADR-0003](0003-use-gradle-as-build-tool.md) - Use Gradle as build tool
 
 <!-- adrlogstop -->
 

diff --git a/external-libraries.txt b/external-libraries.txt
@@ -40,11 +40,6 @@ Project: AppleJavaExtensions
 URL:     https://developer.apple.com/legacy/library/samplecode/AppleJavaExtensions/Introduction/Intro.html
 License: Apple License
 
-Id:      com.github.bkromhout:java-diff-utils
-Project: java-diff-utils
-URL:     https://github.com/bkromhout/java-diff-utils
-License: Apache-2.0
-
 Id:      com.github.tomtung
 Project: latex2unicode
 URL:     https://github.com/tomtung/latex2unicode
@@ -120,6 +115,11 @@ Project: Java String Similarity
 URL:     https://github.com/tdebatty/java-string-similarity
 License: MIT
 
+Id:      io.github.java-diff-utils:java-diff-utils
+Project: java-diff-utils
+URL:     https://github.com/java-diff-utils/java-diff-utils
+License: Apache-1.1
+
 Id:      mysql:mysql-connector-java
 Project: MySQL Connector/J
 URL:     http://www.mysql.de/downloads/connector/j/

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.8-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.9-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/lib/spin.jar b/lib/spin.jar
diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
@@ -35,10 +35,6 @@
 
 public class JabRefGUI {
 
-    private static final String NIMBUS_LOOK_AND_FEEL = "javax.swing.plaf.nimbus.NimbusLookAndFeel";
-    private static final String WINDOWS_LOOK_AND_FEEL = "com.sun.java.swing.plaf.windows.WindowsLookAndFeel";
-    private static final String OSX_AQUA_LOOK_AND_FEEL = "apple.laf.AquaLookAndFeel";
-
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefGUI.class);
 
     private static JabRefFrame mainFrame;