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

* upstream/master: (41 commits) update xmlunit from 2.3.0 -> 2.4.0 update wiremock from 2.6.0 -> 2.7.0 update controlsfx from 8.40.12 -> 8.40.13 Fix group freeze by running markBasechange in swing thread (#3058) Localization: French: translation of new entries (#3050) Fix ads fetcher (#3048) Update translation (#3041) Translate new strings (#3040) Fix navigation in entry editor increases modifies font size (#3037) Initial idea for architectural decision records (#3033) Readd comment Readd comment Fix keybdining in entry editor in localized installation (#3030) Structuring Upgrade shadowJar Modernizer improvements Replace Reimplement MappedList.kt (#3032) Use https for the maven ej-technologies repo Upgrade modernizer plugin Remove separator next to search bar ...
JabRef · Jul 31, 2017 · b6d43dc · b6d43dc
2 parents 136a844 + ed815b4
commit b6d43dc
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diff --git a/.mailmap b/.mailmap
@@ -118,3 +118,6 @@ Saulius Gražulis <grazulis@ibt.lt>
 Rolf Starre <rolf.starre@gmail.com> <RolfStarre@users.noreply.github.com>
 Owen Huang <ohuang12@users.noreply.github.com>
 Anita Armbruster <armbruan@gmail.com>
+Fabian Bauer <125m125@users.noreply.github.com>
+Jong-Ho Shinn <jhshinn@kaist.edu>
+Nadeem Mahmood <mahmoodn@purdue.edu>
diff --git a/.travis.yml b/.travis.yml
@@ -18,6 +18,7 @@ env:
     - TEST_SUITE=fetcherTest
     - TEST_SUITE=databaseTest
     - TEST_SUITE=guiTest
+    - TEST_SUITE=checkstyle
 
 matrix:
     fast_finish: true
@@ -37,9 +38,10 @@ before_script:
   - mysql -u root -e 'create database jabref'
 
 script:
-  # -Dscan enables the Gradle build scan, which can be used to investiage the time each action consumes
+  # --scan enables the Gradle build scan, which can be used to investiage the time each action consumes
   # For more information see https://gradle.com/scans/get-started
-  - if [ "$TEST_SUITE" != "guiTest" ]; then ./gradlew $TEST_SUITE $OPTIONS -Dscan; fi
+  - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
+  - if [ "$TEST_SUITE" == "checkstyle" ]; then ./gradlew checkstyleMain checkstyleTest checkstyleJmh; fi
   - if [ "$TEST_SUITE" == "guiTest" ]; then ./buildres/gui-tests.sh; fi
 
 after_success:

diff --git a/AUTHORS b/AUTHORS
@@ -47,6 +47,7 @@ Egon Willighagen
 Ellen Reitmayr
 Erik Putrycz
 Ervin Kolenovic
+Fabian Bauer
 Fabian Bieker
 Fabrice Dessaint
 Fedor Bezrukov
@@ -79,6 +80,7 @@ John David
 John Relph
 John Zedlewski
 Jonathan Powell
+Jong-Ho Shinn
 Jorge Tornero
 Joshua Ramon Enslin
 Jörg Lenhard
@@ -119,7 +121,9 @@ Michel Baylac
 Mike Smoot
 Moritz Ringler
 Morten Alver
+mpele
 Mélanie Tremblay
+Nadeem Mahmood
 Nathan Dunn
 Nathan Sheffield
 Nicolas Pavillon
@@ -166,12 +170,14 @@ Sven Jäger
 The Gitter Badger
 Thiago Toledo
 Thomas Arildsen
+Thomas Ilsche
 Thorsten Dahlheimer
 Tim van Rossum
 Tobias Boceck
 Tobias Denkinger
 Tobias Diez
 tokkot
+Tony K
 Toralf Senger
 uid112001
 Ulrich Stärk
@@ -185,3 +191,4 @@ wuw
 Yang Zongze
 Yara Grassi Gouffon
 Yifan Peng
+zacmks
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,41 +11,10 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
-- We moved the `adsurl` field to `url` field when fetching with the ADS fetcher.
-- We continued to improve the new groups interface:
-  - You can now again select multiple groups (and a few related settings were added to the preferences) [#2786](https://github.com/JabRef/jabref/issues/2786).
-  - We further improved performance of group operations, especially of the new filter feature [#2852](https://github.com/JabRef/jabref/issues/2852).
-  - It is now possible to resort groups using drag & drop [#2785](https://github.com/JabRef/jabref/issues/2785).
-- The entry editor got a fresh coat of paint:
-  - Homogenize the size of text fields.
-  - The buttons were changed to icons.
-  - Completely new interface to add or modify linked files.
-  - Removed the hidden feature that a double click in the editor inserted the current date.
-  - Complete new implementation of the the auto complete feature.
-- All authors and editors are separated using semicolons when exporting to csv. [#2762](https://github.com/JabRef/jabref/issues/2762)
-- Improved wording of "Show recommendations: into "Show 'Related Articles' tab" in the preferences
-- We added integration of the Library of Congress catalog as a fetcher based on the [LCCN identifier](https://en.wikipedia.org/wiki/Library_of_Congress_Control_Number). [Feature request 636 in the forum](http://discourse.jabref.org/t/loc-marc-mods-connection/636)
-- The integrity check for person names now also tests that the names are specified in one of the standard BibTeX formats.
-- Links in the Recommended Articles tab (Mr.DLib), when clicked, are now opened in the system's default browser. [2931](https://github.com/JabRef/jabref/issues/2931)
-- We improved the duplicate checker such that different editions of the same publication are not marked as duplicates. [2960](https://github.com/JabRef/jabref/issues/2960)
 
 ### Fixed
-- We fixed a bug that leaves .sav file after SaveAs [#2947](https://github.com/JabRef/jabref/issues/2947)
-- We fixed the function "Edit - Copy BibTeX key and link" to pass a hyperlink rather than an HTML statement.
-- We fixed the adding of a new entry from DOI which led to a connection error. The DOI resolution now uses HTTPS to protect the user's privacy.[#2879](https://github.com/JabRef/jabref/issues/2897)
-- We fixed the IEEE Xplore web search functionality [#2789](https://github.com/JabRef/jabref/issues/2789)
-- We fixed an error in the CrossRef fetcher that occurred if one of the fetched entries had no title
-- We fixed an issue that prevented new entries to be automatically assigned to the currently selected group [#2783](https://github.com/JabRef/jabref/issues/2783).
-- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/2839)
-- We fixed a bug that did not allow the correct re-export of the MS-Office XML field `msbib-accessed` with a different date format [#2859](https://github.com/JabRef/jabref/issues/2859).
-- We fixed some bugs that prevented the display of FileAnnotations that were created using the Foxit Reader. [#2839, comment](https://github.com/JabRef/jabref/issues/2839#issuecomment-302058227).
-- We fixed an error that prevented the FileAnnotation tab to load when the entry had no bibtexkey [#2903](https://github.com/JabRef/jabref/issues/2903).
-- We fixed a bug which which could result in an exception when opening/saving files from/to a nonexistent directory [#2917](https://github.com/JabRef/jabref/issues/2917).
-- We fixed a bug where recursive RegExpBased search found a file in a subdirectory multiple times and non-recursive RegExpBased search erroneously found files in subdirectories.
-- We fixed a bug where new groups information was not stored on save [#2932](https://github.com/JabRef/jabref/issues/2932)
-- We fixed a bug where the language files for Brazilian Portugese could not be loaded and the GUI localization remained in English [#1128](https://github.com/JabRef/jabref/issues/1182)
-- We fixed a bug where the database was not marked as dirty when entries or groups were changed [#2787](https://github.com/JabRef/jabref/issues/2787)
-- We restored the original functionality that when browsing through the MainTable, the Entry Editor remembers which tab was opened before [#2896](https://github.com/JabRef/jabref/issues/2896)
+We fixed an issue where the fetcher for the Astrophysics Data System (ADS) added some non-bibtex data to the entry returned from the search [#3035](https://github.com/JabRef/jabref/issues/3035)
+We fixed an issue where assigning an entry via drag and drop to a group caused JabRef to stop/freeze completely [#3036](https://github.com/JabRef/jabref/issues/3036)
 ### Removed
 
 
@@ -88,6 +57,56 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
+
+
+
+
+
+
+
+
+
+
+## [4.0-beta2] – 2017-07-18
+
+### Changed
+- We moved the `adsurl` field to `url` field when fetching with the ADS fetcher.
+- We continued to improve the new groups interface:
+  - You can now again select multiple groups (and a few related settings were added to the preferences) [#2786](https://github.com/JabRef/jabref/issues/2786).
+  - We further improved performance of group operations, especially of the new filter feature [#2852](https://github.com/JabRef/jabref/issues/2852).
+  - It is now possible to resort groups using drag & drop [#2785](https://github.com/JabRef/jabref/issues/2785).
+- The entry editor got a fresh coat of paint:
+  - Homogenize the size of text fields.
+  - The buttons were changed to icons.
+  - Completely new interface to add or modify linked files.
+  - Removed the hidden feature that a double click in the editor inserted the current date.
+  - Complete new implementation of the the auto complete feature.
+- All authors and editors are separated using semicolons when exporting to csv. [#2762](https://github.com/JabRef/jabref/issues/2762)
+- Improved wording of "Show recommendations: into "Show 'Related Articles' tab" in the preferences
+- We added integration of the Library of Congress catalog as a fetcher based on the [LCCN identifier](https://en.wikipedia.org/wiki/Library_of_Congress_Control_Number). [Feature request 636 in the forum](http://discourse.jabref.org/t/loc-marc-mods-connection/636)
+- The integrity check for person names now also tests that the names are specified in one of the standard BibTeX formats.
+- Links in the Recommended Articles tab (Mr.DLib), when clicked, are now opened in the system's default browser. [2931](https://github.com/JabRef/jabref/issues/2931)
+- We improved the duplicate checker such that different editions of the same publication are not marked as duplicates. [2960](https://github.com/JabRef/jabref/issues/2960)
+
+### Fixed
+- We fixed a bug that leaves .sav file after SaveAs [#2947](https://github.com/JabRef/jabref/issues/2947)
+- We fixed the function "Edit - Copy BibTeX key and link" to pass a hyperlink rather than an HTML statement.
+- We fixed the adding of a new entry from DOI which led to a connection error. The DOI resolution now uses HTTPS to protect the user's privacy.[#2879](https://github.com/JabRef/jabref/issues/2897)
+- We fixed the IEEE Xplore web search functionality [#2789](https://github.com/JabRef/jabref/issues/2789)
+- We fixed an error in the CrossRef fetcher that occurred if one of the fetched entries had no title
+- We fixed an issue that prevented new entries to be automatically assigned to the currently selected group [#2783](https://github.com/JabRef/jabref/issues/2783).
+- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/2839)
+- We fixed a bug that did not allow the correct re-export of the MS-Office XML field `msbib-accessed` with a different date format [#2859](https://github.com/JabRef/jabref/issues/2859).
+- We fixed some bugs that prevented the display of FileAnnotations that were created using the Foxit Reader. [#2839, comment](https://github.com/JabRef/jabref/issues/2839#issuecomment-302058227).
+- We fixed an error that prevented the FileAnnotation tab to load when the entry had no bibtexkey [#2903](https://github.com/JabRef/jabref/issues/2903).
+- We fixed a bug which which could result in an exception when opening/saving files from/to a nonexistent directory [#2917](https://github.com/JabRef/jabref/issues/2917).
+- We fixed a bug where recursive RegExpBased search found a file in a subdirectory multiple times and non-recursive RegExpBased search erroneously found files in subdirectories.
+- We fixed a bug where new groups information was not stored on save [#2932](https://github.com/JabRef/jabref/issues/2932)
+- We fixed a bug where the language files for Brazilian Portugese could not be loaded and the GUI localization remained in English [#1128](https://github.com/JabRef/jabref/issues/1182)
+- We fixed a bug where the database was not marked as dirty when entries or groups were changed [#2787](https://github.com/JabRef/jabref/issues/2787)
+- We fixed a bug where editors in the DocBook export were not exported [#3020](https://github.com/JabRef/jabref/issues/3020)
+- We fixed a bug where the source tab was not updated when one the fields was changed [#2888](https://github.com/JabRef/jabref/issues/2888)
+- We restored the original functionality that when browsing through the MainTable, the Entry Editor remembers which tab was opened before [#2896](https://github.com/JabRef/jabref/issues/2896)
 
 ## [4.0-beta] – 2017-04-17
 
@@ -878,7 +897,8 @@ Since much functionality has changed during development, a release of this versi
 
 The changelog of 2.11 and versions before is maintained as [text file](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG) in the [v2.11.1 tag](https://github.com/JabRef/jabref/tree/v2.11.1).
 
-[unreleased]: https://github.com/JabRef/jabref/compare/v4.0-beta...HEAD
+[unreleased]: https://github.com/JabRef/jabref/compare/v4.0-beta2...HEAD
+[4.0-beta2]: https://github.com/JabRef/jabref/compare/v4.0-beta...v4.0-beta2
 [4.0-beta]: https://github.com/JabRef/jabref/compare/v3.8.2...v4.0-beta
 [3.8.2]: https://github.com/JabRef/jabref/compare/v3.8.1...v3.8.2
 [3.8.1]: https://github.com/JabRef/jabref/compare/v3.8...v3.8.1

diff --git a/DEVELOPERS b/DEVELOPERS
@@ -6,3 +6,4 @@ Matthias Geiger (since 2015)
 Oscar Gustafsson (since 2015)
 Tobias Diez (since 2015)
 Christoph Schwentker (since 2016)
+Linus Dietz (since 2017)
diff --git a/build.gradle b/build.gradle
@@ -2,24 +2,14 @@ import org.gradle.internal.os.OperatingSystem
 
 // to update the gradle wrapper, execute ./gradlew wrapper --gradle-version 3.0
 
-buildscript {
-    repositories {
-        maven {
-            url 'http://maven.ej-technologies.com/repository'
-        }
-    }
-    dependencies {
-        classpath 'com.github.edwgiz:maven-shade-plugin.log4j2-cachefile-transformer:2.1'
-    }
-}
-
 plugins {
     id 'com.gradle.build-scan' version '1.8'
-    id "com.install4j.gradle" version "6.1.5"
-    id 'com.github.johnrengelman.shadow' version '1.2.4'
-    id "com.simonharrer.modernizer" version "1.4.0-1"
-    id 'me.champeau.gradle.jmh' version '0.3.1'
-    id "net.ltgt.errorprone" version "0.0.10"
+    id 'com.install4j.gradle' version '6.1.5'
+    id 'com.github.johnrengelman.shadow' version '2.0.1'
+    id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.0"
+    id "com.simonharrer.modernizer" version '1.5.0-1'
+    id 'me.champeau.gradle.jmh' version '0.4.3'
+    id 'net.ltgt.errorprone' version '0.0.11'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -28,22 +18,21 @@ buildScan {
     licenseAgree = 'yes'
 }
 
-apply plugin: "java"
-apply plugin: "application"
-apply plugin: "project-report"
+apply plugin: 'java'
+apply plugin: 'application'
+apply plugin: 'project-report'
 apply plugin: 'jacoco'
 apply plugin: 'install4j'
 apply plugin: 'me.champeau.gradle.jmh'
-
 apply plugin: 'checkstyle'
 
 apply from: 'eclipse.gradle'
 apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.0.0-dev"
-project.ext.threeDotVersion = "4.0.0.1"
+version = "4.0-dev"
+project.ext.threeDotVersion = "4.0.1.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
@@ -53,7 +42,6 @@ install4j {
     installDir = file(project.ext.install4jDir)
 }
 
-
 repositories {
     mavenLocal()
     jcenter()
@@ -68,12 +56,14 @@ configurations {
 }
 
 dependencies {
+    compile fileTree(dir: 'lib', includes: ['*.jar'])
+
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
     compile 'com.jgoodies:jgoodies-looks:2.7.0'
 
     // Later versions cannot be used. Tested until 1.6.5-1.
-    // See https://github.com/JabRef/jabref/issues/271 for details
+    // See https://github.com/JabRef/jabref/issues/271 for details.
     compile 'org.swinglabs.swingx:swingx-core:1.6.4'
 
     // update to 2.0.x is not possible - see https://github.com/JabRef/jabref/pull/1096#issuecomment-208857517
@@ -105,34 +95,30 @@ dependencies {
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
-    compile fileTree(dir: 'lib', includes: ['*.jar'])
 
     compile 'com.google.guava:guava:22.0'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
     compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
-    compile 'org.controlsfx:controlsfx:8.40.12'
+    compile 'org.controlsfx:controlsfx:8.40.13'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
-    compile 'net.corda:jfx:0.12.1'
+
     compile 'org.fxmisc.flowless:flowless:0.5.2'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'org.fxmisc.richtext:richtextfx:0.7-M5'
 
-
     compile 'commons-logging:commons-logging:1.2'
 
-    compile 'org.apache.commons:commons-lang3:3.6'
-
     compile 'org.jsoup:jsoup:1.10.3'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
     compile 'info.debatty:java-string-similarity:0.24'
 
     compile 'org.apache.logging.log4j:log4j-jcl:2.8.2'
     compile 'org.apache.logging.log4j:log4j-api:2.8.2'
     compile 'org.apache.logging.log4j:log4j-core:2.8.2'
-    compile 'org.xmlunit:xmlunit-core:2.3.0'
-    compile 'org.xmlunit:xmlunit-matchers:2.3.0'
+    compile 'org.xmlunit:xmlunit-core:2.4.0'
+    compile 'org.xmlunit:xmlunit-matchers:2.4.0'
 
     // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
@@ -146,9 +132,12 @@ dependencies {
 
     testCompile 'junit:junit:4.12'
     testCompile 'org.mockito:mockito-core:2.8.47'
-    testCompile 'com.github.tomakehurst:wiremock:2.6.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.6.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.7.0'
+    testCompile 'org.assertj:assertj-swing-junit:3.7.0'
     testCompile 'org.reflections:reflections:0.9.11'
+
+    testCompile 'com.tngtech.archunit:archunit-junit:0.4.0'
+    testCompile 'org.slf4j:slf4j-jcl:1.7.25' // required by ArchUnit to enable logging over jcl
 }
 
 sourceSets {
@@ -285,6 +274,7 @@ processTestResources.dependsOn copyTestResources
 
 tasks.withType(Test) {
     reports.html.destination = file("${reporting.baseDir}/${name}")
+
     jacoco {
         append = true
     }
@@ -306,33 +296,6 @@ jacocoTestReport {
 
 shadowJar {
     classifier 'fat'
-
-    transform(new com.github.jengelman.gradle.plugins.shadow.transformers.Transformer() {
-
-        // this is an adapter required for generating a fat jar with correct log4j2 output
-
-        com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer target = new com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer()
-
-        @Override
-        boolean canTransformResource(FileTreeElement element) {
-            return target.canTransformResource(element.getPath())
-        }
-
-        @Override
-        void transform(String path, InputStream is, List<com.github.jengelman.gradle.plugins.shadow.relocation.Relocator> relocators) {
-            target.processResource(path, is, relocators)
-        }
-
-        @Override
-        boolean hasTransformedResource() {
-            return target.hasTransformedResource()
-        }
-
-        @Override
-        void modifyOutputStream(org.apache.tools.zip.ZipOutputStream jos) {
-            target.modifyOutputStream(jos)
-        }
-    })
 }
 
 /*

diff --git a/docs/adr/0000-use-architectural-decision-records.md b/docs/adr/0000-use-architectural-decision-records.md
@@ -0,0 +1,16 @@
+# Use Architectural Decision Records
+
+We need to record the architectural decisions made on this project.
+
+## Considered Alternatives
+
+* No record
+* [DecisionRecord](https://github.com/schubmat/DecisionCapture)
+* [Michael Nygard's template](http://thinkrelevance.com/blog/2011/11/15/documenting-architecture-decisions), maintainable by [adr-tools](https://github.com/npryce/adr-tools)
+* [Sustainable Architectural Decisions](https://www.infoq.com/articles/sustainable-architectural-design-decisions)
+* [Other templates](https://github.com/joelparkerhenderson/architecture_decision_record)
+
+## Conclusion
+
+* *Chosen Alternative: Decision Record*
+* That template is lean and fits most the development style
diff --git a/docs/adr/index.md b/docs/adr/index.md
@@ -0,0 +1,8 @@
+# Architectural Decision Records
+
+This lists the architectural decisions for JabRef.
+
+- [0000-use-architectural-decision-records.md](0000-use-architectural-decision-records) - Use Architectural Decision Records
+- [template.md](template/) - the template
+
+More information on architectural decision records is available at <https://adr.github.io/>.