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

* upstream/master: (91 commits)
  fixed #2613 (#2623)
  Add MathSciNet as ID-based fetcher (#2621)
  Add icon + color and description to groups (#2612)
  Fixed wrong logger import (#2618)
  Cleanup window has a scrollbar now. (#2614)
  Added the locale to a newly created class
  Move ExportComparator and CustomExportList to the correct package (only used in preferences)
  Fixes displaying of Mr DLib recommendations (#2616)
  Fix title-related key patterns in BibtexKeyPatternUtil (#2610)
  Remove OrdinalsToSuperscriptFormatter from recommended biblatex save actions (#2601)
  Update pgjdbc to new major version
  Update Dependenices String Similary log4j wiremock mockito
  Fix exception when parsing groups which contain a top level group (#2611)
  Add "Remove group and subgroups" option (#2587)
  Fix #1104: group selection is preserved under tab change
  Fix several File Cleanup + Rename issues  (#2415)
  Fixed a small error in the code comments
  Implement #1904: filter groups (#2588)
  Braces checking followup (#2598)
  Improve braces checking (#2593)
  ...

.mailmap

@@ -108,3 +108,4 @@ Ali Ayan <ali.ayan@hotmail.de>
 Arno Blouin <blouin.arno@gmail.com>
 Jeff Miller <miller@psy.otago.ac.nz>
 Alain Vaucher <avaucher@users.noreply.github.com>
+Daniel Mair <mairdl.dev@gmail.com> <mairdl.dev@googlemail.com>

AUTHORS

@@ -93,6 +93,7 @@ Laura Hernández Gómez
 Lee Patton
 Leonardo Haddad
 Ling Wang
+Linus Dietz
 Lorenzo Genta
 Luciana de Melo e Abud
 Mairieli Wessel
@@ -128,6 +129,7 @@ Olaf Lenz
 Oliver Beckmann
 Oliver Kopp
 Oscar Gustafsson
+Paul Martin
 payload
 Peter Ansell
 Philip Johnson
@@ -149,6 +151,7 @@ Shitikanth
 Simon Harrer
 Simon Rutishauser
 speed9
+Stefan Feyer
 Stefan Kolb
 Stefan Robert
 Stefano Gariazzo

CHANGELOG.md

@@ -17,6 +17,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
     - Redesigned group panel.
       - Number of matched entries is always shown.
       - The background color of the hit counter signals whether the group contains all/any of the entries selected in the main table. 
+      - Added a possibility to filter the groups panel [#1904](https://github.com/JabRef/jabref/issues/1904)
+      - Removed edit mode.
     - Redesigned about dialog.
     - Redesigned key bindings dialog.
     - Redesigned journal abbreviations dialog.
@@ -32,6 +34,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
     - Font sizes can now be increased <kbd>Ctrl</kbd> + <kbd>Plus</kbd>, decreased <kbd>Ctrl</kbd> + <kbd>Minus</kbd>, and reset to default <kbd>CTRL</kbd> + <kbd>0</kbd>.
 - We integrated support for the [paper recommender system Mr.DLib](http://help.jabref.org/en/EntryEditor#related-articles-tab) in a new tab in the entry editor.
 - We renamed "database" to "library" to have a real distinction to SQL and NoSQL databases. [#2095](https://github.com/JabRef/jabref/issues/2095)
+- We added MathSciNet as a ID-based fetcher in the `BibTeX -> New entry` dialog (implements a [feature request in the forum](http://discourse.jabref.org/t/allow-to-search-by-mr-number-mathscinet))
+- Removed the apache.commons.collections library
+- We removed the ordinals-to-superscript formatter from the recommendations for biblatex save actions [#2596](https://github.com/JabRef/jabref/issues/2596)
+- The `Move linked files to default file directory`-Cleanup operation respects the `File directory pattern` setting 
+- We separated the `Move file` and `Rename Pdfs` logic and context menu entries in the `General`-Tab for the Field `file` to improve the semantics
+- A scrollbar was added to the cleanup panel, as a result of issue [#2501](https://github.com/JabRef/jabref/issues/2501)
 
 ### Fixed
  - We fixed an issue where authors with multiple surnames were not presented correctly in the main table. [#2534](https://github.com/JabRef/jabref/issues/2534)
@@ -40,7 +48,21 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We fixed the export of the `number` field in MS-Office XML export. [#2509](https://github.com/JabRef/jabref/issues/2509)
  - The field `issue` is now always exported to the corresponding `issue` field in MS-Office XML.
  - We fixed an issue with repeated escaping of the %-sign when running the LaTeXCleanup more than once. [#2451](https://github.com/JabRef/jabref/issues/2451)
-
+ - We fixed the import of MS-Office XML files, when the `month` field contained an invalid value.
+ - ArXiV fetcher now checks similarity of entry when using DOI retrieval to avoid false positives [#2575](https://github.com/JabRef/jabref/issues/2575)
+ - Sciencedirect/Elsevier fetcher is now able to scrape new HTML structure [#2576](https://github.com/JabRef/jabref/issues/2576)
+ - Fixed the synchronization logic of keywords and special fields and vice versa [#2580](https://github.com/JabRef/jabref/issues/2580)
+ - Fixed a display issue when removing a group with a long name [#1407](https://github.com/JabRef/jabref/issues/1407)
+ - The group selection is no longer lost when switching tabs [#1104](https://github.com/JabRef/jabref/issues/1104)
+ - We fixed an issue where the "find unlinked files" functionality threw an error when only one PDF was imported but not assigned to an entry [#2577](https://github.com/JabRef/jabref/issues/2577)
+ - We fixed issue where escaped braces were incorrectly counted when calculating brace balance in a field [#2561](https://github.com/JabRef/jabref/issues/2561)
+ - We fixed an issue introduced with Version 3.8.2 where executing the `Rename PDFs`-cleanup operation moved the files to the file directory. [#2526](https://github.com/JabRef/jabref/issues/2526)
+ - We fixed an issue where the `Move linked files to default file directory`- cleanup operation did not move the files to the location of the bib-file. [#2454](https://github.com/JabRef/jabref/issues/2454)
+ - We fixed an issue where executing `Move file` on a selected file in the `general`-tab could overwrite an existing file. [#2385](https://github.com/JabRef/jabref/issues/2358)
+ - We fixed an issue with importing groups and subgroups [#2600](https://github.com/JabRef/jabref/issues/2600)
+ - Fixed an issue where title-related key patterns did not correspond to the documentation [#2604](https://github.com/JabRef/jabref/issues/2604) [#2589](https://github.com/JabRef/jabref/issues/2589)
+ - We fixed an issue which prohibited the citation export to external programms on MacOS  [#2613](https://github.com/JabRef/jabref/issues/2613)
+
 ### Removed
 
 

build.gradle

@@ -42,13 +42,13 @@ apply from: 'eclipse.gradle'
 apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
-group = "net.sf.jabref"
+group = "org.jabref"
 version = "4.0.0-dev"
 project.ext.threeDotVersion = "4.0.0.0"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
-mainClassName = "net.sf.jabref.JabRefMain"
+mainClassName = "org.jabref.JabRefMain"
 
 install4j {
     installDir = file(project.ext.install4jDir)
@@ -102,7 +102,7 @@ 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:5.1.40'
 
-    compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.6'
+    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'])
@@ -118,16 +118,15 @@ dependencies {
 
     compile 'commons-logging:commons-logging:1.2'
 
-    compile 'org.apache.commons:commons-collections4:4.0'
     compile 'org.apache.commons:commons-lang3:3.5'
 
     compile 'org.jsoup:jsoup:1.10.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
-    compile 'info.debatty:java-string-similarity:0.21'
+    compile 'info.debatty:java-string-similarity:0.23'
 
-    compile 'org.apache.logging.log4j:log4j-jcl:2.7'
-    compile 'org.apache.logging.log4j:log4j-api:2.7'
-    compile 'org.apache.logging.log4j:log4j-core:2.7'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.8'
+    compile 'org.apache.logging.log4j:log4j-api:2.8'
+    compile 'org.apache.logging.log4j:log4j-core:2.8'
     compile 'org.xmlunit:xmlunit-core:2.3.0'
     compile 'org.xmlunit:xmlunit-matchers:2.3.0'
 
@@ -141,8 +140,8 @@ dependencies {
     compile 'com.github.tomtung:latex2unicode_2.12:0.2-SNAPSHOT'
 
     testCompile 'junit:junit:4.12'
-    testCompile 'org.mockito:mockito-core:2.6.2'
-    testCompile 'com.github.tomakehurst:wiremock:2.5.0'
+    testCompile 'org.mockito:mockito-core:2.7.12'
+    testCompile 'com.github.tomakehurst:wiremock:2.5.1'
     testCompile 'org.assertj:assertj-swing-junit:3.5.0'
     testCompile 'org.reflections:reflections:0.9.10'
 }
@@ -187,15 +186,15 @@ task generateBstGrammarSource(type: JavaExec) {
     group 'JabRef'
     description 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.'
 
-    File antlrSource = file('src/main/antlr3/net/sf/jabref/bst/Bst.g')
+    File antlrSource = file('src/main/antlr3/org/jabref/bst/Bst.g')
 
     inputs.file antlrSource
-    outputs.file file('src/main/gen/net/sf/jabref/logic/bst/BstLexer.java')
-    outputs.file file('src/main/gen/net/sf/jabref/logic/bst/BstParser.java')
+    outputs.file file('src/main/gen/org/jabref/logic/bst/BstLexer.java')
+    outputs.file file('src/main/gen/org/jabref/logic/bst/BstParser.java')
 
     main = 'org.antlr.Tool'
     classpath = configurations.antlr3
-    args = ["-o", file('src/main/gen/net/sf/jabref/logic/bst/'), antlrSource]
+    args = ["-o", file('src/main/gen/org/jabref/logic/bst/'), antlrSource]
 }
 
 task generateSearchGrammarSource(type: JavaExec) {
@@ -204,7 +203,7 @@ task generateSearchGrammarSource(type: JavaExec) {
     group 'JabRef'
     description "Generates java files for ${grammarFile}.g antlr4."
 
-    String packagePath = "net/sf/jabref/search"
+    String packagePath = "org/jabref/search"
     File antlrPath = file("src/main/antlr4")
     File genPath = file("src/main/gen")
 
@@ -221,7 +220,7 @@ task generateSearchGrammarSource(type: JavaExec) {
 
     main = 'org.antlr.v4.Tool'
     classpath = configurations.antlr4
-    args = ["-o", destinationDir, "-visitor", "-no-listener", "-package", "net.sf.jabref.search", antlrSource]
+    args = ["-o", destinationDir, "-visitor", "-no-listener", "-package", "org.jabref.search", antlrSource]
 }
 
 compileJava {
@@ -244,9 +243,9 @@ javadoc {
 
 test {
     useJUnit {
-        excludeCategories 'net.sf.jabref.testutils.category.DatabaseTests'
-        excludeCategories 'net.sf.jabref.testutils.category.FetcherTests'
-        excludeCategories 'net.sf.jabref.testutils.category.GUITests'
+        excludeCategories 'org.jabref.testutils.category.DatabaseTests'
+        excludeCategories 'org.jabref.testutils.category.FetcherTests'
+        excludeCategories 'org.jabref.testutils.category.GUITests'
     }
     testLogging {
         events "failed"
@@ -256,19 +255,19 @@ test {
 
 task databaseTest(type: Test) {
     useJUnit {
-        includeCategories 'net.sf.jabref.testutils.category.DatabaseTests'
+        includeCategories 'org.jabref.testutils.category.DatabaseTests'
     }
 }
 
 task fetcherTest(type: Test) {
     useJUnit {
-        includeCategories 'net.sf.jabref.testutils.category.FetcherTests'
+        includeCategories 'org.jabref.testutils.category.FetcherTests'
     }
 }
 
 task guiTest(type: Test) {
     useJUnit {
-        includeCategories 'net.sf.jabref.testutils.category.GUITests'
+        includeCategories 'org.jabref.testutils.category.GUITests'
     }
 }
 

config/IntelliJ Code Style.xml

@@ -12,7 +12,7 @@
       <emptyLine />
       <package name="javafx" withSubpackages="true" static="false" />
       <emptyLine />
-      <package name="net.sf.jabref" withSubpackages="true" static="false" />
+      <package name="org.jabref" withSubpackages="true" static="false" />
       <emptyLine />
       <package name="" withSubpackages="true" static="false" />
       <emptyLine />

config/checkstyle/checkstyle.xml

@@ -42,7 +42,7 @@
         <module name="IllegalImport"/>
 
         <module name="ImportOrder">
-            <property name="groups" value="java,javax,javafx,net.sf.jabref,*"/>
+            <property name="groups" value="java,javax,javafx,org.jabref,*"/>
             <property name="ordered" value="true"/>
             <property name="separated" value="true"/>
             <property name="option" value="bottom"/>

external-libraries.txt

@@ -55,11 +55,6 @@ Project: Apache Commons Lang
 URL:     https://commons.apache.org/proper/commons-lang/
 License: Apache-2.0
 
-Id:      org.apache.commons:commons-collections4
-Project: Apache Commons Collections
-URL:     https://commons.apache.org/proper/commons-collections/
-License: Apache-2.0
-
 Id:      com.github.bkromhout:java-diff-utils
 Project: java-diff-utils
 URL:     https://github.com/bkromhout/java-diff-utils

jabref.install4j

@@ -68,7 +68,7 @@
           <versionLine x="20" y="40" text="version ${compiler:sys.version}" fontSize="8" fontColor="0,0,0" bold="false" />
         </text>
       </splashScreen>
-      <java mainClass="net.sf.jabref.JabRefMain" vmParameters="" arguments="" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
+      <java mainClass="org.jabref.JabRefMain" vmParameters="" arguments="" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
         <classPath>
           <archive location="${compiler:buildFileName}" failOnError="false" />
         </classPath>

src/jmh/java/net/sf/jabref/benchmarks/Benchmarks.java → src/jmh/java/org/jabref/benchmarks/Benchmarks.java

@@ -1,33 +1,33 @@
-package net.sf.jabref.benchmarks;
+package org.jabref.benchmarks;
 
 import java.io.IOException;
 import java.io.StringReader;
 import java.util.List;
 import java.util.Random;
 import java.util.stream.Collectors;
 
-import net.sf.jabref.Globals;
-import net.sf.jabref.logic.exporter.BibtexDatabaseWriter;
-import net.sf.jabref.logic.exporter.SavePreferences;
-import net.sf.jabref.logic.exporter.StringSaveSession;
-import net.sf.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;
-import net.sf.jabref.logic.importer.ParseException;
-import net.sf.jabref.logic.importer.ParserResult;
-import net.sf.jabref.logic.importer.fileformat.BibtexParser;
-import net.sf.jabref.logic.layout.format.HTMLChars;
-import net.sf.jabref.logic.layout.format.LatexToUnicodeFormatter;
-import net.sf.jabref.logic.search.SearchQuery;
-import net.sf.jabref.model.Defaults;
-import net.sf.jabref.model.database.BibDatabase;
-import net.sf.jabref.model.database.BibDatabaseContext;
-import net.sf.jabref.model.database.BibDatabaseMode;
-import net.sf.jabref.model.database.BibDatabaseModeDetection;
-import net.sf.jabref.model.entry.BibEntry;
-import net.sf.jabref.model.groups.GroupHierarchyType;
-import net.sf.jabref.model.groups.KeywordGroup;
-import net.sf.jabref.model.groups.WordKeywordGroup;
-import net.sf.jabref.model.metadata.MetaData;
-import net.sf.jabref.preferences.JabRefPreferences;
+import org.jabref.Globals;
+import org.jabref.logic.exporter.BibtexDatabaseWriter;
+import org.jabref.logic.exporter.SavePreferences;
+import org.jabref.logic.exporter.StringSaveSession;
+import org.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;
+import org.jabref.logic.importer.ParseException;
+import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.importer.fileformat.BibtexParser;
+import org.jabref.logic.layout.format.HTMLChars;
+import org.jabref.logic.layout.format.LatexToUnicodeFormatter;
+import org.jabref.logic.search.SearchQuery;
+import org.jabref.model.Defaults;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.database.BibDatabaseMode;
+import org.jabref.model.database.BibDatabaseModeDetection;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.groups.GroupHierarchyType;
+import org.jabref.model.groups.KeywordGroup;
+import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
+import org.jabref.preferences.JabRefPreferences;
 
 import org.openjdk.jmh.Main;
 import org.openjdk.jmh.annotations.Benchmark;

src/main/antlr3/net/sf/jabref/bst/Bst.g → src/main/antlr3/org/jabref/bst/Bst.g

@@ -13,15 +13,15 @@ tokens {
 
 // applies only to the parser:
 @header {// Generated by ANTLR
-package net.sf.jabref.logic.bst;}
+package org.jabref.logic.bst;}
 
 // applies only to the lexer:
 @lexer::header {// Generated by ANTLR
-package net.sf.jabref.logic.bst;}
+package org.jabref.logic.bst;}
 
 program : commands+ -> ^(COMMANDS commands+);
 
-commands 
+commands
 	: STRINGS^ idList
 	| INTEGERS^ idList
 	| FUNCTION^ id stack
@@ -33,28 +33,28 @@ commands
 	| ENTRY^ idList0 idList0 idList0
 	| SORT^;
 
-identifier 
+identifier
 	: IDENTIFIER;
 
-id 
+id
 	: '{'! identifier '}'!;
-	
-idList 
+
+idList
 	: '{' identifier+ '}' -> ^(IDLIST identifier+);
-	
-idList0 
+
+idList0
 	: '{' identifier* '}' -> ^(IDLIST identifier*);
 
-function 
+function
 	: '<' | '>' | '=' | '+' | '-' | ':=' | '*' | identifier;
-	
-stack 
+
+stack
 	: '{' stackitem+ '}' -> ^(STACK stackitem+);
-	
+
 stackitem
 	: function
-	| STRING 
-	| INTEGER 
+	| STRING
+	| INTEGER
 	| QUOTED
 	| stack;
 
@@ -80,17 +80,17 @@ fragment LETTER
 
 STRING
 	: '"' (~('"'))* '"';
-	
-INTEGER   
+
+INTEGER
 	: '#' ('+'|'-')? NUMERAL+ ;
 
 fragment NUMERAL
 	: ('0'..'9');
-	
+
 WS
 	: (' '|'\t'|'\n'|'\r')+ {_channel=99;} ;
-	
+
 LINE_COMMENT
     : '%' ~('\n'|'\r')* '\r'? '\n' {_channel=99;}
     ;
-	
+