CyraxSector · CyraxSector · Aug 20, 2019 · Jun 19, 2019 · Jun 19, 2019 · Jun 20, 2019
diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -1,12 +1,12 @@
 # These are supported funding model platforms
 
 github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
-patreon: koppor
+patreon: # Patreon user account
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username
 tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
 community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
-liberapay: koppor
+liberapay: JabRef
 issuehunt: # Replace with a single IssueHunt username
 otechie: # Replace with a single Otechie username
 custom: https://github.com/JabRef/jabref/wiki/Donations # Replace with a single custom sponsorship URL
diff --git a/.github/autoapproval.yml b/.github/autoapproval.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- All fields are now properly sorted alphabetically (in the subgroups of required/optional fields) when the entry is written to the bib file.
+- We fixed an issue where some importers used the field `pubstatus` instead of the standard BibTeX field `pubstate`.
 - We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)
 - We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
   - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
@@ -53,6 +55,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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 change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
+- We added description of how recommendations where 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)
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
 - We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
@@ -69,6 +72,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We moved the dropdown menu for selecting the push-application from the toolbar into the external application preferences. [#674](https://github.com/JabRef/jabref/issues/674)
 - We removed the alphabetical ordering of the custom tabs and updated the error message when trying to create a general field with a name containing an illegal character. [#5019](https://github.com/JabRef/jabref/issues/5019)
 - We added a context menu to the bib(la)tex-source-editor to copy'n'paste. [#5007](https://github.com/JabRef/jabref/pull/5007)
+- We added a tool that allows searching for citations in LaTeX files. It scans directories and shows which entries are used, how many times and where.
+- We added a 'LaTeX citations' tab to the entry editor, to search for citations to the active entry in the LaTeX file directory. It can be disabled in the preferences dialog.
+- We added an option in preferences to allow for integers in field "edition" when running database in bibtex mode. [#4680](https://github.com/JabRef/jabref/issues/4680)
 
 
 ### Fixed
@@ -125,6 +131,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the same menu for changing entry type had two different sizes and weights. [#4977](https://github.com/JabRef/jabref/issues/4977)
 - We fixed an issue where the "Attach file" dialog, in the right-click menu for an entry, started on the working directory instead of the user's main directory. [#4995](https://github.com/JabRef/jabref/issues/4995)
 - We fixed an issue where the JabRef Icon in the macOS launchpad was not displayed correctly [#5003](https://github.com/JabRef/jabref/issues/5003)
+- We fixed an issue where the "Search for unlinked local files" would throw an exception when parsing the content of a PDF-file with missing "series" information [#5128](https://github.com/JabRef/jabref/issues/5128)
 
 
 ### Removed

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright © 2003-2018 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS)
+Copyright © 2003-2019 [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/README.md b/README.md
@@ -3,6 +3,7 @@
 [![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)
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
+[![Crowdin](https://d322cqt584bo4o.cloudfront.net/jabref/localized.svg)](https://crowdin.com/project/jabref)
 
 JabRef is an open-source, cross-platform citation and reference management tool licensed under the  [MIT license](https://tldrlegal.com/license/mit-license).
 

diff --git a/build.gradle b/build.gradle
@@ -16,13 +16,13 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '2.3'
-    id 'com.install4j.gradle' version '7.0.11'
-    id 'com.github.johnrengelman.shadow' version '5.0.0'
-    id "com.simonharrer.modernizer" version '1.6.0-1'
+    id 'com.gradle.build-scan' version '2.4'
+    id 'com.install4j.gradle' version '7.0.12'
+    id 'com.github.johnrengelman.shadow' version '5.1.0'
+    id "com.simonharrer.modernizer" version '1.8.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
     id 'net.ltgt.errorprone' version '0.8.1'
-    id 'com.github.ben-manes.versions' version '0.21.0'
+    id 'com.github.ben-manes.versions' version '0.22.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -90,11 +90,11 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.15'
-    compile 'org.apache.pdfbox:fontbox:2.0.15'
-    compile 'org.apache.pdfbox:xmpbox:2.0.15'
+    compile 'org.apache.pdfbox:pdfbox:2.0.16'
+    compile 'org.apache.pdfbox:fontbox:2.0.16'
+    compile 'org.apache.pdfbox:xmpbox:2.0.16'
 
-    compile group: 'org.apache.tika', name: 'tika-core', version: '1.21'
+    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
     compile 'org.bouncycastle:bcprov-jdk15on:1.62'
@@ -115,7 +115,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile 'mysql:mysql-connector-java:8.0.16'
+    compile 'mysql:mysql-connector-java:8.0.17'
 
     compile 'org.postgresql:postgresql:42.2.6'
 
@@ -143,37 +143,37 @@ dependencies {
 
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:2.0.0-alpha0'
-    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-api:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-core:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.12.1'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.12.1'
+    compile 'org.apache.logging.log4j:log4j-api:2.12.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.12.1'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.4.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.4.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.5.1'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.5.1'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.5.1'
 
-    testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.28.2'
-    testCompile 'com.github.tomakehurst:wiremock:2.23.2'
+    testRuntime 'org.apache.logging.log4j:log4j-core:2.12.0'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.12.1'
+    testCompile 'org.mockito:mockito-core:3.0.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.2'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.11.0'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.11.0'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.22'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.23'
     xjc 'com.sun.xml.bind:jaxb-xjc:2.2.4-1'
     jython 'org.python:jython-standalone:2.7.1'
 }

diff --git a/src/jmh/java/org/jabref/benchmarks/Benchmarks.java b/src/jmh/java/org/jabref/benchmarks/Benchmarks.java
@@ -22,6 +22,9 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.database.BibDatabaseModeDetection;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.field.UnknownField;
 import org.jabref.model.groups.GroupHierarchyType;
 import org.jabref.model.groups.KeywordGroup;
 import org.jabref.model.groups.WordKeywordGroup;
@@ -54,12 +57,12 @@ public void init() throws Exception {
         for (int i = 0; i < 1000; i++) {
             BibEntry entry = new BibEntry();
             entry.setCiteKey("id" + i);
-            entry.setField("title", "This is my title " + i);
-            entry.setField("author", "Firstname Lastname and FirstnameA LastnameA and FirstnameB LastnameB" + i);
-            entry.setField("journal", "Journal Title " + i);
-            entry.setField("keyword", "testkeyword");
-            entry.setField("year", "1" + i);
-            entry.setField("rnd", "2" + randomizer.nextInt());
+            entry.setField(StandardField.TITLE, "This is my title " + i);
+            entry.setField(StandardField.AUTHOR, "Firstname Lastname and FirstnameA LastnameA and FirstnameB LastnameB" + i);
+            entry.setField(StandardField.JOURNAL, "Journal Title " + i);
+            entry.setField(StandardField.KEYWORDS, "testkeyword");
+            entry.setField(StandardField.YEAR, "1" + i);
+            entry.setField(new UnknownField("rnd"), "2" + randomizer.nextInt());
             database.insertEntry(entry);
         }
 
@@ -72,7 +75,7 @@ public void init() throws Exception {
 
     private StringWriter getOutputWriter() throws IOException {
         StringWriter outputWriter = new StringWriter();
-        BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class));
+        BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class), new BibEntryTypesManager());
         databaseWriter.savePartOfDatabase(
                 new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
         return outputWriter;
@@ -128,7 +131,7 @@ public String htmlToLatexConversion() {
 
     @Benchmark
     public boolean keywordGroupContains() {
-        KeywordGroup group = new WordKeywordGroup("testGroup", GroupHierarchyType.INDEPENDENT, "keyword", "testkeyword", false, ',', false);
+        KeywordGroup group = new WordKeywordGroup("testGroup", GroupHierarchyType.INDEPENDENT, StandardField.KEYWORDS, "testkeyword", false, ',', false);
         return group.containsAll(database.getEntries());
     }
 

diff --git a/src/main/java/org/jabref/Globals.java b/src/main/java/org/jabref/Globals.java
@@ -21,6 +21,7 @@
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.server.RemoteListenerServerLifecycle;
 import org.jabref.logic.util.BuildInfo;
+import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -61,6 +62,7 @@ public class Globals {
     public static StateManager stateManager = new StateManager();
     public static ExporterFactory exportFactory;
     public static CountingUndoManager undoManager = new CountingUndoManager();
+    public static BibEntryTypesManager entryTypesManager = new BibEntryTypesManager();
     // Key binding preferences
     private static KeyBindingRepository keyBindingRepository;
     private static DefaultFileUpdateMonitor fileUpdateMonitor;

diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
@@ -22,9 +22,7 @@
 import org.jabref.logic.util.JavaVersion;
 import org.jabref.logic.util.OS;
 import org.jabref.migrations.PreferencesMigrations;
-import org.jabref.model.EntryTypes;
 import org.jabref.model.database.BibDatabaseMode;
-import org.jabref.model.entry.InternalBibtexFields;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.slf4j.Logger;
@@ -153,21 +151,14 @@ private static boolean handleMultipleAppInstances(String[] args) {
     }
 
     private static void applyPreferences(JabRefPreferences preferences) {
-        // Update handling of special fields based on preferences
-        InternalBibtexFields.updateSpecialFields(Globals.prefs.getBoolean(JabRefPreferences.SERIALIZESPECIALFIELDS));
-        // Update name of the time stamp field based on preferences
-        InternalBibtexFields.updateTimeStampField(Globals.prefs.getTimestampPreferences().getTimestampField());
-        // Update which fields should be treated as numeric, based on preferences:
-        InternalBibtexFields.setNumericFields(Globals.prefs.getStringList(JabRefPreferences.NUMERIC_FIELDS));
-
         // Read list(s) of journal names and abbreviations
         Globals.journalAbbreviationLoader = new JournalAbbreviationLoader();
 
         // Build list of Import and Export formats
         Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
                                                         Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
-        EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
-                                        preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
+        Globals.entryTypesManager.addCustomizedEntryTypes(preferences.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
+                preferences.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
         Globals.exportFactory = Globals.prefs.getExporterFactory(Globals.journalAbbreviationLoader);
 
         // Initialize protected terms loader

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -44,7 +44,6 @@
 import org.jabref.logic.util.OS;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.model.Defaults;
-import org.jabref.model.EntryTypes;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -391,7 +390,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             System.out.println(Localization.lang("Saving") + ": " + subName);
             SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
             AtomicFileWriter fileWriter = new AtomicFileWriter(Paths.get(subName), prefs.getEncoding());
-            BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs);
+            BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs, Globals.entryTypesManager);
             Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
             databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults));
 
@@ -458,8 +457,8 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
     private void importPreferences() {
         try {
             Globals.prefs.importPreferences(cli.getPreferencesImport());
-            EntryTypes.loadCustomEntryTypes(Globals.prefs.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
-                    Globals.prefs.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
+            Globals.entryTypesManager.addCustomizedEntryTypes(Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
+                    Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
             List<TemplateExporter> customExporters = Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationLoader);
             LayoutFormatterPreferences layoutPreferences = Globals.prefs
                     .getLayoutFormatterPreferences(Globals.journalAbbreviationLoader);

diff --git a/src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java b/src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java
@@ -16,7 +16,7 @@
 import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.identifier.DOI;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -53,7 +53,7 @@ public static void main(String[] args) throws IOException, InterruptedException
 
                     @Override
                     public void run() {
-                        Optional<DOI> origDOI = entry.getField(FieldName.DOI).flatMap(DOI::parse);
+                        Optional<DOI> origDOI = entry.getField(StandardField.DOI).flatMap(DOI::parse);
                         if (origDOI.isPresent()) {
                             dois.incrementAndGet();
                             try {

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
@@ -1015,6 +1015,11 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-fill: -jr-warn;
 }
 
+.warning-message {
+    -fx-fill: -jr-error;
+    -fx-text-fill: -jr-error;
+}
+
 .error-icon {
     -fx-text-fill: -jr-error;
     -fx-fill: -jr-error;