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

* upstream/master: (67 commits)
  Medline fix test (#2463)
  Fix conversion of tilde n (#2459)
  ctrl+f selects current query while the searchbar is focusd (#2457)
  incorrect log name of JabRefExecutorService (#2452)
  unregister DateChangeListener in manual update method (#2450)
  Escaping of escape symbols in the MetaData (#2445)
  Fix typo
  Update gradle from 3.2.1 to 3.3
  Use instanceof
  Remove unused import
  Avoid ClassCastException in AutoCompleteListener
  Fix typo in CHANGELOG.md
  Add support for pages in the format 2:1-2:33 (#2440)
  L10N-ru update (#2441)
  Change https to http
  Update DBLP API endpoint
  Revert "Chistmas edition colors"
  Show development information
  Release v3.8.1
  Result of generate-authors.sh
  ...

# Conflicts:
#	CHANGELOG.md
#	src/main/java/net/sf/jabref/gui/date/DatePickerButton.java

.gitattributes

@@ -6,7 +6,7 @@ gradlew eol=lf
 *.properties text
 *.java text
 
-# disalbe after a release
+# disable after a release
 # CHANGELOG.md merge=union
 
 src/main/resources/l10n/*.properties merge=union

AUTHORS

@@ -15,6 +15,7 @@ Andreas Rudert
 Anh Nghia Tran
 Antonio Ribeiro
 Arno Blouin
+avaucher
 Behrouz Javanmardi
 Bernd Kalbfuss
 Bernhard Tempel

CHANGELOG.md

@@ -8,30 +8,26 @@ Here, the categories "Changed" for added and changed functionality,
 
 We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`.
 
+
 ## [Unreleased]
 
 ### Changed
-- When [adding a new entry](http://help.jabref.org/en/BaseFrame#adding-a-new-entry), one can select "title" to create a full BibTeX entry based on a title.
-- When editing an article, the tab "Optional fields" now shows "ISSN".
-- When editing a book, the tab "Optional fields" now shows "ISBN".
-- When using "Copy citation (HTML)" and pasting into a text editor, plain text is always pasted.
-- When using the "Download from URL" functionality, one is not limited to http(s) URLs, but can, for instance, enter ftp URLs.
-- When using the "Look up full text documents" functionality, JabRef warns more explicitly about multiple requests.
-- The entry received from DOI does no longer contain the DOI as URL. Implements [#2417](https://github.com/JabRef/jabref/issues/2417).
-- We use following parameters for the JVM on Windows and OSX: `-XX:+UseG1GC -XX:+UseStringDeduplication -XX:StringTableSize=1000003`.
 
 ### Fixed
-- Fixed [#2391](https://github.com/JabRef/jabref/issues/2391): Clicking on "Get Fulltext" button sets links correctly for the entry being edited.
-- The integrity check now determines the set of BibLaTeX-only fields differently. Fixes [#2390](https://github.com/JabRef/jabref/issues/2390).
-- We fixed an issue where groups containing brackets were not working properly. Fixes [#2394](https://github.com/JabRef/jabref/issues/2394).
-- We fixed issues with the [timestamp](http://help.jabref.org/en/TimeStamp) field. However, clearing with the clear button is not possible if timestamp format does not match the current settings. Fixes [#2403](https://github.com/JabRef/jabref/issues/2403).
-- Fixes [#2406](https://github.com/JabRef/jabref/issues/2406) so that the integrity check filter works again
-- Closing of subtrees in the groups panel using "close subtree" is working again. Fixes [#2319](https://github.com/JabRef/jabref/issues/2319).
-- The proxy settings are now also applied to HTTPS connections. Fixes [#2249](https://github.com/JabRef/jabref/issues/2249).
+- The formatter for normalizing pages now also can treat ACM pages such as `2:1--2:33`.
+- Backslashes in content selectors are now correctly escaped. Fixes [#2426](https://github.com/JabRef/jabref/issues/2426).
+- Non-ISO timestamp settings prevented the opening of the entry editor (see [#2447](https://github.com/JabRef/jabref/issues/2447))
+- When pressing <kbd>Ctrl</kbd> + <kbd>F</kbd> and the searchbar is already focused the text will be selected.
+- LaTeX symbols are now displayed as Unicode for the author column in the main table. Fixes [#2458](https://github.com/JabRef/jabref/issues/2458).
+
+### Removed
+
+
+
+
 
 
 
-### Removed
 
 
 
@@ -72,6 +68,31 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
+
+
+
+
+## [3.8.1] – 2016-12-24
+
+### Changed
+- When [adding a new entry](https://help.jabref.org/en/BaseFrame#adding-a-new-entry), one can select "title" to create a full BibTeX entry based on a title.
+- When [editing](https://help.jabref.org/en/EntryEditor) an article, the tab "Optional fields" now shows "ISSN".
+- When editing a book, the tab "Optional fields" now shows "ISBN".
+- When using "Copy citation (HTML)" and pasting into a text editor, plain text is always pasted.
+- When using the "Download from URL" functionality, one is not limited to http(s) URLs, but can, for instance, enter ftp URLs.
+- When using the "Look up full text documents" functionality, JabRef warns more explicitly about multiple requests.
+- The entry received from DOI does no longer contain the DOI as URL. Implements [#2417](https://github.com/JabRef/jabref/issues/2417).
+- We use following parameters for the JVM on Windows and OSX: `-XX:+UseG1GC -XX:+UseStringDeduplication -XX:StringTableSize=1000003`.
+
+### Fixed
+- Clicking on "Get Fulltext" button sets links correctly for the entry being edited. Fixes [#2391](https://github.com/JabRef/jabref/issues/2391).
+- The [integrity check](https://help.jabref.org/en/CheckIntegrity) now determines the set of BibLaTeX-only fields differently. Fixes [#2390](https://github.com/JabRef/jabref/issues/2390).
+- The integrity check filter works again. Fixes [#2406](https://github.com/JabRef/jabref/issues/2406).
+- The [ArXiv fetcher](http://help.jabref.org/en/arXiv) also accepts identifiers that include the "arXiv:" prefix. Fixes [#2427](https://github.com/JabRef/jabref/issues/2427).
+- We fixed an issue where groups containing brackets were not working properly. Fixes [#2394](https://github.com/JabRef/jabref/issues/2394).
+- Closing of subtrees in the groups panel using "close subtree" is working again. Fixes [#2319](https://github.com/JabRef/jabref/issues/2319).
+- We fixed issues with the [timestamp](http://help.jabref.org/en/TimeStamp) field. However, clearing with the clear button is not possible if timestamp format does not match the current settings. Fixes [#2403](https://github.com/JabRef/jabref/issues/2403).
+- The proxy settings are now also applied to HTTPS connections. Fixes [#2249](https://github.com/JabRef/jabref/issues/2249).
 
 
 ## [3.8] – 2016-12-16
@@ -722,7 +743,8 @@ 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/v3.8...HEAD
+[unreleased]: https://github.com/JabRef/jabref/compare/v3.8.1...HEAD
+[3.8.1]: https://github.com/JabRef/jabref/compare/v3.8...v3.8.1
 [3.8]: https://github.com/JabRef/jabref/compare/v3.7...v3.8
 [3.7]: https://github.com/JabRef/jabref/compare/v3.6...v3.7
 [3.6]: https://github.com/JabRef/jabref/compare/v3.5...v3.6

build.gradle

@@ -43,8 +43,8 @@ apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "net.sf.jabref"
-version = "3.8.1-dev"
-project.ext.threeDotVersion = "3.8.0.1"
+version = "3.8.2-dev"
+project.ext.threeDotVersion = "3.8.1.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Tue Dec 06 07:56:11 CET 2016
+#Thu Jan 05 09:52:38 CET 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.3-bin.zip

gradlew

@@ -155,13 +155,14 @@ if $cygwin ; then
 fi
 
 # Escape application args
-for s in "${@}" ; do
-    s=\"$s\"
-    APP_ARGS=$APP_ARGS" "$s
-done
+save ( ) {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=$(save "$@")
 
 # Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- "$DEFAULT_JVM_OPTS" "$JAVA_OPTS" "$GRADLE_OPTS" "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
 # by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
 if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then

src/main/java/net/sf/jabref/JabRefExecutorService.java

@@ -8,8 +8,6 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 
-import net.sf.jabref.gui.undo.UndoableInsertEntry;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -18,7 +16,7 @@
  */
 public class JabRefExecutorService implements Executor {
 
-    private static final Log LOGGER = LogFactory.getLog(UndoableInsertEntry.class);
+    private static final Log LOGGER = LogFactory.getLog(JabRefExecutorService.class);
 
     public static final JabRefExecutorService INSTANCE = new JabRefExecutorService();
 

src/main/java/net/sf/jabref/gui/IconTheme.java

@@ -32,12 +32,12 @@ public class IconTheme {
     /* Colors */
 
     // JabRef's default colors
-    //public static final Color DEFAULT_COLOR = new Color(79, 95, 143); // The purple color of the logo
-    //public static final Color DEFAULT_DISABLED_COLOR = new Color(200, 200, 200);
+    public static final Color DEFAULT_COLOR = new Color(79, 95, 143); // The purple color of the logo
+    public static final Color DEFAULT_DISABLED_COLOR = new Color(200, 200, 200);
 
     // Christmas edition
-    public static final Color DEFAULT_COLOR = new Color(0x155115);
-    public static final Color DEFAULT_DISABLED_COLOR = new Color(0x990000);
+    //public static final Color DEFAULT_COLOR = new Color(0x155115);
+    //public static final Color DEFAULT_DISABLED_COLOR = new Color(0x990000);
 
 
     public static final int DEFAULT_SIZE = 24;

src/main/java/net/sf/jabref/gui/autocompleter/AutoCompleteListener.java

@@ -164,7 +164,7 @@ private boolean atEndOfWord(JTextComponent textField) {
      * @param wordSeperatorTyped indicates whether the user has typed a white space character or a
      */
     private void setUnmodifiedTypedLetters(JTextComponent comp, boolean lastBeginningContainsTypedCharacter,
-            boolean wordSeperatorTyped) {
+                                           boolean wordSeperatorTyped) {
         if (lastBeginning == null) {
             LOGGER.debug("No last beginning found");
             // There was no previous input (if the user typed a word, where no autocompletion is available)
@@ -268,14 +268,15 @@ public void keyTyped(KeyEvent e) {
         }
 
         // don't do auto completion inside words
-        if (!atEndOfWord((JTextComponent) e.getSource())) {
+        if (!(e.getSource() instanceof JTextComponent) || !atEndOfWord((JTextComponent) e.getSource())) {
             return;
         }
 
         if ((e.getModifiers() | InputEvent.SHIFT_MASK) == InputEvent.SHIFT_MASK) {
             // plain key or SHIFT + key is pressed, no handling of CTRL+key,  META+key, ...
             if (Character.isLetter(ch) || Character.isDigit(ch)
                     || (Character.isWhitespace(ch) && completer.isSingleUnitField())) {
+
                 JTextComponent comp = (JTextComponent) e.getSource();
 
                 if (toSetIn == null) {

src/main/java/net/sf/jabref/gui/date/DatePickerButton.java

@@ -79,6 +79,9 @@ public JComponent getDatePicker() {
      * @param dateString
      */
     public void updateDatePickerDate(String dateString) {
+        // unregister DateChangeListener before update to prevent circular calls resulting in IllegalStateExceptions
+        datePicker.removeDateChangeListener(this);
+
         if(dateString!=null && !dateString.isEmpty()) {
             try {
                 datePicker.setDate(LocalDate.parse(dateString, dateTimeFormatter));
@@ -87,5 +90,7 @@ public void updateDatePickerDate(String dateString) {
                         + "Clear button in calender popup will not work.");
             }
         }
+
+        datePicker.addDateChangeListener(this);
     }
 }

src/main/java/net/sf/jabref/gui/maintable/MainTableColumn.java

@@ -104,7 +104,7 @@ public Object getColumnValue(BibEntry entry) {
         String result = content.orElse(null);
 
         if (isNameColumn) {
-            result = MainTableNameFormatter.formatName(result);
+            result = MainTableNameFormatter.formatName(toUnicode.format(result));
         }
 
         if (result != null) {

src/main/java/net/sf/jabref/gui/search/GlobalSearchBar.java

@@ -290,8 +290,8 @@ public void endSearch() {
     public void focus() {
         if (!searchField.hasFocus()) {
             searchField.requestFocus();
-            searchField.selectAll();
         }
+        searchField.selectAll();
     }
 
     private void clearSearch(BasePanel currentBasePanel) {

src/main/java/net/sf/jabref/logic/exporter/MetaDataSerializer.java

@@ -61,7 +61,7 @@ private static Map<String, String> serializeMetaData(Map<String, List<String>> s
             StringBuilder stringBuilder = new StringBuilder();
             for (String dataItem : metaItem.getValue()) {
                 stringBuilder.append(StringUtil.quote(dataItem, MetaData.SEPARATOR_STRING, MetaData.ESCAPE_CHARACTER)).append(MetaData.SEPARATOR_STRING);
-
+                
                 //in case of save actions, add an additional newline after the enabled flag
                 if (metaItem.getKey().equals(MetaData.SAVE_ACTIONS)
                         && (FieldFormatterCleanups.ENABLED.equals(dataItem)

src/main/java/net/sf/jabref/logic/formatter/bibtexfields/NormalizePagesFormatter.java

@@ -10,20 +10,21 @@
 import com.google.common.base.Strings;
 
 /**
- * This class includes sensible defaults for consistent formatting of BibTex page numbers.
+ * This class includes sensible defaults for consistent formatting of BibTeX page numbers.
  *
- * From BibTex manual:
+ * From BibTeX manual:
  * One or more page numbers or range of numbers, such as 42--111 or 7,41,73--97 or 43+
  * (the '+' in this last example indicates pages following that don't form a simple range).
  * To make it easier to maintain Scribe-compatible databases, the standard styles convert
  * a single dash (as in 7-33) to the double dash used in TEX to denote number ranges (as in 7--33).
  */
 public class NormalizePagesFormatter implements Formatter {
 
-    private static final Pattern PAGES_DETECT_PATTERN = Pattern.compile("\\A(\\d+)(?:-{1,2}(\\d+))?\\Z");
+    // "startpage" and "endpage" are named groups. See http://stackoverflow.com/a/415635/873282 for a documentation
+    private static final Pattern PAGES_DETECT_PATTERN = Pattern.compile("\\A(?<startpage>(\\d+:)?\\d+)(?:-{1,2}(?<endpage>(\\d+:)?\\d+))?\\Z");
 
-    private static final String REJECT_LITERALS = "[^a-zA-Z0-9,\\-\\+,]";
-    private static final String PAGES_REPLACE_PATTERN = "$1--$2";
+    private static final String REJECT_LITERALS = "[^a-zA-Z0-9,\\-\\+,:]";
+    private static final String PAGES_REPLACE_PATTERN = "${startpage}--${endpage}";
     private static final String SINGLE_PAGE_REPLACE_PATTERN = "$1";
 
 
@@ -66,9 +67,9 @@ public String format(String value) {
         cleanValue = cleanValue.replaceAll("\u2013|\u2014", "-").replaceAll(REJECT_LITERALS, "");
         // try to find pages pattern
         Matcher matcher = PAGES_DETECT_PATTERN.matcher(cleanValue);
-        if(matcher.matches()) {
+        if (matcher.matches()) {
             // replace
-            if(Strings.isNullOrEmpty(matcher.group(2))) {
+            if (Strings.isNullOrEmpty(matcher.group("endpage"))) {
                 return matcher.replaceFirst(SINGLE_PAGE_REPLACE_PATTERN);
             } else {
                 return matcher.replaceFirst(PAGES_REPLACE_PATTERN);

src/main/java/net/sf/jabref/logic/importer/fetcher/ArXiv.java

@@ -107,8 +107,9 @@ private Optional<ArXivEntry> searchForEntry(String searchQuery) throws FetcherEx
     }
 
     private Optional<ArXivEntry> searchForEntryById(String identifier) throws FetcherException {
+        identifier = identifier.replaceAll("(?i)arxiv:", "");
         List<ArXivEntry> entries = queryApi("", Collections.singletonList(identifier), 0, 1);
-        if (entries.size() == 1) {
+        if (entries.size() >= 1) {
             return Optional.of(entries.get(0));
         } else {
             return Optional.empty();

src/main/java/net/sf/jabref/logic/importer/fetcher/DBLPFetcher.java

@@ -26,7 +26,7 @@
  */
 public class DBLPFetcher implements SearchBasedParserFetcher {
 
-    private static final String BASIC_SEARCH_URL = "http://www.dblp.org/search/api/";
+    private static final String BASIC_SEARCH_URL = "http://dblp.org/search/publ/api";
 
     private final ImportFormatPreferences importFormatPreferences;
 

src/main/java/net/sf/jabref/logic/importer/util/MetaDataParser.java

@@ -16,6 +16,7 @@
 import net.sf.jabref.model.metadata.ContentSelectors;
 import net.sf.jabref.model.metadata.MetaData;
 import net.sf.jabref.model.metadata.SaveOrderConfig;
+import net.sf.jabref.model.strings.StringUtil;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -53,7 +54,7 @@ public static MetaData parse(MetaData metaData, Map<String, String> data, Charac
                 metaData.setUserFileDirectory(user, getSingleItem(value));
                 continue;
             } else if(entry.getKey().startsWith(MetaData.SELECTOR_META_PREFIX)){
-                metaData.addContentSelector(ContentSelectors.parse(entry.getKey().substring(MetaData.SELECTOR_META_PREFIX.length()), entry.getValue()));
+                metaData.addContentSelector(ContentSelectors.parse(entry.getKey().substring(MetaData.SELECTOR_META_PREFIX.length()), StringUtil.unquote(entry.getValue(), MetaData.ESCAPE_CHARACTER)));
                 continue;
             }
 

src/main/resources/l10n/Menu_ru.properties

@@ -1,5 +1,5 @@
 #!
-#! created/edited by Popeye version 0.55 (github.com/JabRef/popeye)
+#! created/edited by wuw (30/12/16)
 #! encoding:UTF-8
 
 Abbreviate_journal_names_(ISO)=Сокращения_названий_журналов_(ISO)
@@ -105,7 +105,7 @@ Decrease_table_font_size=Уменьшить_шрифт_в_таблице
 Forward=Вперед
 Back=Назад
 
-Look_up_full_text_documents=
+Look_up_full_text_documents=Поиск_цитируемых_документов
 Set/clear/rename_fields=Задать/очистить/переименовать_поля
 
 Resolve_duplicate_BibTeX_keys=Разрешение_дубликатов_ключей_BibTeX
@@ -119,7 +119,7 @@ Find_unlinked_files...=Найти_несвязанные_файлы...
 Hide/show_toolbar=Показать/скрыть_панель_инструментов
 
 Fork_me_on_GitHub=Моя_ветка_на_GitHub
-Save_selected_as_plain_BibTeX...=Сохранить_выбранное_как_неформатированный_BibTeX_...
+Save_selected_as_plain_BibTeX...=Сохранить_выбранное_как_неформатированный_BibTeX...
 
 Groups=Группы
 Delete_entry=Удалить_запись
@@ -133,7 +133,7 @@ Blog=Блог
 JabRef_resources=Ресурсы_JabRef
 Development_version=Версия_для_разработчиков
 View_change_log=Просмотр_журнала_изменений
-Copy_BibTeX_key_and_link=
-Copy_DOI_url=
+Copy_BibTeX_key_and_link=Копировать_ключ_BibTeX_и_ссылку
+Copy_DOI_url=Копировать_URL-адрес_DOI
 
-Copy_citation=
+Copy_citation=Копировать_цитату

src/test/java/net/sf/jabref/logic/exporter/BibtexDatabaseWriterTest.java

@@ -1,5 +1,7 @@
 package net.sf.jabref.logic.exporter;
 
+import java.io.IOException;
+import java.io.StringReader;
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
@@ -560,4 +562,20 @@ public void writeEntriesInOriginalOrderWhenNoSaveOrderConfigIsSetInMetadata() th
                 , session.getStringValue());
     }
 
+    @Test
+    public void roundtripWithContentSelectorsAndUmlauts() throws IOException, SaveException {
+        String fileContent = "% Encoding: UTF-8" + OS.NEWLINE + OS.NEWLINE + "@Comment{jabref-meta: selector_journal:Test {\\\\\"U}mlaut;}" + OS.NEWLINE;
+        Charset encoding = StandardCharsets.UTF_8;
+
+        ParserResult firstParse = new BibtexParser(importFormatPreferences).parse(new StringReader(fileContent));
+
+        SavePreferences preferences = new SavePreferences().withEncoding(encoding).withSaveInOriginalOrder(true);
+        BibDatabaseContext context = new BibDatabaseContext(firstParse.getDatabase(), firstParse.getMetaData(),
+                new Defaults(BibDatabaseMode.BIBTEX));
+
+        StringSaveSession session = databaseWriter.savePartOfDatabase(context, firstParse.getDatabase().getEntries(), preferences);
+
+        assertEquals(fileContent, session.getStringValue());
+    }
+
 }