Merge branch 'master' into fileChooserRefactor

* master:
  Fixed OO/LO manual connection dialog on Linux
  Removed thrown Exception declarations (JabRef#1673)
  Fix JabRef#1288 Newly opened bib-file is not focused (JabRef#1671)
  Refactor DB loading
  Fix OutOfBoundsException when importing multiple entries in medline format (JabRef#1611)
  Removed the possibility to auto show or hide the groups interface (JabRef#1668)
  Add test to describe workaround for JabRef#1633
  Fixed JabRef#1643: Searching with double quotes in a specific field ignores the last character
  fix build
  Fixes JabRef#1554: JabRefFrame is set as owner for ImportInspectionDialog
  Fixed most of the ErrorProne warnings
  Replaced output of getResolvedField to Optional<String> (JabRef#1650)
  PushToApplication cleanup and refactoring (JabRef#1659)
  Replaced Object with appropriate class where possible (JabRef#1660)
  Replaced some array return types (JabRef#1661)
  Fix XMP test
  Localization
  Moved the main part of XMPUtil to jabref.XMPUtilMain and injected a b… (JabRef#1642)
  Made possible to make the OO/LO panel a bit more narrow (JabRef#1652)
  French localization: Jabref_fr: empty strings + some cleaning

CHANGELOG.md

@@ -38,9 +38,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Fixed [#1321](https://github.com/JabRef/jabref/issues/1321): LaTeX commands in fields not displayed in the list of references
 - Fixed [#1639](https://github.com/JabRef/jabref/issues/1639): Google Scholar fetching works again.
 - Date fields in the BibLatex standard are now always formatted in the correct way, independent of the preferences
+- Fixed [#1554](https://github.com/JabRef/jabref/issues/1554): Import dialog is no longer hidden behind main window
+- Fixed [#1643](https://github.com/JabRef/jabref/issues/1643): Searching with double quotes in a specific field ignores the last character
+- Fixed [#1288](https://github.com/JabRef/jabref/issues/1288): Newly opened bib-file is not focused
+- Fixed [#1669](https://github.com/JabRef/jabref/issues/1669): Dialog for manual connection to OpenOffice/LibreOffice works again on Linux
+
 
 ### Removed
 - It is not longer possible to choose to convert HTML sub- and superscripts to equations
+- [#1610](https://github.com/JabRef/jabref/issues/1610) Removed the possibility to auto show or hide the groups interface
 
 
 
@@ -489,4 +495,4 @@ The changelog of 2.11 and versions before is maintained as [text file](https://g
 [3.1]: https://github.com/JabRef/jabref/compare/v3.0...v3.1
 [3.0]: https://github.com/JabRef/jabref/compare/v2.11.1...v3.0
 [dev_2.11]: https://github.com/JabRef/jabref/compare/v2.11.1...dev_2.11
-[2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1
+[2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1

build.gradle

@@ -47,7 +47,7 @@ install4j {
 }
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '2.14'
+    gradleVersion = '2.14.1'
 }
 
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Mon Jun 27 17:21:50 CEST 2016
+#Wed Aug 03 11:49:15 CEST 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.14-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.14.1-bin.zip

gradlew

@@ -6,12 +6,30 @@
 ##
 ##############################################################################
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
 
 APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
@@ -30,6 +48,7 @@ die ( ) {
 cygwin=false
 msys=false
 darwin=false
+nonstop=false
 case "`uname`" in
   CYGWIN* )
     cygwin=true
@@ -40,26 +59,11 @@ case "`uname`" in
   MINGW* )
     msys=true
     ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
 esac
 
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
 # Determine the Java command to use to start the JVM.
@@ -85,7 +89,7 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
     MAX_FD_LIMIT=`ulimit -H -n`
     if [ $? -eq 0 ] ; then
         if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then

gradlew.bat

@@ -8,14 +8,14 @@
 @rem Set local scope for the variables with windows NT shell
 if "%OS%"=="Windows_NT" setlocal
 
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
-
 set DIRNAME=%~dp0
 if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 

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

@@ -127,7 +127,7 @@ public boolean keywordGroupContains() throws ParseException {
     }
 
     @Benchmark
-    public boolean keywordGroupContainsWord() throws ParseException {
+    public boolean keywordGroupContainsWord() {
         return KeywordGroup.containsWord("testWord", "Some longer test string containing testWord the test word");
     }
 

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

@@ -41,7 +41,6 @@
 import net.sf.jabref.importer.OpenDatabaseAction;
 import net.sf.jabref.importer.ParserResult;
 import net.sf.jabref.logic.l10n.Localization;
-import net.sf.jabref.logic.preferences.LastFocusedTabPreferences;
 import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.Version;
 import net.sf.jabref.logic.util.VersionPreferences;
@@ -58,16 +57,25 @@ public class JabRefGUI {
 
     private static JabRefFrame mainFrame;
 
-    private final List<ParserResult> loaded;
+    private final List<ParserResult> bibDatabases;
     private final boolean isBlank;
-
     private final List<File> postponed = new ArrayList<>();
     private final List<ParserResult> failed = new ArrayList<>();
     private final List<ParserResult> toOpenTab = new ArrayList<>();
 
-    public JabRefGUI(List<ParserResult> loaded, boolean isBlank) {
-        this.loaded = loaded;
+    private String focusedFile;
+
+    public JabRefGUI(List<ParserResult> argsDatabases, boolean isBlank) {
+        this.bibDatabases = argsDatabases;
         this.isBlank = isBlank;
+
+        // passed file (we take the first one) should be focused
+        if (!argsDatabases.isEmpty()) {
+            focusedFile = argsDatabases.get(0).getFile().getAbsolutePath();
+        } else {
+            focusedFile = Globals.prefs.get(JabRefPreferences.LAST_FOCUSED);
+        }
+
         openWindow();
         JabRefGUI.checkForNewVersion(false);
     }
@@ -102,9 +110,8 @@ private void openWindow() {
         setLookAndFeel();
 
         // If the option is enabled, open the last edited databases, if any.
-        if (!isBlank && Globals.prefs.getBoolean(JabRefPreferences.OPEN_LAST_EDITED)
-                && (Globals.prefs.get(JabRefPreferences.LAST_EDITED) != null)) {
-            openLastEditedDatabase();
+        if (!isBlank && Globals.prefs.getBoolean(JabRefPreferences.OPEN_LAST_EDITED)) {
+            openLastEditedDatabases();
         }
 
         GUIGlobals.init();
@@ -114,19 +121,20 @@ private void openWindow() {
         LOGGER.debug("Initializing frame");
         JabRefGUI.mainFrame = new JabRefFrame();
 
-        // Add all loaded databases to the frame:
-        boolean first = true;
-        if (!loaded.isEmpty()) {
-            for (Iterator<ParserResult> i = loaded.iterator(); i.hasNext();) {
-                ParserResult pr = i.next();
+        // Add all bibDatabases databases to the frame:
+        boolean first = false;
+        if (!bibDatabases.isEmpty()) {
+            for (Iterator<ParserResult> parserResultIterator = bibDatabases.iterator(); parserResultIterator.hasNext();) {
+                ParserResult pr = parserResultIterator.next();
 
-                if (new LastFocusedTabPreferences(Globals.prefs).hadLastFocus(pr.getFile())) {
+                // Define focused tab
+                if (focusedFile != null && pr.getFile().getAbsolutePath().equals(focusedFile)) {
                     first = true;
                 }
 
                 if (pr.isInvalid()) {
                     failed.add(pr);
-                    i.remove();
+                    parserResultIterator.remove();
                 } else if (!pr.isPostponedAutosaveFound()) {
                     if (pr.toOpenTab()) {
                         // things to be appended to an opened tab should be done after opening all tabs
@@ -137,7 +145,7 @@ private void openWindow() {
                         first = false;
                     }
                 } else {
-                    i.remove();
+                    parserResultIterator.remove();
                     postponed.add(pr.getFile());
                 }
             }
@@ -177,7 +185,7 @@ private void openWindow() {
 
         if (Globals.prefs.getBoolean(JabRefPreferences.DISPLAY_KEY_WARNING_DIALOG_AT_STARTUP)) {
             int i = 0;
-            for (ParserResult pr : loaded) {
+            for (ParserResult pr : bibDatabases) {
                 ParserResultWarningDialog.showParserResultWarningDialog(pr, JabRefGUI.getMainFrame(), i++);
             }
         }
@@ -189,10 +197,10 @@ private void openWindow() {
         // in this version of JabRef.
         // Note that we have to check whether i does not go over getBasePanelCount().
         // This is because importToOpen might have been used, which adds to
-        // loaded, but not to getBasePanelCount()
+        // loadedDatabases, but not to getBasePanelCount()
 
-        for (int i = 0; (i < loaded.size()) && (i < JabRefGUI.getMainFrame().getBasePanelCount()); i++) {
-            ParserResult pr = loaded.get(i);
+        for (int i = 0; (i < bibDatabases.size()) && (i < JabRefGUI.getMainFrame().getBasePanelCount()); i++) {
+            ParserResult pr = bibDatabases.get(i);
             BasePanel panel = JabRefGUI.getMainFrame().getBasePanelAt(i);
             OpenDatabaseAction.performPostOpenActions(panel, pr, true);
         }
@@ -206,33 +214,43 @@ private void openWindow() {
             SwingUtilities.invokeLater(asp);
         }
 
-        if (!loaded.isEmpty()) {
+        if (!bibDatabases.isEmpty()) {
             new FocusRequester(JabRefGUI.getMainFrame().getCurrentBasePanel().getMainTable());
         }
     }
 
-    private void openLastEditedDatabase() {
-        // How to handle errors in the databases to open?
-        List<String> names = Globals.prefs.getStringList(JabRefPreferences.LAST_EDITED);
-        lastEdLoop: for (String name : names) {
-            File fileToOpen = new File(name);
+    private void openLastEditedDatabases() {
+        if (Globals.prefs.get(JabRefPreferences.LAST_EDITED) == null) {
+            return;
+        }
+
+        List<String> lastFiles = Globals.prefs.getStringList(JabRefPreferences.LAST_EDITED);
 
-            for (ParserResult pr : loaded) {
-                if ((pr.getFile() != null) && pr.getFile().equals(fileToOpen)) {
-                    continue lastEdLoop;
-                }
+        for (String fileName : lastFiles) {
+            File dbFile = new File(fileName);
+
+            // Already parsed via command line parameter, e.g., "jabref.jar somefile.bib"
+            if (isLoaded(dbFile) || !dbFile.exists()) {
+                continue;
             }
 
-            if (fileToOpen.exists()) {
-                ParserResult pr = OpenDatabaseAction.loadDatabaseOrAutoSave(name, false);
+            ParserResult parsedDatabase = OpenDatabaseAction.loadDatabaseOrAutoSave(fileName, false);
 
-                if (pr.isNullResult()) {
-                    LOGGER.error(Localization.lang("Error opening file") + " '" + fileToOpen.getPath() + "'");
-                } else {
-                    loaded.add(pr);
-                }
+            if (parsedDatabase.isNullResult()) {
+                LOGGER.error(Localization.lang("Error opening file") + " '" + dbFile.getPath() + "'");
+            } else {
+                bibDatabases.add(parsedDatabase);
+            }
+        }
+    }
+
+    private boolean isLoaded(File fileToOpen) {
+        for (ParserResult pr : bibDatabases) {
+            if (pr.getFile() != null && pr.getFile().equals(fileToOpen)) {
+                return true;
             }
         }
+        return false;
     }
 
     private void setLookAndFeel() {

src/main/java/net/sf/jabref/cli/ArgumentProcessor.java

@@ -51,15 +51,13 @@
 import org.apache.commons.logging.LogFactory;
 
 public class ArgumentProcessor {
+    private static final Log LOGGER = LogFactory.getLog(ArgumentProcessor.class);
 
     public enum Mode {
         INITIAL_START,
         REMOTE_START
     }
 
-
-    private static final Log LOGGER = LogFactory.getLog(ArgumentProcessor.class);
-
     private final JabRefCLI cli;
 
     private final List<ParserResult> parserResults;
@@ -230,7 +228,7 @@ private void doAuxImport(List<ParserResult> loaded) {
     private List<ParserResult> importAndOpenFiles() {
         List<ParserResult> loaded = new ArrayList<>();
         List<String> toImport = new ArrayList<>();
-        if (!cli.isBlank() && (cli.getLeftOver().length > 0)) {
+        if (!cli.isBlank() && (!cli.getLeftOver().isEmpty())) {
             for (String aLeftOver : cli.getLeftOver()) {
                 // Leftover arguments that have a "bib" extension are interpreted as
                 // BIB files to open. Other files, and files that could not be opened

src/main/java/net/sf/jabref/cli/JabRefCLI.java

@@ -15,6 +15,9 @@
 */
 package net.sf.jabref.cli;
 
+import java.util.Arrays;
+import java.util.List;
+
 import net.sf.jabref.Globals;
 import net.sf.jabref.logic.exporter.ExportFormats;
 import net.sf.jabref.logic.l10n.Localization;
@@ -32,7 +35,7 @@ public class JabRefCLI {
 
     private static final Log LOGGER = LogFactory.getLog(JabRefCLI.class);
 
-    private String[] leftOver;
+    private List<String> leftOver;
     private final CommandLine cl;
 
 
@@ -42,7 +45,7 @@ public JabRefCLI(String[] args) {
 
         try {
             this.cl = new DefaultParser().parse(options, args);
-            this.leftOver = cl.getArgs();
+            this.leftOver = Arrays.asList(cl.getArgs());
         } catch (ParseException e) {
             LOGGER.warn("Problem parsing arguments", e);
 
@@ -262,7 +265,7 @@ private String getVersionInfo() {
         return String.format("JabRef %s", Globals.BUILD_INFO.getVersion());
     }
 
-    public String[] getLeftOver() {
+    public List<String> getLeftOver() {
         return leftOver;
     }