Merge pull request #1 from JabRef/master

Updating my repo

.gitignore

@@ -12,7 +12,6 @@ buildant/
 build.number
 classes/
 user.properties
-src/main/resources/resource/build.properties
 src/main/resources/windows/nsis/dist/
 
 # Gradle

CHANGELOG

@@ -1,4 +1,11 @@
 [master]
+    - All duplicate whitespaces / tabs / newlines are now removed from non-multiline fields
+    - Fixed a bug in the IEEEXploreFetcher
+    - Replaced some deprecated DefaultFormBuilder with FormBuilder
+    - Added more characters to HTML/Unicode converter
+    - Feature: Push citations to Texmaker (SF: #318, #582)
+    - Case changers improved to honor words (not yet more than single words) within {}
+    - Feature: Added converters from HTML and Unicode to LaTeX on right click in text fields (#191)
     - Fixed bug 1282 (SourceForge) related to backslashes duplication.
     - Feature: Add an option to the FileList context menu to delete an associated file from the file system
     - Breaking API change: String[] is replaced by List<String> in BibtexEntryType
@@ -8,19 +15,28 @@
     - Feature: When pasting a Google search URL, meta data will be automatically stripped before insertion.
     - No longer write JabRef version to BibTex file header.
     - No longer add blank lines inside a bibtex entry
+    - Feature: PDF auto download from ACS, arXiv, ScienceDirect, SpringerLink, and Google Scholar
     - Perform syntax improvements enabled by Java 1.7+ (diamond operator, try-with-resources)
     - List of authors is now auto generated `scripts/generate-authors.sh` and inserted into L10N About.html
     - Remove Mr.DLib support as MR.DLib will be shut down in 2015
     - Streamline logging API: Replace usages of java.util.logging with commons.logging
     - BREAKING: Remove plugin functionality.
     - Fixes Bug#1297: No console message on closing.
     - Fix bug #1285: Editing position is not lost on saving
+    - Fix bug #194: JabRef starts again on Win XP and Win Vista
     - Remove support for custom icon themes. The user has to use the default one.
     - Bugfix: Tooltips are now shown for the #-field when the bibtex entry is incomplete.
     - Solved feature request #767: New subdatabase based on AUX file (biblatex)
     - Fixes GH Bug #173: Personal journal abbreviation list is not loaded twice
     - Bugfix: Preview of external journal abbreviation list now displays the correct list
+    - Feature: DOItoBibTeX fetcher now also handles HTTP URLs
+    - Feature: "Normalize to BibTeX name format" also removes newlines
+    - Tweak of preference defaults: Autolink requires that the filename starts with the given BibTeX key and the default filename patterns is key followed by title
+    - Remove support to the move-to-SysTray action
+    - Feature: case changers now leave protected areas (enclosed with curly brakets) alone
+    - Fix #223: Window is displayed in visible area even when having multiple screens
 [dev_2.11]
+    - Backports from 2.80: Fix bug #194: JabRef starts again on Win XP and Win Vista
     - Backports from 2.80: Fixes #103: JDialog for auto set links is openend and closed correctly
 2.11 beta 4
     - Add of Persian localization (by Behrouz Javanmardi)

CONTRIBUTING.md

@@ -59,6 +59,8 @@ gets
  *  Copyright (C) 2015 Stefan Jauch
 ```
 
+Please, **do not add yourself at `@authors`**.
+We have track this information in the header only.
 
 ### Write a good commit message
 See [good commit message] or [commit guidelines section of Pro Git].
@@ -76,6 +78,28 @@ In any case, describe the library at [external-libraries.txt](external-libraries
 We need that information for our package maintainers (e.g., those of the [debian package](https://tracker.debian.org/pkg/jabref)).
 
 
+### When making an architectural decision
+In case you add a library or do mayor code rewrites, we ask you to document your decision.
+Recommended reading: http://www.infoq.com/articles/sustainable-architectural-design-decisions
+
+Template:
+```
+In the context of <use case/user story u>,
+facing <concern c>
+we decided for <option o>
+and neglected <other options>,
+to achieve <system qualities/desired consequences>,
+accepting <downside d/undesired consequences>.
+because <additional rationale>.
+```
+
+
+### When adding a new Localization.lang entry
+Run `python scripts/syncLang.py -s` to search for new untranslated strings.
+If everything is OK, run `python scripts/syncLang.py -s -u` to update `JabRef_en.properties`.
+
+
+
 ### Create a pull request
 Create a pull request on GitHub.
 For text inspirations, consider [How to write the perfect pull request](https://github.com/blog/1943-how-to-write-the-perfect-pull-request).

README.md

@@ -6,6 +6,7 @@
 [![License](https://img.shields.io/badge/license-GPLv2-blue.svg)](http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt)
 [![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![Donation](https://img.shields.io/badge/donate-paypal-orange.svg)](https://www.paypal.com/cgi-bin/webscr?item_name=JabRef+Bibliography+Manager&cmd=_donations&lc=US&currency_code=EUR&business=jabrefmail%40gmail.com)
+[![Flattr this git repo](http://api.flattr.com/button/flattr-badge-large.png)](https://flattr.com/submit/auto?user_id=koppor&url=https%3A%2F%2Fgithub.com%2FJabRef%2Fjabref&title=JabRef&language=Java&tags=github&category=software)
 
 This version is a development version. Features may not work as expected.
 

build.gradle

@@ -1,7 +1,7 @@
 import org.gradle.internal.os.OperatingSystem
 
 plugins {
-    id "eu.appsatori.fatjar" version "0.3"
+    id 'com.github.johnrengelman.shadow' version '1.2.2'
     id "edu.sc.seis.launch4j" version "1.1.4"
     id "com.github.kt3k.coveralls" version "2.4.0"
     id "edu.sc.seis.macAppBundle" version "2.1.1"
@@ -26,7 +26,7 @@ targetCompatibility = 1.8
 mainClassName = "net.sf.jabref.JabRefMain"
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '2.6'
+    gradleVersion = '2.7'
 }
 
 repositories {
@@ -63,18 +63,21 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.5.1-1'
 
     compile 'mysql:mysql-connector-java:5.1.36'
-    compile 'org.postgresql:postgresql:9.4-1201-jdbc41'
+    compile 'org.postgresql:postgresql:9.4-1203-jdbc42'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'net.java.dev.jna:jna:4.1.0'
+    compile 'net.java.dev.jna:jna:4.2.0'
 
     compile 'com.google.guava:guava:18.0'
 
     compile 'commons-logging:commons-logging:1.2'
 
     compile 'junit:junit:4.12'
+
+    compile 'org.jsoup:jsoup:1.8.3'
+    compile 'com.mashape.unirest:unirest-java:1.4.6'
 }
 
 sourceSets {
@@ -92,7 +95,7 @@ processResources {
                 "authors": new File('AUTHORS').readLines().findAll {!it.startsWith("#")}.join(", "))
     }
 
-    filesMatching("resource/build.properties") {
+    filesMatching("build.properties") {
         expand version: project.version
     }
 
@@ -189,11 +192,8 @@ format {
     //files = sourceSets.main.java
 }
 
-fatJar {
+shadowJar {
     classifier 'fat'
-    manifest {
-        attributes 'Main-Class': project.mainClassName
-    }
 }
 
 
@@ -229,9 +229,9 @@ launch4j {
     initialHeapSize = 32
     maxHeapSize = 512
 }
-createExe.dependsOn "fatJar"
+createExe.dependsOn "shadowJar"
 
-task releaseJar(dependsOn: "fatJar") {
+task releaseJar(dependsOn: "shadowJar") {
     group = 'JabRef - Release'
     description "Creates a Jar release."
 
@@ -338,3 +338,10 @@ task releaseSourceTar(type: Exec) {
         mkdir("$buildDir/releases")
     }
 }
+
+// workaround until https://issues.gradle.org/browse/GRADLE-2274 is resolved
+eclipseJdt << {
+    File f = file('.settings/org.eclipse.core.resources.prefs')
+    f.write('eclipse.preferences.version=1\n')
+    f.append('encoding/<project>=UTF-8')
+}

circle.yml

@@ -10,7 +10,7 @@ dependencies:
     - chmod +x launch4j/launch4j
     - wget http://nsis.sourceforge.net/mediawiki/images/5/54/WinShell.zip
     - unzip WinShell.zip
-    - sudo cp Plugins/x86-unicode/WinShell.dll /usr/share/nsis/Plugins/
+    - sudo cp Plugins/x86-ansi/WinShell.dll /usr/share/nsis/Plugins/
   override:
     - TERM=dumb ./gradlew dependencies
 

external-libraries.txt

@@ -49,6 +49,11 @@ Project: JGoodies Looks
 URL:     http://www.jgoodies.com/downloads/libraries/
 License: BSD
 
+Id:      com.mashape.unirest
+Project: Unirest for Java
+URL:     https://github.com/Mashape/unirest-java
+License: MIT
+
 Id:      mysql:mysql-connector-java
 Project: MySQL Connector/J
 URL:     http://www.mysql.de/downloads/connector/j/
@@ -79,6 +84,11 @@ Project: Apache PDFBox
 URL:     http://pdfbox.apache.org
 License: Apache 2.0
 
+Id:      org.jsoup:jsoup
+Project: jsoup
+URL:     https://github.com/jhy/jsoup/
+License: MIT
+
 Id:      org.openoffice:juh
 Project: OpenOffice.org
 URL:     http://www.openoffice.org/api/SDK

gradle/wrapper/gradle-wrapper.properties

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.6-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.7-all.zip

scripts/syncLang.py

@@ -2,7 +2,7 @@
 import os
 import re
 
-res_dir = "../src/main/resources/l10n"
+res_dir = "src/main/resources/l10n"
 
 keyFiles = {}
 

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

@@ -33,6 +33,7 @@
 import javax.swing.plaf.FontUIResource;
 
 import net.sf.jabref.gui.*;
+import net.sf.jabref.gui.nativeext.WindowsExtensions;
 import net.sf.jabref.importer.fetcher.EntryFetcher;
 import net.sf.jabref.importer.fetcher.EntryFetchers;
 import net.sf.jabref.logic.journals.Abbreviations;
@@ -61,12 +62,6 @@
 import net.sf.jabref.logic.logging.CacheableHandler;
 import net.sf.jabref.wizard.auximport.AuxCommandLine;
 
-import com.sun.jna.Native;
-import com.sun.jna.NativeLong;
-import com.sun.jna.Pointer;
-import com.sun.jna.WString;
-import com.sun.jna.ptr.PointerByReference;
-
 /**
  * JabRef Main Class - The application gets started here.
  */
@@ -150,10 +145,8 @@ public void start(String[] args) {
         Globals.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
 
         if (OS.WINDOWS) {
-            // Set application user model id so that pinning JabRef to the Win7/8 taskbar works
-            // Based on http://stackoverflow.com/a/1928830
-            JabRef.setCurrentProcessExplicitAppUserModelID("JabRef." + Globals.BUILD_INFO.getVersion());
-            //System.out.println(getCurrentProcessExplicitAppUserModelID());
+            // activate pin to taskbar for Windows 7 and up
+            WindowsExtensions.enablePinToTaskbar();
         }
 
         Vector<ParserResult> loaded = processArguments(args, true);
@@ -165,46 +158,12 @@ public void start(String[] args) {
 
         openWindow(loaded);
     }
-    
+
     private void setupLogHandlerForErrorConsole() {
         Globals.handler = new CacheableHandler();
         ((Jdk14Logger)LOGGER).getLogger().addHandler(Globals.handler);
     }
 
-    // Do not use this code in release version, it contains some memory leaks
-    public static String getCurrentProcessExplicitAppUserModelID()
-    {
-        final PointerByReference r = new PointerByReference();
-
-        if (JabRef.GetCurrentProcessExplicitAppUserModelID(r).longValue() == 0)
-        {
-            final Pointer p = r.getValue();
-
-            return p.getString(0, true); // here we leak native memory by lazyness
-        }
-        return "N/A";
-    }
-
-    private static void setCurrentProcessExplicitAppUserModelID(final String appID)
-    {
-        if (JabRef.SetCurrentProcessExplicitAppUserModelID(new WString(appID)).longValue() != 0) {
-            throw new RuntimeException("unable to set current process explicit AppUserModelID to: " + appID);
-        }
-    }
-
-    private static native NativeLong GetCurrentProcessExplicitAppUserModelID(PointerByReference appID);
-
-    private static native NativeLong SetCurrentProcessExplicitAppUserModelID(WString appID);
-
-
-    static
-    {
-        if (OS.WINDOWS) {
-            Native.register("shell32");
-        }
-    }
-
-
     public Vector<ParserResult> processArguments(String[] args, boolean initialStartup) {
 
         cli = new JabRefCLI(args);

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

@@ -76,7 +76,9 @@ public class JabRefPreferences {
     public static final String FONT_FAMILY = "fontFamily";
     public static final String WIN_LOOK_AND_FEEL = "lookAndFeel";
     public static final String LATEX_EDITOR_PATH = "latexEditorPath";
+    public static final String TEXSTUDIO_PATH = "TeXstudioPath";
     public static final String WIN_EDT_PATH = "winEdtPath";
+    public static final String TEXMAKER_PATH = "texmakerPath";
     public static final String SHOW_SHORT = "showShort";
     public static final String LANGUAGE = "language";
     public static final String NAMES_LAST_ONLY = "namesLastOnly";
@@ -291,7 +293,9 @@ public class JabRefPreferences {
     public static final String CITE_COMMAND_LED = "citeCommandLed";
     public static final String CITE_COMMAND_WIN_EDT = "citeCommandWinEdt";
     public static final String CITE_COMMAND_EMACS = "citeCommandEmacs";
+    public static final String CITE_COMMAND_TEXMAKER = "citeCommandTexmaker";
     public static final String CITE_COMMAND_VIM = "citeCommandVim";
+    public static final String CITE_COMMAND_TEXSTUDIO = "citeCommandTeXstudio";
     public static final String CITE_COMMAND = "citeCommand";
     public static final String EXTERNAL_JOURNAL_LISTS = "externalJournalLists";
     public static final String PERSONAL_JOURNAL_LIST = "personalJournalList";
@@ -312,7 +316,7 @@ public class JabRefPreferences {
     public static final String NUMERIC_FIELDS = "numericFields";
     public static final String DEFAULT_REG_EXP_SEARCH_EXPRESSION_KEY = "defaultRegExpSearchExpression";
     public static final String REG_EXP_SEARCH_EXPRESSION_KEY = "regExpSearchExpression";
-    public static final String USE_REG_EXP_SEARCH_KEY = "useRegExpSearch";
+    public static final String AUTOLINK_USE_REG_EXP_SEARCH_KEY = "useRegExpSearch";
     public static final String DB_CONNECT_USERNAME = "dbConnectUsername";
     public static final String DB_CONNECT_DATABASE = "dbConnectDatabase";
     public static final String DB_CONNECT_HOSTNAME = "dbConnectHostname";
@@ -438,6 +442,7 @@ private JabRefPreferences() {
             defaults.put(WIN_LOOK_AND_FEEL, "com.jgoodies.looks.windows.WindowsLookAndFeel");
             defaults.put(WIN_EDT_PATH, "C:\\Program Files\\WinEdt Team\\WinEdt\\WinEdt.exe");
             defaults.put(LATEX_EDITOR_PATH, "C:\\Program Files\\LEd\\LEd.exe");
+            defaults.put(TEXMAKER_PATH, "C:\\Program Files\\Texmaker\\texmaker.exe");
             defaults.put(EMACS_PATH, "emacsclient.exe");
             defaults.put(EMACS_23, true);
             defaults.put(EMACS_ADDITIONAL_PARAMETERS, "-n -e");
@@ -454,6 +459,8 @@ private JabRefPreferences() {
             defaults.put(EMACS_PATH, "gnuclient");
             defaults.put(EMACS_23, false);
             defaults.put(EMACS_ADDITIONAL_PARAMETERS, "-batch -eval");
+            defaults.put(TEXMAKER_PATH, "texmaker");
+
         }
         defaults.put(USE_PROXY, Boolean.FALSE);
         defaults.put(PROXY_HOSTNAME, "my proxy host");
@@ -737,7 +744,9 @@ private JabRefPreferences() {
         defaults.put(CITE_COMMAND_VIM, "\\cite");
         defaults.put(CITE_COMMAND_EMACS, "\\cite");
         defaults.put(CITE_COMMAND_WIN_EDT, "\\cite");
+        defaults.put(CITE_COMMAND_TEXSTUDIO, "\\cite");
         defaults.put(CITE_COMMAND_LED, "\\cite");
+        defaults.put(CITE_COMMAND_TEXMAKER, "\\cite");
         defaults.put(FLOAT_MARKED_ENTRIES, Boolean.TRUE);
 
         defaults.put(USE_NATIVE_FILE_DIALOG_ON_MAC, Boolean.FALSE);
@@ -751,7 +760,7 @@ private JabRefPreferences() {
         defaults.put(SEARCH_DIALOG_WIDTH, 650);
         defaults.put(SEARCH_DIALOG_HEIGHT, 500);
         defaults.put(SHOW_FILE_LINKS_UPGRADE_WARNING, Boolean.TRUE);
-        defaults.put(AUTOLINK_EXACT_KEY_ONLY, Boolean.TRUE);
+        defaults.put(AUTOLINK_EXACT_KEY_ONLY, Boolean.FALSE);
         defaults.put(NUMERIC_FIELDS, "mittnum;author");
         defaults.put(RUN_AUTOMATIC_FILE_SEARCH, Boolean.FALSE);
         defaults.put(USE_LOCK_FILES, Boolean.TRUE);
@@ -810,7 +819,7 @@ private JabRefPreferences() {
         String defaultExpression = "**/.*[bibtexkey].*\\\\.[extension]";
         defaults.put(DEFAULT_REG_EXP_SEARCH_EXPRESSION_KEY, defaultExpression);
         defaults.put(REG_EXP_SEARCH_EXPRESSION_KEY, defaultExpression);
-        defaults.put(USE_REG_EXP_SEARCH_KEY, Boolean.FALSE);
+        defaults.put(AUTOLINK_USE_REG_EXP_SEARCH_KEY, Boolean.FALSE);
         defaults.put(USE_IEEE_ABRV, Boolean.FALSE);
         defaults.put(USE_CONVERT_TO_EQUATION, Boolean.FALSE);
         defaults.put(USE_CASE_KEEPER_ON_SEARCH, Boolean.TRUE);