Merge branch 'master' into xmlunit

* master:
  Remove obsolete wrapper task
  Added error dialog when setting invalid main file directory (#1921)
  Add filteringCharset = 'UTF-8' (#1945)
  Include https://github.com/grimes2
  Searchbar across all bib files instead each having its own (#1549)
  Some OO/LO cleanups (#1927)
  Update link
  Removed external dependency in logic (#1934)

Author: Siedlerchr

AUTHORS

@@ -79,6 +79,7 @@ Jörg Lenhard
 Jörg Wegner
 Jörg Zieren
 Jørgen Kvalsvik
+Jürgen Lange
 Kai Mindermann
 Koji Yokota
 Kolja Brix

CHANGELOG.md

@@ -12,6 +12,13 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- Implemented [#825](https://github.com/JabRef/jabref/issues/825): Search Bar across all bib files instead each having its own
+- Implemented [#573](https://github.com/JabRef/jabref/issues/573): Add key shortcut for global search (`ctrl+shift+f`, if the searchfield is empty it will be focused instead)
+- The search result Window will now show which entry belongs to which bib file
+- The search result Window will now remember its location
+- The search result Window won't stay on top anymore if the main Window is focused and will be present in the taskbar
+- The user can jump from the searchbar to the maintable  with `ctrl+enter`
+- Implemented [#573 (comment)](https://github.com/JabRef/jabref/issues/573#issuecomment-232284156): Added shortcut: closing the search result window with `ctrl+w`
 - Added integrity check for fields with BibTeX keys, e.g., `crossref` and `related`, to check that the key exists
 - [#1496](https://github.com/JabRef/jabref/issues/1496) Keep track of which entry a downloaded file belongs to
 - Made it possible to download multiple entries in one action
@@ -26,16 +33,25 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Fixed
 - Fixed selecting an entry out of multiple duplicates
+- Fixed [#617](https://github.com/JabRef/jabref/issues/617): `Enter` in global search opens the selected entry & `Enter` in search dialog window opens the selected entry
+- Entries in the SearchResultPanel will be shown correctly (Latex to Unicode)
+- Suggestions in the autocomplete will be shown correctly (Latex to Unicode)
+- Fixed: When searching the first match will be selected if the current selection is no match
+- Selecting an entry in the search result Window will now select the correct entry in the bib file
+- Entries in the SearchResultDialog are now converted to Unicode
+- Suggestions in the autocomplete (search) are now in Unicode
 - Fixed NullPointerException when opening search result window for an untitled database 
 - Fixed entry table traversal with Tab (no column traversal thus no double jump)
 - Fixed [#1757](https://github.com/JabRef/jabref/issues/1757): Crash after saving illegal argument in entry editor
 - Fixed [#1663](https://github.com/JabRef/jabref/issues/1663): Better multi-monitor support
 - Fixed [#1882](https://github.com/JabRef/jabref/issues/1882): Crash after saving illegal bibtexkey in entry editor
 - Fixed field `location` containing only city is not exported correctly to MS-Office 2007 xml format
 - Fixed field `key` field is not exported to MS-Office 2008 xml format
+- Fixed download files failed silently when an invalid directory is selected
 
 ### Removed
 - The non-supported feature of being able to define file directories for any extension is removed. Still, it should work for older databases using the legacy `ps` and `pdf` fields, although we strongly encourage using the `file` field. 
+- Automatic migration for the `evastar_pdf` field is removed.
 
 
 

CONTRIBUTING.md

@@ -101,4 +101,4 @@ You can add the prefix `[WIP]` to indicate that the pull request is not yet comp
 
 [commit guidelines section of Pro Git]: http://git-scm.com/book/en/Distributed-Git-Contributing-to-a-Project#Commit-Guidelines
 [good commit message]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
-[help documentation]: https://help.github.com/articles/using-pull-requests/
+[help documentation]: https://help.github.com/articles/about-pull-requests/

build.gradle

@@ -1,5 +1,7 @@
 import org.gradle.internal.os.OperatingSystem
 
+// to update the gradle wrapper, execute ./gradlew wrapper --gradle-version 3.0
+
 buildscript {
     repositories {
         maven {
@@ -46,11 +48,6 @@ install4j {
     installDir = file(project.ext.install4jDir)
 }
 
-task wrapper(type: Wrapper) {
-    gradleVersion = '2.14.1'
-}
-
-
 repositories {
     jcenter()
 }
@@ -154,6 +151,8 @@ processResources {
                 "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
                 "authors": new File('AUTHORS').readLines().findAll { !it.startsWith("#") }.join(", "),
                 "developers": new File('DEVELOPERS').readLines().findAll { !it.startsWith("#") }.join(", "))
+
+                filteringCharset = 'UTF-8'
     }
 
     filesMatching("resource/**/meta.xml") {

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

@@ -18,7 +18,7 @@
 import net.sf.jabref.Globals;
 import net.sf.jabref.JabRefException;
 import net.sf.jabref.MetaData;
-import net.sf.jabref.external.AutoSetLinks;
+import net.sf.jabref.gui.externalfiles.AutoSetLinks;
 import net.sf.jabref.gui.importer.fetcher.EntryFetcher;
 import net.sf.jabref.gui.importer.fetcher.EntryFetchers;
 import net.sf.jabref.logic.CustomEntryTypesManager;
@@ -47,6 +47,7 @@
 import net.sf.jabref.model.database.BibDatabaseMode;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.preferences.JabRefPreferences;
+import net.sf.jabref.preferences.SearchPreferences;
 import net.sf.jabref.shared.prefs.SharedDatabasePreferences;
 
 import org.apache.commons.logging.Log;
@@ -166,9 +167,10 @@ private boolean exportMatches(List<ParserResult> loaded) {
         BibDatabaseContext databaseContext = pr.getDatabaseContext();
         BibDatabase dataBase = pr.getDatabase();
 
+        SearchPreferences searchPreferences = new SearchPreferences(Globals.prefs);
         SearchQuery query = new SearchQuery(searchTerm,
-                Globals.prefs.getBoolean(JabRefPreferences.SEARCH_CASE_SENSITIVE),
-                Globals.prefs.getBoolean(JabRefPreferences.SEARCH_REG_EXP));
+                searchPreferences.isCaseSensitive(),
+                searchPreferences.isRegularExpression());
         List<BibEntry> matches = new DatabaseSearcher(query, dataBase).getMatches();
 
         //export matches

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

@@ -47,13 +47,6 @@
 import net.sf.jabref.collab.FileUpdateListener;
 import net.sf.jabref.collab.FileUpdatePanel;
 import net.sf.jabref.event.source.EntryEventSource;
-import net.sf.jabref.external.AttachFileAction;
-import net.sf.jabref.external.ExternalFileMenuItem;
-import net.sf.jabref.external.ExternalFileType;
-import net.sf.jabref.external.ExternalFileTypes;
-import net.sf.jabref.external.FindFullTextAction;
-import net.sf.jabref.external.SynchronizeFileField;
-import net.sf.jabref.external.WriteXMPAction;
 import net.sf.jabref.gui.actions.Actions;
 import net.sf.jabref.gui.actions.BaseAction;
 import net.sf.jabref.gui.actions.CleanupAction;
@@ -62,7 +55,16 @@
 import net.sf.jabref.gui.entryeditor.EntryEditor;
 import net.sf.jabref.gui.exporter.ExportToClipboardAction;
 import net.sf.jabref.gui.exporter.SaveDatabaseAction;
+import net.sf.jabref.gui.externalfiles.FindFullTextAction;
+import net.sf.jabref.gui.externalfiles.SynchronizeFileField;
+import net.sf.jabref.gui.externalfiles.WriteXMPAction;
+import net.sf.jabref.gui.externalfiletype.ExternalFileMenuItem;
+import net.sf.jabref.gui.externalfiletype.ExternalFileType;
+import net.sf.jabref.gui.externalfiletype.ExternalFileTypes;
 import net.sf.jabref.gui.fieldeditors.FieldEditor;
+import net.sf.jabref.gui.filelist.AttachFileAction;
+import net.sf.jabref.gui.filelist.FileListEntry;
+import net.sf.jabref.gui.filelist.FileListTableModel;
 import net.sf.jabref.gui.groups.GroupAddRemoveDialog;
 import net.sf.jabref.gui.groups.GroupSelector;
 import net.sf.jabref.gui.groups.GroupTreeNodeViewModel;
@@ -76,7 +78,6 @@
 import net.sf.jabref.gui.mergeentries.FetchAndMergeEntry;
 import net.sf.jabref.gui.mergeentries.MergeEntriesDialog;
 import net.sf.jabref.gui.plaintextimport.TextInputDialog;
-import net.sf.jabref.gui.search.SearchBar;
 import net.sf.jabref.gui.undo.CountingUndoManager;
 import net.sf.jabref.gui.undo.NamedCompound;
 import net.sf.jabref.gui.undo.UndoableChangeType;
@@ -105,6 +106,7 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.layout.Layout;
 import net.sf.jabref.logic.layout.LayoutHelper;
+import net.sf.jabref.logic.search.SearchQuery;
 import net.sf.jabref.logic.util.FileExtensions;
 import net.sf.jabref.logic.util.UpdateField;
 import net.sf.jabref.logic.util.io.FileBasedLock;
@@ -203,9 +205,10 @@ public class BasePanel extends JPanel implements ClipboardOwner, FileUpdateListe
 
     private final SidePaneManager sidePaneManager;
 
-    private final SearchBar searchBar;
     private ContentAutoCompleters autoCompleters;
 
+    private SearchQuery currentSearchQuery;
+
 
     public BasePanel(JabRefFrame frame, BibDatabaseContext bibDatabaseContext) {
         Objects.requireNonNull(frame);
@@ -217,17 +220,16 @@ public BasePanel(JabRefFrame frame, BibDatabaseContext bibDatabaseContext) {
         this.frame = frame;
         this.tableModel = new MainTableDataModel(getBibDatabaseContext());
 
-        searchBar = new SearchBar(this);
-
         setupMainPanel();
 
         setupActions();
 
-        Optional<File> file = bibDatabaseContext.getDatabaseFile();
+        this.getDatabase().registerListener(new SearchListener());
 
         // ensure that at each addition of a new entry, the entry is added to the groups interface
         this.bibDatabaseContext.getDatabase().registerListener(new GroupTreeListener());
 
+        Optional<File> file = bibDatabaseContext.getDatabaseFile();
         if (file.isPresent()) {
             // Register so we get notifications about outside changes to the file.
             try {
@@ -517,7 +519,8 @@ public void update() {
 
         actions.put(Actions.MERGE_ENTRIES, (BaseAction) () -> new MergeEntriesDialog(BasePanel.this));
 
-        actions.put(Actions.SEARCH, (BaseAction) searchBar::focus);
+        actions.put(Actions.SEARCH, (BaseAction) frame.getGlobalSearchBar()::focus);
+        actions.put(Actions.GLOBAL_SEARCH, (BaseAction) frame.getGlobalSearchBar()::performGlobalSearch);
 
         // The action for copying the selected entry's key.
         actions.put(Actions.COPY_KEY, (BaseAction) () -> copyKey());
@@ -1164,11 +1167,6 @@ public BibEntry newEntry(EntryType type) {
         return null;
     }
 
-    public SearchBar getSearchBar() {
-        return searchBar;
-    }
-
-
     private class GroupTreeListener {
 
         private final Runnable task = new Runnable() {
@@ -1271,6 +1269,21 @@ public void listen(EntryChangedEvent entryChangedEvent) {
         }
     }
 
+    /**
+     * Ensures that the results of the current search are updated when a new entry is inserted into the database
+     */
+    private class SearchListener {
+        @Subscribe
+        public void listen(EntryAddedEvent addedEntryEvent) {
+            frame.getGlobalSearchBar().performSearch();
+        }
+
+        @Subscribe
+        public void listen(EntryChangedEvent entryChangedEvent) {
+            frame.getGlobalSearchBar().performSearch();
+        }
+    }
+
 
     /**
      * This method is called from JabRefFrame when the user wants to create a new entry.
@@ -1475,7 +1488,6 @@ public void setupMainPanel() {
 
         setLayout(new BorderLayout());
         removeAll();
-        add(searchBar, BorderLayout.NORTH);
         add(splitPane, BorderLayout.CENTER);
 
         // Set up name autocompleter for search:
@@ -1509,7 +1521,7 @@ public void setupMainPanel() {
     }
 
     public void updateSearchManager() {
-        searchBar.setAutoCompleter(searchAutoCompleter);
+        frame.getGlobalSearchBar().setAutoCompleter(searchAutoCompleter);
     }
 
     private void instantiateSearchAutoCompleter() {
@@ -2412,4 +2424,12 @@ public Map<String, EntryEditor> getEntryEditors() {
     public BibDatabaseContext getDatabaseContext() {
         return bibDatabaseContext;
     }
+
+    public SearchQuery getCurrentSearchQuery() {
+        return currentSearchQuery;
+    }
+
+    public void setCurrentSearchQuery(SearchQuery currentSearchQuery) {
+        this.currentSearchQuery = currentSearchQuery;
+    }
 }

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

@@ -8,8 +8,8 @@
 import javax.swing.JLabel;
 
 import net.sf.jabref.Globals;
-import net.sf.jabref.external.ExternalFileType;
-import net.sf.jabref.external.ExternalFileTypes;
+import net.sf.jabref.gui.externalfiletype.ExternalFileType;
+import net.sf.jabref.gui.externalfiletype.ExternalFileTypes;
 import net.sf.jabref.gui.keyboard.EmacsKeyBindings;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.model.entry.FieldName;

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

@@ -157,6 +157,8 @@ public enum JabRefIcon {
         FORUM("\uf28c"), /* css: forum */
         FACEBOOK("\uf20c"), /* css: facebook */
         BLOG("\uf46b"), /* css: rss */
+        GLOBAL_SEARCH_ON("\uF1E7"), /* css: earth */
+        GLOBAL_SEARCH_OFF("\uF1E8"), /* css: earth-off */
         // STILL MISSING:
         GROUP_REGULAR("\uF4E6", Color.RED);