Merge branch 'ieeFix' of github.com:JabRef/jabref into ieeFix

* 'ieeFix' of github.com:JabRef/jabref: Fix the 'Attach file' dialog for starting on the user's main directory (#4996) Readme TOC (#4986) Fix icon size - the second (#4993) Fix background color of dialogs in dark mode (#4994) NPE-fix for Preferences/Ext-Prog/Settings for X/Browse (#4983) Bump richtextfx from 0.10.0 to 0.10.1 (#4989) Bump tika-core from 1.20 to 1.21 (#4984) Resize different fonts changing entry type (#4980) Extended Hints - Alternative to #4971 (#4975) Fix command line help text (#4979)
JabRef · May 26, 2019 · 62553de · 62553de
2 parents 2fbfaf4 + ef2add7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -56,14 +56,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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)
-- We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
+- We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584)
 - We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
 - We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 - We added an option on the Linked File Viewer to rename the attached file of an entry directly on the JabRef. [#4844](https://github.com/JabRef/jabref/issues/4844)
+- We added an option in the preference dialog box that allows user to enable helpful tooltips.[#3599](https://github.com/JabRef/jabref/issues/3599)
 
 
 ### Fixed
@@ -116,6 +117,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where an NullPointer exception was thrown when a referenced entry in an Open/Libre Office document was no longer present in the library. Now an error message with the reference marker of the missing entry is shown. [#4932](https://github.com/JabRef/jabref/issues/4932)
 - We fixed an issue where a database exception related to a missing timezone was too big. [#4827](https://github.com/JabRef/jabref/issues/4827)
 - We fixed an issue where the IEEE fetcher returned an error if no keywords were present in the result from the IEEE website [#4997](https://github.com/JabRef/jabref/issues/4997)
+- We fixed an issue where the command line help text had several errors, and arguments and descriptions have been rewritten to simplify and detail them better. [#4932](https://github.com/JabRef/jabref/issues/2016)
+- 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)
+
+
+
 
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.

diff --git a/README.md b/README.md
@@ -9,6 +9,14 @@ JabRef is an open-source, cross-platform citation and reference management tool
 Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research.
 ![main table](https://www.jabref.org/img/JabRef-4-0-MainTable.png)
 
+## Table of Contents
+
+- [Features](#features)
+- [Installation](#installation)
+- [Bug Reports, Suggestions, Other Feedback](#bug-reports-suggestions-other-feedback)
+- [Contributing](#contributing)
+- [Acknowledgements](#acknowledgements) / [License](#license)
+
 ## Features
 
 JabRef is a cross-platform application that works on Windows, Linux and Mac OS X. It is available free of charge and is actively developed.

diff --git a/build.gradle b/build.gradle
@@ -94,7 +94,7 @@ dependencies {
     compile 'org.apache.pdfbox:fontbox:2.0.15'
     compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
-    compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
+    compile group: 'org.apache.tika', name: 'tika-core', version: '1.21'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     compile 'org.bouncycastle:bcprov-jdk15on:1.61'
@@ -130,7 +130,7 @@ dependencies {
     compile 'de.saxsys:mvvmfx:1.8.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.10.0'
+    compile 'org.fxmisc.richtext:richtextfx:0.10.1'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
     compile 'com.jfoenix:jfoenix:8.0.8'

diff --git a/src/main/java/org/jabref/cli/JabRefCLI.java b/src/main/java/org/jabref/cli/JabRefCLI.java
@@ -4,7 +4,6 @@
 
 import org.jabref.Globals;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabaseMode;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.DefaultParser;
@@ -17,27 +16,25 @@
 
 public class JabRefCLI {
 
+    private static final int WIDTH = 100; // Number of characters per line
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefCLI.class);
     private final CommandLine cl;
     private List<String> leftOver;
 
     public JabRefCLI(String[] args) {
-
         Options options = getOptions();
-
         try {
             this.cl = new DefaultParser().parse(options, args);
             this.leftOver = cl.getArgList();
         } catch (ParseException e) {
             LOGGER.warn("Problem parsing arguments", e);
-
             this.printUsage();
             throw new RuntimeException();
         }
     }
 
     public static String getExportMatchesSyntax() {
-        return String.format("[%s]searchTerm,outputFile: %s[,%s]",
+        return String.format("[%s]searchTerm,outputFile:%s[,%s]",
                 Localization.lang("field"),
                 Localization.lang("file"),
                 Localization.lang("exportFormat"));
@@ -147,104 +144,97 @@ public String getExportMatches() {
         return cl.getOptionValue("exportMatches");
     }
 
-    public boolean isGenerateBibtexKeys() { return cl.hasOption("generateBibtexKeys"); }
+    public boolean isGenerateBibtexKeys() {
+        return cl.hasOption("generateBibtexKeys");
+    }
 
-    public boolean isAutomaticallySetFileLinks() { return cl.hasOption("automaticallySetFileLinks"); }
+    public boolean isAutomaticallySetFileLinks() {
+        return cl.hasOption("automaticallySetFileLinks");
+    }
 
     private Options getOptions() {
         Options options = new Options();
 
         // boolean options
-        options.addOption("v", "version", false, Localization.lang("Display version"));
-        options.addOption("n", "nogui", false, Localization.lang("No GUI. Only process command line options."));
         options.addOption("h", "help", false, Localization.lang("Display help on command line options"));
+        options.addOption("n", "nogui", false, Localization.lang("No GUI. Only process command line options"));
+        options.addOption("asfl", "automaticallySetFileLinks", false, Localization.lang("Automatically set file links"));
+        options.addOption("g", "generateBibtexKeys", false, Localization.lang("Regenerate all keys for the entries in a BibTeX file"));
         options.addOption("b", "blank", false, Localization.lang("Do not open any files at startup"));
+        options.addOption("v", "version", false, Localization.lang("Display version"));
         options.addOption(null, "debug", false, Localization.lang("Show debug level messages"));
 
         // The "-console" option is handled by the install4j launcher
-        options.addOption(null, "console", false, Localization.lang("Show console output (only necessary when the launcher is used)"));
+        options.addOption(null, "console", false, Localization.lang("Show console output (only when the launcher is used)"));
 
         options.addOption(Option.builder("i").
                 longOpt("import").
-                desc(String.format("%s: %s[,import format]", Localization.lang("Import file"),
-                        Localization.lang("filename"))).
+                desc(String.format("%s: '%s'", Localization.lang("Import file"), "-i library.bib")).
                 hasArg().
-                argName("FILE").build());
+                argName("FILE[,FORMAT]").
+                build());
 
-        options.addOption(
-                Option.builder("ib")
-                      .longOpt("importBibtex")
-                        .desc(String.format("%s: %s[,importBibtex bibtexString]", Localization.lang("Import") + " " + BibDatabaseMode.BIBTEX.getFormattedName(), Localization.lang("filename")))
-                      .hasArg()
-                      .argName("FILE")
-                      .build());
+        options.addOption(Option.builder().
+                longOpt("importToOpen").
+                desc(Localization.lang("Same as --import, but will be imported to the opened tab")).
+                hasArg().
+                argName("FILE[,FORMAT]").
+                build());
 
-        options.addOption(Option.builder("o").
-                longOpt("output").
-                desc(String.format("%s: %s[,export format]", Localization.lang("Output or export file"),
-                        Localization.lang("filename"))).
+        options.addOption(Option.builder("ib").
+                longOpt("importBibtex").
+                desc(String.format("%s: '%s'", Localization.lang("Import BibTeX"), "-ib @article{entry}")).
                 hasArg().
-                argName("FILE").
+                argName("BIBTEXT_STRING").
                 build());
 
-        options.addOption(Option.builder("x").
-                longOpt("prexp").
-                desc(Localization.lang("Export preferences to file")).
+        options.addOption(Option.builder("o").
+                longOpt("output").
+                desc(String.format("%s: '%s'", Localization.lang("Export an input to a file"), "-i db.bib -o db.htm,html")).
                 hasArg().
-                argName("FILE").
+                argName("FILE[,FORMAT]").
                 build());
 
-        options.addOption(Option.builder("p").
-                longOpt("primp").
-                desc(Localization.lang("Import preferences from file")).
+        options.addOption(Option.builder("m").
+                longOpt("exportMatches").
+                desc(String.format("%s: '%s'", Localization.lang("Matching"), "-i db.bib -m author=Newton,search.htm,html")).
                 hasArg().
-                argName("FILE").
+                argName("QUERY,FILE[,FORMAT]").
                 build());
-        options.addOption(Option.builder("d").
-                longOpt("prdef").
-                desc(Localization.lang("Reset preferences (key1,key2,... or 'all')")).
+
+        options.addOption(Option.builder("f").
+                longOpt("fetch").
+                desc(String.format("%s: '%s'", Localization.lang("Run fetcher"), "-f Medline/PubMed:cancer")).
                 hasArg().
-                argName("FILE").
+                argName("FETCHER:QUERY").
                 build());
 
         options.addOption(Option.builder("a").
                 longOpt("aux").
-                desc(String.format("%s: %s[.aux],%s[.bib]", Localization.lang("Sublibrary from AUX"),
-                        Localization.lang("file"),
-                        Localization.lang("new"))).
+                desc(String.format("%s: '%s'", Localization.lang("Sublibrary from AUX to BibTeX"), "-a thesis.aux,new.bib")).
                 hasArg().
-                argName("FILE").
+                argName("FILE[.aux],FILE[.bib] FILE").
                 build());
 
-        options.addOption(Option.builder().
-                longOpt("importToOpen").
-                desc(Localization.lang("Import to open tab")).
+        options.addOption(Option.builder("x").
+                longOpt("prexp").
+                desc(String.format("%s: '%s'", Localization.lang("Export preferences to a file"), "-x prefs.xml")).
                 hasArg().
-                argName("FILE").
+                argName("[FILE]").
                 build());
 
-        options.addOption(Option.builder("f").
-                longOpt("fetch").
-                desc(Localization.lang("Run fetcher, e.g. \"--fetch=Medline:cancer\"")).
+        options.addOption(Option.builder("p").
+                longOpt("primp").
+                desc(String.format("%s: '%s'", Localization.lang("Import preferences from a file"), "-p prefs.xml")).
                 hasArg().
-                argName("FILE").
+                argName("[FILE]").
                 build());
 
-        options.addOption(Option.builder("m").
-                longOpt("exportMatches").
-                desc(JabRefCLI.getExportMatchesSyntax()).
+        options.addOption(Option.builder("d").
+                longOpt("prdef").
+                desc(String.format("%s: '%s'", Localization.lang("Reset preferences"), "-d mainFontSize,newline' or '-d all")).
                 hasArg().
-                argName("FILE").
-                build());
-
-        options.addOption(Option.builder("g").
-                longOpt("generateBibtexKeys").
-                desc(Localization.lang("Regenerate all keys for the entries in a BibTeX file"))
-                .build());
-
-        options.addOption(Option.builder("asfl").
-                longOpt("automaticallySetFileLinks").
-                desc(Localization.lang("Automatically set file links")).
+                argName("KEY1[,KEY2][,KEYn] | all").
                 build());
 
         return options;
@@ -266,7 +256,7 @@ public void printUsage() {
         String footer = '\n' + importFormatsList + outFormatsList + "\nPlease report issues at https://github.com/JabRef/jabref/issues.";
 
         HelpFormatter formatter = new HelpFormatter();
-        formatter.printHelp("jabref [OPTIONS] [BIBTEX_FILE]\n\nOptions:", header, getOptions(), footer, true);
+        formatter.printHelp(WIDTH, "jabref [OPTIONS] [BIBTEX_FILE]\n\nOptions:", header, getOptions(), footer, true);
     }
 
     private String getVersionInfo() {

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
@@ -1032,3 +1032,7 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-font-size: 1.5em;
     -fx-padding: 1em 0em 1em 0em;
 }
+
+.dialog-pane {
+    -fx-background-color: -fx-control-inner-background;
+}
diff --git a/src/main/java/org/jabref/gui/actions/ActionFactory.java b/src/main/java/org/jabref/gui/actions/ActionFactory.java
@@ -4,7 +4,6 @@
 import java.lang.reflect.Method;
 import java.util.Objects;
 
-import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonBase;
 import javafx.scene.control.CheckMenuItem;
@@ -148,13 +147,9 @@ public ButtonBase configureIconButton(Action action, Command command, ButtonBase
         button.getStyleClass().add("icon-button");
 
         // For some reason the graphic is not set correctly, so let's fix this
+        // ToDO: Find a way to reuse JabRefIconView
         button.graphicProperty().unbind();
-        action.getIcon().ifPresent(icon -> {
-            // ToDO: Find a way to reuse JabRefIconView
-            Node graphicNode = icon.getGraphicNode();
-            graphicNode.setStyle(String.format("-fx-font-family: %s; -fx-font-size: %s;", icon.fontFamily(), "1em"));
-            button.setGraphic(graphicNode);
-        });
+        action.getIcon().ifPresent(icon -> button.setGraphic(icon.getGraphicNode()));
 
         return button;
     }

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.css b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.css
@@ -31,6 +31,16 @@
     -fx-background-color: -jr-icon-background-active;
 }
 
+#typeLabel .context-menu {
+    -fx-font-size: 0.92em;
+    -fx-font-weight: normal;
+}
+
+#typeLabel .tooltip {
+    -fx-font-size: 1em;
+    -fx-font-weight: normal;
+}
+
 .icon-button.narrow {
     -fx-padding: 0.1em;
 }

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.fxml b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.fxml
@@ -40,7 +40,14 @@
                     <Tooltip text="%Change entry type"/>
                 </tooltip>
             </Button>
-            <Button fx:id="generateCiteKeyButton" styleClass="narrow"/>
+            <Button styleClass="icon-button,narrow" onAction="#generateCiteKeyButton">
+                <graphic>
+                    <JabRefIconView glyph="MAKE_KEY"/>
+                </graphic>
+                <tooltip>
+                    <Tooltip text="%Generate BibTeX key"/>
+                </tooltip>
+            </Button>
             <Button fx:id="fetcherButton" styleClass="icon-button,narrow">
                 <graphic>
                     <JabRefIconView glyph="REFRESH"/>

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -27,8 +27,6 @@
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.GUIGlobals;
-import org.jabref.gui.actions.ActionFactory;
-import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.bibtexkeypattern.GenerateBibtexKeySingleAction;
 import org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTab;
 import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
@@ -87,7 +85,6 @@ public class EntryEditor extends BorderPane {
     @FXML private Button typeChangeButton;
     @FXML private Button fetcherButton;
     @FXML private Label typeLabel;
-    @FXML private Button generateCiteKeyButton;
 
     private final EntryEditorPreferences preferences;
     private final DialogService dialogService;
@@ -261,6 +258,12 @@ private void deleteEntry() {
         panel.delete(entry);
     }
 
+    @FXML
+    void generateCiteKeyButton() {
+        GenerateBibtexKeySingleAction action = new GenerateBibtexKeySingleAction(getEntry(), databaseContext, dialogService, preferences, undoManager);
+        action.execute();
+    }
+
     @FXML
     private void navigateToPreviousEntry() {
         panel.selectPreviousEntry();
@@ -387,13 +390,6 @@ private void setupToolBar() {
             fetcherMenu.getItems().add(fetcherMenuItem);
         }
         fetcherButton.setOnMouseClicked(event -> fetcherMenu.show(fetcherButton, Side.RIGHT, 0, 0));
-
-        // Configure cite key button
-        new ActionFactory(preferences.getKeyBindings())
-                .configureIconButton(
-                        StandardActions.GENERATE_CITE_KEY,
-                        new GenerateBibtexKeySingleAction(getEntry(), databaseContext, dialogService, preferences, undoManager),
-                        generateCiteKeyButton);
     }
 
     private void fetchAndMerge(EntryBasedFetcher fetcher) {