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

* upstream/master: (49 commits) improve styling of preferences side menu (#4556) Cleanup interfaces (#4553) Bump fontbox from 2.0.12 to 2.0.13 (#4552) Bump pdfbox from 2.0.12 to 2.0.13 (#4551) Bump wiremock from 2.19.0 to 2.20.0 (#4550) Fixes that renaming a group did not change the group name in the interface (#4549) Bump applicationinsights-logging-log4j2 from 2.2.1 to 2.3.0 (#4540) Bump antlr4-runtime from 4.7.1 to 4.7.2 (#4542) Bump applicationinsights-core from 2.2.1 to 2.3.0 (#4541) Bump antlr4 from 4.7.1 to 4.7.2 (#4543) Fix journal name "Astronomy Journal" to "Astronomical Journal" fix-for-issue-4489 (#4538) Sorting of read-status isn't working as expected #4521 (#4536) Add preselect last used export format in export to clipboard dialog (#4533) fixed 4365 put html in clipboard (#4519) [WIP] Convert Exporter Customization Dialog to javafx (#4394) Fixes #4437 (#4531) Bump checkstyle from 8.14 to 8.15 (#4528) Correct PNAS abbrev. (#4524) Create test (#4518) ...
JabRef · Dec 28, 2018 · 928fd8e · 928fd8e
2 parents 5004bbc + b936ba9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,11 +11,19 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
+  - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
+  - DOI/URL: General -> Optional
+  - Internal fields like ranking, read status and priority: Other -> General
+  - Moreover, empty deprecated fields are no longer shown
+- Added server timezone parameter when connecting to a shared database.
 - We updated the dialog for setting up general fields.
 - URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
+- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
+  Because of this change, the last-used cleanup operations were reset.
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
 - We added a button in the tab header which allows you to close the database with one click. https://github.com/JabRef/jabref/issues/494
@@ -28,15 +36,18 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀<kbd>alt</kbd> + <kbd>up/down</kbd>.
 - Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file.
 - Window state is saved on close and restored on start.
+- We made the MathSciNet fetcher more reliable.
+- We added the ISBN fetcher to the list of fetcher available under "Update with bibliographic information from the web" in the entry editor toolbar.
 - Files without a defined external file type are now directly opened with the default application of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
 - We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
 - We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
 - We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
-- We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl<kbd> + <kbd>E<kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
+- We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl</kbd> + <kbd>E</kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
 - We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
 - We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
+- We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
 
 
 
@@ -58,7 +69,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
 - We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
+- We improved the integrity check for page numbers. [#4113](https://github.com/JabRef/jabref/issues/4113) and [feature request in the forum](http://discourse.jabref.org/t/pages-field-allow-use-of-en-dash/1199)
 - We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
+- We fixed an issue where renaming a group did not change the group name in the interface. [#3189](https://github.com/JabRef/jabref/issues/3189)
 - We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
 - We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410
 - We fixed an issue where the number of entries matched was not updated correctly upon adding or removing an entry. [#3537](https://github.com/JabRef/jabref/issues/3537)
@@ -76,8 +89,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the list of XMP Exclusion fields in the preferences was not be saved [#4072](https://github.com/JabRef/jabref/issues/4072)
 - We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [koppor#328](https://github.com/koppor/jabref/issues/328)
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
-
-
+- We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
+- We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
 
 
 

diff --git a/build.gradle b/build.gradle
@@ -96,8 +96,8 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.12'
-    compile 'org.apache.pdfbox:fontbox:2.0.12'
+    compile 'org.apache.pdfbox:pdfbox:2.0.13'
+    compile 'org.apache.pdfbox:fontbox:2.0.13'
     compile 'org.apache.pdfbox:xmpbox:2.0.12'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
@@ -110,30 +110,30 @@ dependencies {
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"
 
-    compile 'io.github.java-diff-utils:java-diff-utils:2.2.0'
+    compile 'io.github.java-diff-utils:java-diff-utils:4.0'
     compile 'info.debatty:java-string-similarity:1.1.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
 
-    antlr4 'org.antlr:antlr4:4.7.1'
-    compile 'org.antlr:antlr4-runtime:4.7.1'
+    antlr4 'org.antlr:antlr4:4.7.2'
+    compile 'org.antlr:antlr4-runtime:4.7.2'
 
     compile 'mysql:mysql-connector-java:8.0.13'
 
     compile 'org.postgresql:postgresql:42.2.5'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:27.0-jre'
+    compile 'com.google.guava:guava:27.0.1-jre'
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.1'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.2'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
     compile 'com.jfoenix:jfoenix:8.0.7'
@@ -157,29 +157,30 @@ dependencies {
 
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.2.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.2.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
+
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.2'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.2'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.3.2'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.1'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.1'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.1'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.3.1'
     testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
-    testCompile 'org.mockito:mockito-core:2.23.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.19.0'
+    testCompile 'org.mockito:mockito-core:2.23.4'
+    testCompile 'com.github.tomakehurst:wiremock:2.20.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.1'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.1'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.3'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.14'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.15'
 }
 
 jacoco {

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -8,7 +8,6 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Locale;
-import java.util.Map;
 import java.util.Optional;
 import java.util.prefs.BackingStoreException;
 
@@ -459,8 +458,7 @@ private void importPreferences() {
             Globals.prefs.importPreferences(cli.getPreferencesImport());
             EntryTypes.loadCustomEntryTypes(Globals.prefs.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
                     Globals.prefs.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
-            Map<String, TemplateExporter> customExporters = Globals.prefs.customExports.getCustomExportFormats(Globals.prefs,
-                    Globals.journalAbbreviationLoader);
+            List<TemplateExporter> customExporters = Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationLoader);
             LayoutFormatterPreferences layoutPreferences = Globals.prefs
                     .getLayoutFormatterPreferences(Globals.journalAbbreviationLoader);
             SavePreferences savePreferences = Globals.prefs.loadForExportFromPreferences();

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
@@ -291,7 +291,6 @@
 .check-box > .box,
 .menu-button,
 .choice-box,
-.color-picker.split-button > .color-picker-label,
 .combo-box-base,
 .combo-box-base:editable > .arrow-button {
     -fx-background-color: transparent;
@@ -956,3 +955,23 @@ We want to have a look that matches our icons in the tool-bar */
 .progress-bar > .track {
     -fx-background-color: -jr-accent;
 }
+
+.jfx-color-picker:armed,
+.jfx-color-picker:hover,
+.jfx-color-picker:focused,
+.jfx-color-picker {
+    -fx-background-color: transparent, transparent, transparent, transparent;
+    -fx-background-radius: 0px;
+    -fx-background-insets: 0px;
+    -fx-effect: null;
+}
+
+.color-palette {
+    -fx-background-color: -fx-background;
+    -fx-background-radius: 0px;
+    -fx-background-insets: 0px;
+}
+
+.color-palette-region .button {
+    -fx-border-width: 0px;
+}
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -272,7 +272,7 @@ public void output(String s) {
     }
 
     private void setupActions() {
-        SaveDatabaseAction saveAction = new SaveDatabaseAction(this);
+        SaveDatabaseAction saveAction = new SaveDatabaseAction(this, Globals.prefs);
         CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs);
 
         actions.put(Actions.UNDO, undoAction);
@@ -429,7 +429,7 @@ private void setupActions() {
         actions.put(Actions.REMOVE_FROM_GROUP, new GroupAddRemoveDialog(this, false, false));
         actions.put(Actions.MOVE_TO_GROUP, new GroupAddRemoveDialog(this, true, true));
 
-        actions.put(Actions.DOWNLOAD_FULL_TEXT, new FindFullTextAction(frame.getDialogService(), this));
+        actions.put(Actions.DOWNLOAD_FULL_TEXT, new FindFullTextAction(this)::execute);
     }
 
     /**

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -454,9 +454,6 @@ private void tearDownJabRef(List<String> filenames) {
         }
 
         fileHistory.storeHistory();
-        prefs.customExports.store(Globals.prefs);
-        prefs.customImports.store();
-
         prefs.flush();
 
         // dispose all windows, even if they are not displayed anymore
@@ -928,7 +925,7 @@ private MenuBar createMenu() {
 
                 factory.createMenuItem(StandardActions.SETUP_GENERAL_FIELDS, new SetupGeneralFieldsAction()),
                 factory.createMenuItem(StandardActions.MANAGE_CUSTOM_IMPORTS, new ManageCustomImportsAction(this)),
-                factory.createMenuItem(StandardActions.MANAGE_CUSTOM_EXPORTS, new ManageCustomExportsAction(this)),
+                factory.createMenuItem(StandardActions.MANAGE_CUSTOM_EXPORTS, new ManageCustomExportsAction()),
                 factory.createMenuItem(StandardActions.MANAGE_EXTERNAL_FILETYPES, new EditExternalFileTypesAction()),
                 factory.createMenuItem(StandardActions.MANAGE_JOURNALS, new ManageJournalsAction()),
                 factory.createMenuItem(StandardActions.CUSTOMIZE_KEYBINDING, new CustomizeKeyBindingAction()),
@@ -1335,7 +1332,7 @@ private boolean confirmClose(BasePanel panel) {
         if (response.isPresent() && response.get().equals(saveChanges)) {
             // The user wants to save.
             try {
-                SaveDatabaseAction saveAction = new SaveDatabaseAction(panel);
+                SaveDatabaseAction saveAction = new SaveDatabaseAction(panel, Globals.prefs);
                 if (!saveAction.save()) {
                     // The action was either canceled or unsuccessful.
                     output(Localization.lang("Unable to save library"));

diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -46,6 +46,9 @@
 import com.google.common.eventbus.Subscribe;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
 
 /**
  * Displays an BibEntry using the given layout format.
@@ -351,7 +354,19 @@ public void close() {
     }
 
     private void copyPreviewToClipBoard() {
-        String previewContent = (String) previewView.getEngine().executeScript("document.documentElement.outerHTML");
-        clipBoardManager.setContent(previewContent);
+        StringBuilder previewStringContent = new StringBuilder();
+        Document document = previewView.getEngine().getDocument();
+        NodeList nodeList = document.getElementsByTagName("*");
+
+        for (int i = 0; i < nodeList.getLength(); i++) {
+            Element element = (Element) nodeList.item(i);
+            previewStringContent.append(element.getNodeValue()).append("\n");
+        }
+
+        ClipboardContent content = new ClipboardContent();
+        content.putString(previewStringContent.toString());
+        content.putHtml((String) previewView.getEngine().executeScript("document.documentElement.outerHTML"));
+
+        clipBoardManager.setContent(content);
     }
 }
diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -10,7 +10,6 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.BackgroundTask;
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -23,11 +22,6 @@ public class CleanupAction implements BaseAction {
     private final BasePanel panel;
     private final DialogService dialogService;
 
-    /**
-     * Global variable to count unsuccessful renames
-     */
-    private int unsuccessfulRenames;
-
     private boolean isCanceled;
     private int modifiedEntriesCount;
     private final JabRefPreferences preferences;
@@ -44,13 +38,31 @@ public void action() {
         if (isCanceled) {
             return;
         }
-        CleanupDialog cleanupDialog = new CleanupDialog(panel.getBibDatabaseContext(), preferences.getCleanupPreset());
+        CleanupDialog cleanupDialog = new CleanupDialog(panel.getBibDatabaseContext(), preferences.getCleanupPreset(), preferences.getFilePreferences());
 
         Optional<CleanupPreset> chosenPreset = cleanupDialog.showAndWait();
-        chosenPreset.ifPresent(cleanupPreset ->
-                BackgroundTask.wrap(() -> cleanup(cleanupPreset))
-                              .onSuccess(x -> showResults())
-                              .executeWith(Globals.TASK_EXECUTOR));
+
+        if (chosenPreset.isPresent()) {
+            if (chosenPreset.get().isRenamePDFActive() && preferences.getBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN)) {
+                boolean confirmed = dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Autogenerate PDF Names"),
+                        Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
+                        Localization.lang("Autogenerate PDF Names"),
+                        Localization.lang("Cancel"),
+                        Localization.lang("Disable this confirmation dialog"),
+                        optOut -> Globals.prefs.putBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN, !optOut));
+
+                if (!confirmed) {
+                    isCanceled = true;
+                    return;
+                }
+            }
+
+            preferences.setCleanupPreset(chosenPreset.get());
+
+            BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
+                          .onSuccess(result -> showResults())
+                          .executeWith(Globals.TASK_EXECUTOR);
+        }
     }
 
     public void init() {
@@ -111,21 +123,6 @@ private void showResults() {
     private void cleanup(CleanupPreset cleanupPreset) {
         preferences.setCleanupPreset(cleanupPreset);
 
-        if (cleanupPreset.isRenamePDF() && preferences.getBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN)) {
-
-            boolean confirmed = DefaultTaskExecutor.runInJavaFXThread(() -> dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Autogenerate PDF Names"),
-                    Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
-                    Localization.lang("Autogenerate PDF Names"),
-                    Localization.lang("Cancel"),
-                    Localization.lang("Disable this confirmation dialog"),
-                    optOut -> Globals.prefs.putBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN, !optOut)));
-
-            if (!confirmed) {
-                isCanceled = true;
-                return;
-            }
-        }
-
         for (BibEntry entry : panel.getSelectedEntries()) {
             // undo granularity is on entry level
             NamedCompound ce = new NamedCompound(Localization.lang("Cleanup entry"));