update 2021.3.11

CHANGELOG.md

@@ -30,6 +30,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The export to MS Office XML now uses the month name for the field `MonthAcessed` instead of the two digit number [#7354](https://github.com/JabRef/jabref/issues/7354)
 - We included some standalone dialogs from the options menu in the main preference dialog and fixed some visual issues in the preferences dialog. [#7384](https://github.com/JabRef/jabref/pull/7384)
 - We improved the linking of the `python3` interpreter via the shebang to dynamically use the systems default Python. Related to [JabRef-Browser-Extension #177](https://github.com/JabRef/JabRef-Browser-Extension/issues/177)
+- Automatically found pdf files now have the linking button to the far left and uses a link icon with a plus instead of a briefcase. The file name also has lowered opacity(70%) until added. [#3607](https://github.com/JabRef/jabref/issues/3607)
 - We simplified the select entry type form by splitting it into two parts ("Recommended" and "Others") based on internal usage data. [#6730](https://github.com/JabRef/jabref/issues/6730)
 
 ### Fixed
@@ -59,6 +60,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where a non valid value as font size results in an uncaught exception. [#7415](https://github.com/JabRef/jabref/issues/7415)
 - We fixed an issue where "Merge citations" in the Openoffice/Libreoffice integration panel did not have a corresponding opposite. [#7454](https://github.com/JabRef/jabref/issues/7454)
 - We fixed an issue where drag and drop of bib files for opening resulted in uncaught exceptions [#7464](https://github.com/JabRef/jabref/issues/7464)
+- We fixed an issue where Content selector does not seem to work for custom fields. [#6819](https://github.com/JabRef/jabref/issues/6819)
 
 ### Removed
 
@@ -95,6 +97,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We changed the title of the window  "Manage field names and content":  to have the same title as the corresponding menu item  [#6895](https://github.com/JabRef/jabref/pull/6895)
 - We improved the detection of "short" DOIs [6880](https://github.com/JabRef/jabref/issues/6880)
 - We improved the duplicate detection when identifiers like DOI or arxiv are semantiaclly the same, but just syntactically differ (e.g. with or without http(s):// prefix). [#6707](https://github.com/JabRef/jabref/issues/6707)
+- We improved JabRef start up time [6057](https://github.com/JabRef/jabref/issues/6057)
 - We changed in the group interface "Generate groups from keywords in a BibTeX field" by "Generate groups from keywords in the following field". [#6983](https://github.com/JabRef/jabref/issues/6983)
 - We changed the name of a group type from "Searching for keywords" to "Searching for a keyword". [6995](https://github.com/JabRef/jabref/pull/6995)
 - We changed the way JabRef displays the title of a tab and of the window. [4161](https://github.com/JabRef/jabref/issues/4161)

docs/adr.md

@@ -16,13 +16,14 @@ Architectural decisions for JabRef:
 * [ADR-0011](https://github.com/JabRef/jabref/tree/master/docs/adr/0011-test-external-links-in-documentation.md) - Test external links in documentation
 * [ADR-0012](https://github.com/JabRef/jabref/tree/master/docs/adr/0012-handle-different-bibEntry-formats-of-fetchers.md) - Handle different bibentry formats of fetchers by adding a layer
 * [ADR-0013](https://github.com/JabRef/jabref/tree/master/docs/adr/0013-add-native-support-biblatex-software.md) - Add Native Support for BibLatex-Software
-
-  fix checkstyle in adr
-
 * [ADR-0014](https://github.com/JabRef/jabref/tree/master/docs/adr/0014-separate-URL-creation-to-enable-proper-logging.md) - Separate URL creation to enable proper logging
 * [ADR-0015](https://github.com/JabRef/jabref/tree/master/docs/adr/0015-support-an-abstract-query-syntax-for-query-conversion.md) - Query syntax design
 * [ADR-0016](https://github.com/JabRef/jabref/tree/master/docs/adr/0016-mutable-preferences-objects.md) - Mutable preferences objects
 * [ADR-0017](https://github.com/JabRef/jabref/tree/master/docs/adr/0017-allow-model-access-logic.md) - Allow org.jabref.model to access org.jabref.logic
+* [ADR-0018](https://github.com/JabRef/jabref/blob/master/docs/adr/0018-use-regular-expression-to-split-multiple-sentence-titles.md) - Use regular expression to split multiple-sentence titles
+* [ADR-0019](https://github.com/JabRef/jabref/blob/master/docs/adr/0019-implement-special-fields-as-seperate-fields.md) - Implement special fields as seperate fields
+* [ADR-0020](https://github.com/JabRef/jabref/blob/master/docs/adr/0020-use-Jackson-to-parse-study-yml.md) - Use Jackson to parse study.yml
+* [ADR-0021](https://github.com/JabRef/jabref/blob/master/docs/adr/0021-keep-study-as-a-dto.md) - Keep study as a DTO
 
 For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/master/docs/adr/template.md) as basis. More information on the used format is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/). Then add them to the above list.
 

src/main/java/org/jabref/gui/Base.css

@@ -646,6 +646,10 @@
     -fx-fill: -jr-search-text;
 }
 
+.file-row-text:opacity{
+    -fx-fill: derive(-jr-search-text, 70%);
+}
+
 .combo-box-base {
     -fx-background-color: -fx-outer-border, -fx-control-inner-background;
     -fx-background-insets: 0, 1;

src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java

@@ -16,6 +16,7 @@
 import org.jabref.gui.LibraryTab;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.ControlHelper;
+import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.field.Field;
 
@@ -68,6 +69,9 @@ public void initialize() {
     private void initFieldNameComponents() {
         initListView(fieldsListView, viewModel::getFieldNamesBackingList);
         viewModel.selectedFieldProperty().bind(fieldsListView.getSelectionModel().selectedItemProperty());
+        new ViewModelListCellFactory<Field>()
+                .withText(Field::getDisplayName)
+                .install(fieldsListView);
         removeFieldNameButton.disableProperty().bind(viewModel.isNoFieldNameSelected());
         EasyBind.subscribe(viewModel.selectedFieldProperty(), viewModel::populateKeywords);
     }

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -4,6 +4,7 @@
 
 import javafx.beans.binding.Bindings;
 import javafx.collections.ObservableList;
+import javafx.css.PseudoClass;
 import javafx.fxml.FXML;
 import javafx.scene.Node;
 import javafx.scene.Parent;
@@ -46,6 +47,7 @@
 import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.views.ViewLoader;
+import com.tobiasdiez.easybind.EasyBind;
 
 public class LinkedFilesEditor extends HBox implements FieldEditorFX {
 
@@ -137,11 +139,16 @@ private void handleOnDragDropped(LinkedFileViewModel originalItem, DragEvent eve
     }
 
     private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
+        PseudoClass opacity = PseudoClass.getPseudoClass("opacity");
+
         Node icon = linkedFile.getTypeIcon().getGraphicNode();
         icon.setOnMouseClicked(event -> linkedFile.open());
+
         Text link = new Text();
         link.textProperty().bind(linkedFile.linkProperty());
         link.getStyleClass().setAll("file-row-text");
+        EasyBind.subscribe(linkedFile.isAutomaticallyFoundProperty(), found -> link.pseudoClassStateChanged(opacity, found));
+
         Text desc = new Text();
         desc.textProperty().bind(linkedFile.descriptionProperty());
         desc.getStyleClass().setAll("file-row-text");
@@ -157,6 +164,7 @@ private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
         Button acceptAutoLinkedFile = IconTheme.JabRefIcons.AUTO_LINKED_FILE.asButton();
         acceptAutoLinkedFile.setTooltip(new Tooltip(Localization.lang("This file was found automatically. Do you want to link it to this entry?")));
         acceptAutoLinkedFile.visibleProperty().bind(linkedFile.isAutomaticallyFoundProperty());
+        acceptAutoLinkedFile.managedProperty().bind(linkedFile.isAutomaticallyFoundProperty());
         acceptAutoLinkedFile.setOnAction(event -> linkedFile.acceptAsLinked());
         acceptAutoLinkedFile.getStyleClass().setAll("icon-button");
 
@@ -169,7 +177,7 @@ private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
         HBox container = new HBox(10);
         container.setPrefHeight(Double.NEGATIVE_INFINITY);
 
-        container.getChildren().addAll(info, acceptAutoLinkedFile, writeXMPMetadata);
+        container.getChildren().addAll(acceptAutoLinkedFile, info, writeXMPMetadata);
 
         return container;
     }

src/main/java/org/jabref/gui/icon/IconTheme.java

@@ -230,7 +230,7 @@ public enum JabRefIcons implements JabRefIcon {
         RENAME(MaterialDesignR.RENAME_BOX),
         DELETE_FILE(MaterialDesignD.DELETE_FOREVER),
         REMOVE_LINK(MaterialDesignL.LINK_OFF),
-        AUTO_LINKED_FILE(MaterialDesignB.BRIEFCASE_CHECK),
+        AUTO_LINKED_FILE(MaterialDesignL.LINK_PLUS),
         QUALITY_ASSURED(MaterialDesignC.CERTIFICATE),
         QUALITY(MaterialDesignC.CERTIFICATE),
         OPEN(MaterialDesignF.FOLDER_OUTLINE),

src/main/java/org/jabref/gui/maintable/columns/FieldColumn.java

@@ -6,8 +6,12 @@
 import org.jabref.gui.maintable.MainTableColumnModel;
 import org.jabref.gui.util.ValueTableCellFactory;
 import org.jabref.gui.util.comparator.NumericFieldComparator;
+import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
 import org.jabref.model.entry.field.OrFields;
+import org.jabref.model.entry.field.UnknownField;
+
+import com.google.common.collect.Iterables;
 
 /**
  * A column that displays the text-value of the field
@@ -26,7 +30,16 @@ public FieldColumn(MainTableColumnModel model) {
         new ValueTableCellFactory<BibEntryTableViewModel, String>()
                 .withText(text -> text)
                 .install(this);
-        this.setComparator(new NumericFieldComparator());
+
+        if (fields.size() == 1) {
+            // comparator can't parse more than one value
+            Field field = Iterables.getOnlyElement(fields);
+
+            if (field instanceof UnknownField || field.isNumeric()) {
+                this.setComparator(new NumericFieldComparator());
+            }
+        }
+
         this.setSortable(true);
     }
 

src/main/java/org/jabref/gui/util/comparator/NumericFieldComparator.java

@@ -2,6 +2,8 @@
 
 import java.util.Comparator;
 
+import org.jabref.model.strings.StringUtil;
+
 /**
  * Comparator for numeric cases. The purpose of this class is to add the numeric comparison, because values are sorted
  * as if they were strings.
@@ -10,51 +12,54 @@ public class NumericFieldComparator implements Comparator<String> {
 
     @Override
     public int compare(String val1, String val2) {
-        // We start by implementing the comparison in the edge cases (if one of the values is null).
-        if (val1 == null && val2 == null) {
-            return 0;
-        }
+        Integer valInt1 = parseInt(val1);
+        Integer valInt2 = parseInt(val2);
 
-        if (val1 == null) {
+        if (valInt1 == null && valInt2 == null) {
+            if (val1 != null && val2 != null) {
+                return val1.compareTo(val2);
+            } else {
+                return 0;
+            }
+        } else if (valInt1 == null) {
             // We assume that "null" is "less than" any other value.
             return -1;
-        }
-
-        if (val2 == null) {
+        } else if (valInt2 == null) {
             return 1;
         }
 
-        // Now we start the conversion to integers.
-        Integer valInt1 = null;
-        Integer valInt2 = null;
-        try {
-            // Trim in case the user added an unnecessary white space (e.g. 1 1 instead of 11).
-            valInt1 = Integer.parseInt(val1.trim());
-        } catch (NumberFormatException ignore) {
-            // do nothing
+        // If we arrive at this stage then both values are actually numeric !
+        return valInt1 - valInt2;
+    }
+
+    private static Integer parseInt(String number) {
+        if (!isNumber(number)) {
+            return null;
         }
+
         try {
-            valInt2 = Integer.parseInt(val2.trim());
+            return Integer.valueOf(number.trim());
         } catch (NumberFormatException ignore) {
-            // do nothing
+            return null;
         }
+    }
 
-        if (valInt1 == null && valInt2 == null) {
-            // None of the values were parsed (i.e both are not numeric)
-            // so we will use the normal string comparison.
-            return val1.compareTo(val2);
+    private static boolean isNumber(String number) {
+        if (StringUtil.isNullOrEmpty(number)) {
+            return false;
         }
-
-        if (valInt1 == null) {
-            // We assume that strings "are less" than integers
-            return -1;
+        if (number.length() == 1 && (number.charAt(0) == '-' || number.charAt(0) == '+')) {
+            return false;
         }
-
-        if (valInt2 == null) {
-            return 1;
+        for (int i = 0; i < number.length(); i++) {
+            char c = number.charAt(i);
+            if (i == 0 && (c == '-' || c == '+')) {
+                continue;
+            } else if (!Character.isDigit(c)) {
+                return false;
+            }
         }
 
-        // If we arrive at this stage then both values are actually numeric !
-        return valInt1 - valInt2;
+        return true;
     }
 }

src/test/java/org/jabref/gui/util/comparator/NumericFieldComparatorTest.java

@@ -42,4 +42,24 @@ public void compareStringWithInteger() {
     public void compareIntegerWithString() {
         assertEquals(1, comparator.compare("4", "hi"));
     }
+
+    @Test
+    public void compareNegativeInteger() {
+        assertEquals(1, comparator.compare("-4", "-5"));
+    }
+
+    @Test
+    public void compareWithMinusString() {
+        assertEquals(-1, comparator.compare("-", "-5"));
+    }
+
+    @Test
+    public void compareWithPlusString() {
+        assertEquals(-1, comparator.compare("+", "-5"));
+    }
+
+    @Test
+    public void compareWordWithMinus() {
+        assertEquals(-1, comparator.compare("-abc", "-5"));
+    }
 }