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

# Conflicts: # src/main/resources/l10n/JabRef_en.properties
ShikunXiong · Feb 20, 2020 · 1dc67db · 1dc67db
2 parents bca3a0b + 5fa1dcf
commit 1dc67db
Show file tree

Hide file tree

Showing 27 changed files with 610 additions and 154 deletions.
diff --git a/.github/workflows/gradle-wrapper-validation.yml b/.github/workflows/gradle-wrapper-validation.yml
@@ -0,0 +1,14 @@
+# This is https://github.com/marketplace/actions/gradle-wrapper-validation
+# It ensures that the jar file is from gradle and not by a strange third party.
+
+name: "Validate Gradle Wrapper"
+on: [push, pull_request]
+
+jobs:
+  validation:
+    name: "Validation"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: gradle/wrapper-validation-action@v1
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
+- We reintroduced the possibility to extract references from plain text (using GROBID) [#5614](https://github.com/JabRef/jabref/pull/5614) 
 - We changed the open office panel to show buttons in rows of three instead of going straight down to save space as the button expanded out to take up unnecessary horizontal space. [#5479](https://github.com/JabRef/jabref/issues/5479)
 - We cleaned up the group add/edit dialog. [#5826](https://github.com/JabRef/jabref/pull/5826)
 - We reintroduced the index column. [#5844](https://github.com/JabRef/jabref/pull/5844)
@@ -22,6 +23,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Fixed
 
+- We fixed an issue where the command line console was always opened in the background. [#5474](https://github.com/JabRef/jabref/issues/5474)
 - We fixed and issue where pdf files will not open under some KDE linux distributions when using okular. [#5253](https://github.com/JabRef/jabref/issues/5253)
 - We fixed an issue where the Medline fetcher was only working when JabRef was running from source. [#5645](https://github.com/JabRef/jabref/issues/5645)
 - We fixed some visual issues in the dark theme. [#5764](https://github.com/JabRef/jabref/pull/5764) [#5753](https://github.com/JabRef/jabref/issues/5753)

diff --git a/build.gradle b/build.gradle
@@ -23,7 +23,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.27.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
-    id 'org.beryx.jlink' version '2.17.1'
+    id 'org.beryx.jlink' version '2.17.2'
 
     // nicer test outputs during running and completion
     id 'com.adarshr.test-logger' version '2.0.0'
@@ -255,7 +255,7 @@ dependencyUpdates.resolutionStrategy = {
         }
         rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /2.0.26-9.1.2/
-                || selection.candidate.version ==~ /2.0.26-9.1.1/ 
+                || selection.candidate.version ==~ /2.0.26-9.1.1/
                 || selection.candidate.version ==~ /2.0.26-9.1.0/) {
                 selection.reject('1.7.22-11 is actually newer (strange version system)')
             }
@@ -590,7 +590,7 @@ jlink {
         requires 'java.rmi'
         requires 'java.xml'
         requires 'com.sun.xml.txw2'
-        requires 'com.google.gson';
+        requires 'com.google.gson'
         requires 'java.desktop'
         requires 'java.security.jgss'
         requires 'jdk.jsobject'
@@ -628,7 +628,6 @@ jlink {
             // This requires WiX to be installed: https://github.com/wixtoolset/wix3/releases
             installerType = "msi"
             imageOptions = [
-                    '--win-console',
                     '--icon', "${projectDir}/src/main/resources/icons/jabref.ico",
             ]
             installerOptions = [

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -486,6 +486,7 @@ private Node createToolbar() {
         HBox rightSide = new HBox(
                 factory.createIconButton(StandardActions.NEW_ARTICLE, new NewEntryAction(this, StandardEntryType.Article, dialogService, Globals.prefs, stateManager)),
                 factory.createIconButton(StandardActions.NEW_ENTRY, new NewEntryAction(this, dialogService, Globals.prefs, stateManager)),
+                factory.createIconButton(StandardActions.NEW_ENTRY_FROM_PLAIN_TEXT, new ExtractBibtexAction(stateManager)),
                 factory.createIconButton(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, stateManager)),
                 new Separator(Orientation.VERTICAL),
                 factory.createIconButton(StandardActions.UNDO, new OldDatabaseCommandWrapper(Actions.UNDO, this, stateManager)),
@@ -734,6 +735,7 @@ private MenuBar createMenu() {
         //@formatter:off
         library.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_ENTRY, new NewEntryAction(this, dialogService, Globals.prefs, stateManager)),
+                factory.createMenuItem(StandardActions.NEW_ENTRY_FROM_PLAIN_TEXT, new ExtractBibtexAction(stateManager)),
                 factory.createMenuItem(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, stateManager)),
 
                 new SeparatorMenuItem(),
@@ -773,7 +775,6 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this, stateManager)),
                 factory.createMenuItem(StandardActions.WRITE_XMP, new WriteXMPAction(stateManager, dialogService)),
                 factory.createMenuItem(StandardActions.COPY_LINKED_FILES, new CopyFilesAction(stateManager, this.getDialogService())),
-                factory.createMenuItem(StandardActions.EXTRACT_BIBTEX, new ExtractBibtexAction(stateManager)),
 
                 new SeparatorMenuItem(),
 

diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -120,7 +120,7 @@ public enum StandardActions implements Action {
 
     NEW_ENTRY(Localization.lang("New entry"), IconTheme.JabRefIcons.ADD_ENTRY, KeyBinding.NEW_ENTRY),
     NEW_ARTICLE(Localization.lang("New article"), IconTheme.JabRefIcons.ADD_ARTICLE),
-    NEW_ENTRY_FROM_PLAINTEX(Localization.lang("New entry from plain text"), KeyBinding.NEW_FROM_PLAIN_TEXT),
+    NEW_ENTRY_FROM_PLAIN_TEXT(Localization.lang("New entry from plain text"), IconTheme.JabRefIcons.NEW_ENTRY_FROM_PLAIN_TEXT, KeyBinding.NEW_ENTRY_FROM_PLAIN_TEXT),
     LIBRARY_PROPERTIES(Localization.lang("Library properties")),
     EDIT_PREAMBLE(Localization.lang("Edit preamble")),
     EDIT_STRINGS(Localization.lang("Edit string constants"), IconTheme.JabRefIcons.EDIT_STRINGS, KeyBinding.EDIT_STRINGS),
@@ -138,7 +138,6 @@ public enum StandardActions implements Action {
     DOWNLOAD_FULL_TEXT(Localization.lang("Search full text documents online"), IconTheme.JabRefIcons.FILE_SEARCH, KeyBinding.DOWNLOAD_FULL_TEXT),
     CLEANUP_ENTRIES(Localization.lang("Cleanup entries"), IconTheme.JabRefIcons.CLEANUP_ENTRIES, KeyBinding.CLEANUP),
     SET_FILE_LINKS(Localization.lang("Automatically set file links"), KeyBinding.AUTOMATICALLY_LINK_FILES),
-    EXTRACT_BIBTEX(Localization.lang("Extract BibTeX from plain text")),
 
     HELP(Localization.lang("Online help"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     HELP_KEY_PATTERNS(Localization.lang("Help on key patterns"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),

diff --git a/src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java b/src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java
@@ -3,40 +3,60 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import javax.swing.undo.UndoManager;
+
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
 
 import org.jabref.Globals;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.externalfiles.ImportHandler;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.importer.fetcher.GrobidCitationFetcher;
+import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.types.EntryType;
-import org.jabref.model.entry.types.StandardEntryType;
+import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.JabRefPreferences;
 
 public class BibtexExtractorViewModel {
 
     private final StringProperty inputTextProperty = new SimpleStringProperty("");
-    private final BibDatabaseContext bibdatabaseContext;
-
-    public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext) {
-        this.bibdatabaseContext = bibdatabaseContext;
+    private DialogService dialogService;
+    private GrobidCitationFetcher currentCitationfetcher;
+    private TaskExecutor taskExecutor;
+    private ImportHandler importHandler;
+
+    public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext, DialogService dialogService,
+                                    JabRefPreferences jabRefPreferences, FileUpdateMonitor fileUpdateMonitor, TaskExecutor taskExecutor, UndoManager undoManager, StateManager stateManager) {
+        this.dialogService = dialogService;
+        currentCitationfetcher = new GrobidCitationFetcher(jabRefPreferences.getImportFormatPreferences());
+        this.taskExecutor = taskExecutor;
+        this.importHandler = new ImportHandler(dialogService, bibdatabaseContext, ExternalFileTypes.getInstance(), jabRefPreferences.getFilePreferences(), jabRefPreferences.getImportFormatPreferences(), jabRefPreferences.getUpdateFieldPreferences(), fileUpdateMonitor, undoManager, stateManager);
     }
 
     public StringProperty inputTextProperty() {
         return this.inputTextProperty;
     }
 
-    public void startExtraction() {
-
-        BibtexExtractor extractor = new BibtexExtractor();
-        BibEntry entity = extractor.extract(inputTextProperty.getValue());
-        this.bibdatabaseContext.getDatabase().insertEntry(entity);
-        trackNewEntry(StandardEntryType.Article);
+    public void startParsing() {
+        BackgroundTask.wrap(() -> currentCitationfetcher.performSearch(inputTextProperty.getValue()))
+                .onRunning(() -> dialogService.notify(Localization.lang("Your text is being parsed...")))
+                .onSuccess(parsedEntries -> {
+                    dialogService.notify(Localization.lang("%0 entries were parsed from your query.", String.valueOf(parsedEntries.size())));
+                    importHandler.importEntries(parsedEntries);
+                    for (BibEntry bibEntry : parsedEntries) {
+                        trackNewEntry(bibEntry);
+                    }
+                }).executeWith(taskExecutor);
     }
 
-    private void trackNewEntry(EntryType type) {
+    private void trackNewEntry(BibEntry bibEntry) {
         Map<String, String> properties = new HashMap<>();
-        properties.put("EntryType", type.getName());
-
-        Globals.getTelemetryClient().ifPresent(client -> client.trackEvent("NewEntry", properties, new HashMap<>()));
+        properties.put("EntryType", bibEntry.typeProperty().getValue().getName());
+        Globals.getTelemetryClient().ifPresent(client -> client.trackEvent("ParseWithGrobid", properties, new HashMap<>()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.fxml b/src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.fxml
@@ -4,11 +4,17 @@
 <?import javafx.scene.control.DialogPane?>
 <?import javafx.scene.control.TextArea?>
 
+<?import javafx.scene.layout.VBox?>
+
 <DialogPane prefHeight="430.0" prefWidth="586.0" xmlns="http://javafx.com/javafx/8.0.171"
             xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.bibtexextractor.ExtractBibtexDialog">
     <content>
-        <TextArea fx:id="input" minHeight="-Infinity" prefHeight="350.0" prefWidth="586.0"/>
+        <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
+        <children>
+            <TextArea fx:id="input" minHeight="-Infinity" prefHeight="350.0" prefWidth="586.0" wrapText="true"/>
+        </children>
+        </VBox>
     </content>
-    <ButtonType fx:id="extractButtonType" buttonData="OK_DONE" text="%Extract"/>
+    <ButtonType fx:id="parseButtonType" buttonData="OK_DONE" text = "%Add to current library"/>
     <ButtonType fx:constant="CANCEL"/>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.java b/src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.java
@@ -1,17 +1,22 @@
 package org.jabref.gui.bibtexextractor;
 
 import javax.inject.Inject;
+import javax.swing.undo.UndoManager;
 
 import javafx.fxml.FXML;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.TextArea;
 import javafx.scene.control.Tooltip;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.JabRefPreferences;
 
 import com.airhacks.afterburner.views.ViewLoader;
 
@@ -20,31 +25,34 @@
  */
 public class ExtractBibtexDialog extends BaseDialog<Void> {
 
-    private final Button buttonExtract;
+    private final Button buttonParse;
     @FXML private TextArea input;
-    @FXML private ButtonType extractButtonType;
+    @FXML private ButtonType parseButtonType;
     private BibtexExtractorViewModel viewModel;
-
     @Inject private StateManager stateManager;
+    @Inject private DialogService dialogService;
+    @Inject private FileUpdateMonitor fileUpdateMonitor;
+    @Inject private TaskExecutor taskExecutor;
+    @Inject private UndoManager undoManager;
 
     public ExtractBibtexDialog() {
-
         ViewLoader.view(this)
                   .load()
                   .setAsDialogPane(this);
-
-        this.setTitle(Localization.lang("Input text to parse"));
-        buttonExtract = (Button) getDialogPane().lookupButton(extractButtonType);
-        buttonExtract.setTooltip(new Tooltip((Localization.lang("Starts the extraction of the BibTeX entry"))));
-        buttonExtract.setOnAction(e -> viewModel.startExtraction());
-        buttonExtract.disableProperty().bind(viewModel.inputTextProperty().isEmpty());
+        this.setTitle(Localization.lang("Plain References Parser"));
+        input.setPromptText(Localization.lang("Please enter the plain references to extract from separated by double empty lines."));
+        input.selectAll();
+
+        buttonParse = (Button) getDialogPane().lookupButton(parseButtonType);
+        buttonParse.setTooltip(new Tooltip((Localization.lang("Starts the extraction and adds the resulting entries to the currently opened database"))));
+        buttonParse.setOnAction(event -> viewModel.startParsing());
+        buttonParse.disableProperty().bind(viewModel.inputTextProperty().isEmpty());
     }
 
     @FXML
     private void initialize() {
         BibDatabaseContext database = stateManager.getActiveDatabase().orElseThrow(() -> new NullPointerException("Database null"));
-        this.viewModel = new BibtexExtractorViewModel(database);
-
+        this.viewModel = new BibtexExtractorViewModel(database, dialogService, JabRefPreferences.getInstance(), fileUpdateMonitor, taskExecutor,undoManager,stateManager);
         input.textProperty().bindBidirectional(viewModel.inputTextProperty());
     }
 }
diff --git a/src/main/java/org/jabref/gui/desktop/os/Linux.java b/src/main/java/org/jabref/gui/desktop/os/Linux.java
@@ -11,8 +11,10 @@
 import java.util.Optional;
 import java.util.StringJoiner;
 
+import org.jabref.JabRefExecutorService;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.util.StreamGobbler;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.slf4j.Logger;
@@ -22,6 +24,7 @@
 import static org.jabref.preferences.JabRefPreferences.USE_PDF_READER;
 
 public class Linux implements NativeDesktop {
+
     private static final Logger LOGGER = LoggerFactory.getLogger(Linux.class);
 
     @Override
@@ -34,14 +37,13 @@ public void openFile(String filePath, String fileType) throws IOException {
         } else {
             viewer = "xdg-open";
         }
-        String[] cmdArray = { viewer, filePath };
-        Process p = Runtime.getRuntime().exec(cmdArray);
-        // When the stream is full at some point, then blocks the execution of the program
-        // See https://stackoverflow.com/questions/10981969/why-is-going-through-geterrorstream-necessary-to-run-a-process.
-        BufferedReader in = new BufferedReader(new InputStreamReader(p.getErrorStream()));
-        String line;
-        line = in.readLine();
-        LOGGER.debug("Received output: " + line);
+        ProcessBuilder processBuilder = new ProcessBuilder(viewer, filePath);
+        Process process = processBuilder.start();
+        StreamGobbler streamGobblerInput = new StreamGobbler(process.getInputStream(), LOGGER::debug);
+        StreamGobbler streamGobblerError = new StreamGobbler(process.getErrorStream(), LOGGER::debug);
+
+        JabRefExecutorService.INSTANCE.execute(streamGobblerInput);
+        JabRefExecutorService.INSTANCE.execute(streamGobblerError);
     }
 
     @Override
@@ -53,17 +55,18 @@ public void openFileWithApplication(String filePath, String application) throws
         } else {
             openWith = new String[] {"xdg-open"};
         }
-
         String[] cmdArray = new String[openWith.length + 1];
         System.arraycopy(openWith, 0, cmdArray, 0, openWith.length);
         cmdArray[cmdArray.length - 1] = filePath;
-        Process p = Runtime.getRuntime().exec(cmdArray);
-        // When the stream is full at some point, then blocks the execution of the program
-        // See https://stackoverflow.com/questions/10981969/why-is-going-through-geterrorstream-necessary-to-run-a-process.
-        BufferedReader in = new BufferedReader(new InputStreamReader(p.getErrorStream()));
-        String line;
-        line = in.readLine();
-        LOGGER.debug("Received output: " + line);
+
+        ProcessBuilder processBuilder = new ProcessBuilder(cmdArray);
+        Process process = processBuilder.start();
+
+        StreamGobbler streamGobblerInput = new StreamGobbler(process.getInputStream(), LOGGER::debug);
+        StreamGobbler streamGobblerError = new StreamGobbler(process.getErrorStream(), LOGGER::debug);
+
+        JabRefExecutorService.INSTANCE.execute(streamGobblerInput);
+        JabRefExecutorService.INSTANCE.execute(streamGobblerError);
     }
 
     @Override
@@ -118,7 +121,7 @@ public void openPdfWithParameters(String filePath, List<String> parameters) thro
 
             openFileWithApplication(filePath, sj.toString());
         } else {
-            openFile( filePath, "PDF");
+            openFile(filePath, "PDF");
         }
     }
 

diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -298,7 +298,8 @@ public enum JabRefIcons implements JabRefIcon {
         OPEN_ABBREVIATION_LIST(MaterialDesignIcon.FOLDER_OUTLINE),
         REMOVE_ABBREVIATION_LIST(MaterialDesignIcon.FOLDER_REMOVE),
         ADD_ABBREVIATION(MaterialDesignIcon.PLAYLIST_PLUS),
-        REMOVE_ABBREVIATION(MaterialDesignIcon.PLAYLIST_MINUS);
+        REMOVE_ABBREVIATION(MaterialDesignIcon.PLAYLIST_MINUS),
+        NEW_ENTRY_FROM_PLAIN_TEXT(MaterialDesignIcon.PLUS_BOX);
 
         private final JabRefIcon icon;
 

diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
@@ -48,7 +48,7 @@ public enum KeyBinding {
     NEW_ARTICLE("New article", Localization.lang("New article"), "ctrl+shift+A", KeyBindingCategory.BIBTEX),
     NEW_BOOK("New book", Localization.lang("New book"), "ctrl+shift+B", KeyBindingCategory.BIBTEX),
     NEW_ENTRY("New entry", Localization.lang("New entry"), "ctrl+N", KeyBindingCategory.BIBTEX),
-    NEW_FROM_PLAIN_TEXT("New from plain text", Localization.lang("New from plain text"), "ctrl+shift+N", KeyBindingCategory.BIBTEX),
+    NEW_ENTRY_FROM_PLAIN_TEXT("New entry from plain text", Localization.lang("New entry from plain text"), "ctrl+shift+N", KeyBindingCategory.BIBTEX),
     NEW_INBOOK("New inbook", Localization.lang("New inbook"), "ctrl+shift+I", KeyBindingCategory.BIBTEX),
     NEW_MASTERSTHESIS("New mastersthesis", Localization.lang("New mastersthesis"), "ctrl+shift+M", KeyBindingCategory.BIBTEX),
     NEW_PHDTHESIS("New phdthesis", Localization.lang("New phdthesis"), "ctrl+shift+T", KeyBindingCategory.BIBTEX),