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

* upstream/master:
  builds.jabref.org: Keep html files and just remove *.exe, *.dmg, *.jar during upload of a new build
  Fix comment typo
  Fix typos in comments in .travis.yml
  Switch to LGoodDatePicker (#2340)
  Gradle build scans should only run on TravisCI, not on the other CI services
  Try scans.gradle.com
  Remove reference to GPL - we are MIT now
  fix date changes in medline fetcher results
  Fix #2336: shutdown is working again (#2338)

.travis.yml

@@ -2,7 +2,7 @@ language: java
 
 # we test at Ubuntu Trusty (Ubuntu 14.04 LTS)
 # see https://docs.travis-ci.com/user/trusty-ci-environment/
-# This environment is continuosly updated as described in https://docs.travis-ci.com/user/build-environment-updates/
+# This environment is continuously updated as described in https://docs.travis-ci.com/user/build-environment-updates/
 dist: trusty
 sudo: required
 
@@ -20,8 +20,8 @@ before_script:
   - mysql -u root -e 'create database jabref'
 
 script:
-  - ./gradlew check
-  - ./gradlew databaseTest
+  - ./gradlew check -Dscan
+  - ./gradlew databaseTest -Dscan
   # Prepare integration tests
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
@@ -30,7 +30,7 @@ script:
   # currently does not work: "stop: Unknown instance:" - sudo service mysql stop
   - sudo service postgresql stop
   # following services identified by "sudo service --status-all" do not need to run, too
-  # excluded: rsyslog (feels wrong), udev (feels wrong), friendly-recovery ("Unkonwn instance" error)
+  # excluded: rsyslog (feels wrong), udev (feels wrong), friendly-recovery ("Unknown instance" error)
   - sudo service acpid stop
   - sudo service atd stop
   - sudo service cron stop
@@ -40,8 +40,8 @@ script:
   - sudo service resolvconf stop
   - sudo service sshguard stop
   - sudo service ssh stop
-  # Integratation tests run in a timeout. Just start them and kill them after 60s
-  - timeout 60 ./gradlew integrationTest --info || true
+  # Integration tests run in a timeout. Just start them and kill them after 60s.
+  - timeout 60 ./gradlew integrationTest -Dscan --info || true
 
 after_script:
   # enable codecov report

CHANGELOG.md

@@ -26,6 +26,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 ### Fixed
+- We fixed an issue which prevented JabRef from closing using the "Quit" menu command. [#2336](https://github.com/JabRef/jabref/issues/2336)
 - We fixed an issue which caused a metadata loss on reconnection to shared database. [#2219](https://github.com/JabRef/jabref/issues/2219)
 - We fixed an issue which caused an internal error when leaving the file path field empty and connecting to a shared database.
 - We fixed an issue where the file permissions of the .bib-file were changed upon saving [#2279](https://github.com/JabRef/jabref/issues/2279).

build.gradle

@@ -14,13 +14,20 @@ buildscript {
 }
 
 plugins {
+    id 'com.gradle.build-scan' version '1.3'
     id "com.install4j.gradle" version "6.1.3"
     id 'com.github.johnrengelman.shadow' version '1.2.3'
     // If this is updated to 0.0.9, check configurations.errorprone
     id "net.ltgt.errorprone" version "0.0.8"
     id 'me.champeau.gradle.jmh' version '0.3.1'
 }
 
+// use the gradle build scan feature: https://scans.gradle.com/get-started
+buildScan {
+    licenseAgreementUrl = 'https://gradle.com/terms-of-service'
+    licenseAgree = 'yes'
+}
+
 apply plugin: "java"
 apply plugin: "application"
 apply plugin: "project-report"
@@ -123,6 +130,8 @@ dependencies {
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
     compile 'org.citationstyles:locales:1.0.1-SNAPSHOT'
     compile 'de.undercouch:citeproc-java:1.0.1'
+
+    compile 'com.github.lgooddatepicker:LGoodDatePicker:8.2.2'
 
     testCompile 'junit:junit:4.12'
     testCompile 'org.mockito:mockito-core:2.2.26'

external-libraries.txt

@@ -145,11 +145,10 @@ Project: SwingX
 URL:     https://swingx.java.net/
 License: LGPL-3.0
 
-Id:      microba
-Path:    lib/microba.jar
-Project: Microba
-URL:     https://github.com/tdbear/microba
-License: BSD
+Id:      com.github.lgooddatepicker:LGoodDatePicker
+Project: LGoodDatePicker
+URL:     https://github.com/LGoodDatePicker/LGoodDatePicker
+License: MIT
 
 Id:      spin
 Path:    lib/spin.jar

scripts/upload-to-builds.jabref.org.sh

@@ -23,7 +23,7 @@ command="cd www/\n"
 # then, "snapshot" is extracted
 if [ "snapshot" != "$branch" ] ; then
   # change into dir and delete old snapshots
-  command="${command}mkdir $branch\ncd $branch\nrm *\n"
+  command="${command}mkdir $branch\ncd $branch\nrm *.dmg\nrm *.jar\nrm *.exe\n"
 fi
 
 #only upload [Jr]ab[Rr]ef*, not md5sums, updates.xml, etc.

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

@@ -158,6 +158,7 @@ public enum JabRefIcon {
         FACEBOOK("\uf20c"), /* css: facebook */
         BLOG("\uf46b"), /* css: rss */
         GLOBAL_SEARCH("\uF1E7"), /* css: earth */
+        DATE_PICKER("\uF0ED;"), /* css: calendar */
         // STILL MISSING:
         GROUP_REGULAR("\uF4E6", Color.RED);
 

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

@@ -1684,9 +1684,7 @@ public void addTab(BasePanel basePanel, boolean raisePanel) {
             autosaver.registerListener(new AutosaveUIManager(basePanel));
         }
 
-        if (readyForBackup(context)) {
-            BackupManager.start(context);
-        }
+        BackupManager.start(context);
     }
 
     public BasePanel addTab(BibDatabaseContext databaseContext, boolean raisePanel) {
@@ -1702,9 +1700,6 @@ private boolean readyForAutosave(BibDatabaseContext context) {
                 context.getDatabaseFile().isPresent();
     }
 
-    private boolean readyForBackup(BibDatabaseContext context) {
-        return context.getLocation() == DatabaseLocation.LOCAL && context.getDatabaseFile().isPresent();
-    }
 
     /**
      * Creates icons for the disabled state for all JMenuItems with FontBasedIcons in the given menuElement.

src/main/java/net/sf/jabref/gui/date/DatePickerButton.java

@@ -1,51 +1,60 @@
 package net.sf.jabref.gui.date;
 
 import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Date;
+import java.time.LocalDate;
+import java.time.ZonedDateTime;
+import java.time.format.DateTimeFormatter;
 
 import javax.swing.JComponent;
 import javax.swing.JPanel;
 
 import net.sf.jabref.Globals;
+import net.sf.jabref.gui.IconTheme;
 import net.sf.jabref.gui.fieldeditors.FieldEditor;
 import net.sf.jabref.logic.util.date.EasyDateFormat;
 import net.sf.jabref.preferences.JabRefPreferences;
 
-import com.michaelbaranov.microba.calendar.DatePicker;
+import com.github.lgooddatepicker.components.DatePicker;
+import com.github.lgooddatepicker.components.DatePickerSettings;
+import com.github.lgooddatepicker.optionalusertools.DateChangeListener;
+import com.github.lgooddatepicker.zinternaltools.DateChangeEvent;
 
 /**
  * wrapper and service class for the DatePicker handling at the EntryEditor
  */
-public class DatePickerButton implements ActionListener {
+public class DatePickerButton implements DateChangeListener {
 
-    private final DatePicker datePicker = new DatePicker();
+    private final DatePicker datePicker;
     private final JPanel panel = new JPanel();
     private final FieldEditor editor;
     private final boolean isoFormat;
 
 
     public DatePickerButton(FieldEditor pEditor, Boolean isoFormat) {
         this.isoFormat = isoFormat;
-        datePicker.showButtonOnly(true);
-        datePicker.addActionListener(this);
-        datePicker.setShowTodayButton(true);
+        // Create a date picker with hidden text field (showing button only).
+        DatePickerSettings dateSettings = new DatePickerSettings();
+        dateSettings.setVisibleDateTextField(false);
+        dateSettings.setGapBeforeButtonPixels(0);
+
+        datePicker = new DatePicker(dateSettings);
+        datePicker.addDateChangeListener(this);
+        datePicker.getComponentToggleCalendarButton().setIcon(IconTheme.JabRefIcon.DATE_PICKER.getIcon());
+        datePicker.getComponentToggleCalendarButton().setText("");
+
         panel.setLayout(new BorderLayout());
         panel.add(datePicker, BorderLayout.WEST);
         editor = pEditor;
     }
 
     @Override
-    public void actionPerformed(ActionEvent e) {
-        Date date = datePicker.getDate();
+    public void dateChanged(DateChangeEvent dateChangeEvent) {
+        LocalDate date = datePicker.getDate();
         if (date != null) {
             if (isoFormat) {
-                editor.setText(EasyDateFormat.isoDateFormat().getDateAt(date));
+                editor.setText(date.format(DateTimeFormatter.ISO_DATE));
             } else {
-                editor.setText(EasyDateFormat
-                        .fromTimeStampFormat(Globals.prefs.get(JabRefPreferences.TIME_STAMP_FORMAT))
-                        .getDateAt(date));
+                EasyDateFormat.fromTimeStampFormat(Globals.prefs.get(JabRefPreferences.TIME_STAMP_FORMAT)).getDateAt(ZonedDateTime.from(date));
             }
         } else {
             // in this case the user selected "none" in the date picker, so we just clear the field

src/main/java/net/sf/jabref/logic/autosaveandbackup/BackupManager.java

@@ -1,6 +1,5 @@
 package net.sf.jabref.logic.autosaveandbackup;
 
-import java.io.File;
 import java.io.IOException;
 import java.nio.charset.Charset;
 import java.nio.file.Files;
@@ -31,7 +30,8 @@
 
 /**
  * Backups the given bib database file from {@link BibDatabaseContext} on every {@link BibDatabaseContextChangedEvent}.
- * An intelligent {@link ExecutorService} with a {@link BlockingQueue} prevents a high load while making backups and rejects all redundant backup tasks.
+ * An intelligent {@link ExecutorService} with a {@link BlockingQueue} prevents a high load while making backups and
+ * rejects all redundant backup tasks.
  * This class does not manage the .bak file which is created when opening a database.
  */
 public class BackupManager {
@@ -44,63 +44,19 @@ public class BackupManager {
 
     private final BibDatabaseContext bibDatabaseContext;
     private final JabRefPreferences preferences;
-    private final BlockingQueue<Runnable> workerQueue;
     private final ExecutorService executor;
-    private final Charset charset;
-
-    private Path originalPath;
-    private Path backupPath;
+    private final Runnable backupTask = () -> determineBackupPath().ifPresent(this::performBackup);
 
 
     private BackupManager(BibDatabaseContext bibDatabaseContext) {
         this.bibDatabaseContext = bibDatabaseContext;
         this.preferences = JabRefPreferences.getInstance();
-        this.workerQueue = new ArrayBlockingQueue<>(1);
+        BlockingQueue<Runnable> workerQueue = new ArrayBlockingQueue<>(1);
         this.executor = new ThreadPoolExecutor(1, 1, 0, TimeUnit.SECONDS, workerQueue);
-        this.charset = bibDatabaseContext.getMetaData().getEncoding().orElse(preferences.getDefaultEncoding());
-    }
-
-
-    private final Runnable backupTask = new Runnable() {
-        @Override
-        public void run() {
-            try {
-                SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(preferences).withEncoding(charset).withMakeBackup(false);
-                new BibtexDatabaseWriter<>(FileSaveSession::new).saveDatabase(bibDatabaseContext, prefs).commit(backupPath);
-            } catch (SaveException e) {
-                LOGGER.error("Error while saving file.", e);
-            }
-        }
-    };
-
-    @Subscribe
-    public synchronized void listen(@SuppressWarnings("unused") BibDatabaseContextChangedEvent event) {
-        startBackupTask();
-    }
-
-    private void startBackupTask() {
-        try {
-            executor.submit(backupTask);
-        } catch (RejectedExecutionException e) {
-            LOGGER.debug("Rejecting while another backup process is already running.");
-        }
-    }
 
-    /**
-     * Unregisters the BackupManager from the eventBus of {@link BibDatabaseContext} and deletes the backup file.
-     * This method should only be used when closing a database/JabRef legally.
-     */
-    private void shutdown() {
-        bibDatabaseContext.getDatabase().unregisterListener(this);
-        bibDatabaseContext.getMetaData().unregisterListener(this);
-        executor.shutdown();
-        try {
-            if (Files.exists(backupPath) && !Files.isDirectory(backupPath)) {
-                Files.delete(backupPath);
-            }
-        } catch (IOException e) {
-            LOGGER.error("Error while deleting the backup file.", e);
-        }
+        // Listen for change events
+        bibDatabaseContext.getDatabase().registerListener(this);
+        bibDatabaseContext.getMetaData().registerListener(this);
     }
 
     static Path getBackupPath(Path originalPath) {
@@ -109,38 +65,26 @@ static Path getBackupPath(Path originalPath) {
 
     /**
      * Starts the BackupManager which is associated with the given {@link BibDatabaseContext}.
-     * If no database file is present in {@link BibDatabaseContext}, {@link BackupManager} will do nothing.
+     * As long as no database file is present in {@link BibDatabaseContext}, the {@link BackupManager} will do nothing.
      *
      * @param bibDatabaseContext Associated {@link BibDatabaseContext}
      */
     public static BackupManager start(BibDatabaseContext bibDatabaseContext) {
         BackupManager backupManager = new BackupManager(bibDatabaseContext);
-
-        Optional<File> originalFile = bibDatabaseContext.getDatabaseFile();
-
-        if (originalFile.isPresent()) {
-            backupManager.originalPath = originalFile.get().toPath();
-            backupManager.backupPath = getBackupPath(backupManager.originalPath);
-            backupManager.startBackupTask();
-            bibDatabaseContext.getDatabase().registerListener(backupManager);
-            bibDatabaseContext.getMetaData().registerListener(backupManager);
-            runningInstances.add(backupManager);
-        }
-
+        backupManager.startBackupTask();
+        runningInstances.add(backupManager);
         return backupManager;
     }
 
     /**
-     * Shuts down the BackupManager which is associated with the given {@link BibDatabaseContext}
+     * Shuts down the BackupManager which is associated with the given {@link BibDatabaseContext}.
      *
      * @param bibDatabaseContext Associated {@link BibDatabaseContext}
      */
     public static void shutdown(BibDatabaseContext bibDatabaseContext) {
-        runningInstances.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).findAny()
-                .ifPresent(instance -> {
-                    instance.shutdown();
-                    runningInstances.remove(instance);
-                });
+        runningInstances.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(
+                BackupManager::shutdown);
+        runningInstances.removeIf(instance -> instance.bibDatabaseContext == bibDatabaseContext);
     }
 
     /**
@@ -166,4 +110,54 @@ public static void restoreBackup(Path originalPath) {
             LOGGER.error("Error while restoring the backup file.", e);
         }
     }
+
+    private Optional<Path> determineBackupPath() {
+        return bibDatabaseContext.getDatabasePath().map(BackupManager::getBackupPath);
+    }
+
+    private void performBackup(Path backupPath) {
+        try {
+            Charset charset = bibDatabaseContext.getMetaData().getEncoding().orElse(preferences.getDefaultEncoding());
+            SavePreferences savePreferences = SavePreferences.loadForSaveFromPreferences(preferences).withEncoding
+                    (charset).withMakeBackup(false);
+            new BibtexDatabaseWriter<>(FileSaveSession::new).saveDatabase(bibDatabaseContext, savePreferences).commit
+                    (backupPath);
+        } catch (SaveException e) {
+            LOGGER.error("Error while saving file.", e);
+        }
+    }
+
+    @Subscribe
+    public synchronized void listen(@SuppressWarnings("unused") BibDatabaseContextChangedEvent event) {
+        startBackupTask();
+    }
+
+    private void startBackupTask() {
+        try {
+            executor.submit(backupTask);
+        } catch (RejectedExecutionException e) {
+            LOGGER.debug("Rejecting while another backup process is already running.");
+        }
+    }
+
+    /**
+     * Unregisters the BackupManager from the eventBus of {@link BibDatabaseContext} and deletes the backup file.
+     * This method should only be used when closing a database/JabRef legally.
+     */
+    private void shutdown() {
+        bibDatabaseContext.getDatabase().unregisterListener(this);
+        bibDatabaseContext.getMetaData().unregisterListener(this);
+        executor.shutdown();
+        determineBackupPath().ifPresent(this::deleteBackupFile);
+    }
+
+    private void deleteBackupFile(Path backupPath) {
+        try {
+            if (Files.exists(backupPath) && !Files.isDirectory(backupPath)) {
+                Files.delete(backupPath);
+            }
+        } catch (IOException e) {
+            LOGGER.error("Error while deleting the backup file.", e);
+        }
+    }
 }