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

* upstream/master:
  Add throttle to AutosaveUIManager (#5680)
  Do not couple search position to sidebar width (#5716)
  fix springer fetcher tests
  Bump controlsfx from 11.0.0 to 11.0.1 (#5714)
  Add CHANGELOG.md entry for Oracle
  Enable oracle tests (#5683)

.github/workflows/refresh-csl-subtrees.yml

@@ -2,7 +2,7 @@ name: Refresh Citation Style Language Files
 
 on:
  schedule:
- # run on 1th and 15th of each month
+ # run on 1st and 15th of each month
  - cron: '1 2 1,15 * *'
 
 jobs:

.github/workflows/tests-oracle.yml

@@ -0,0 +1,66 @@
+name: Oracle Tests
+
+on:
+ push:
+ paths:
+ - 'src/test/java/org/jabref/model/database/**'
+ - 'src/test/java/org/jabref/logic/shared/**'
+ - '.github/workflows/tests-oracle.yml'
+ - 'build.gradle'
+ schedule:
+ # run on each Wednesday
+ - cron: '2 3 * * 3'
+
+jobs:
+ oracletests:
+ name: Oracle tests
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout source
+ uses: actions/checkout@v1
+ with:
+ depth: 1
+ submodules: false
+ - name: Set up JDK
+ uses: actions/setup-java@v1
+ with:
+ java-version: 13
+ - uses: actions/cache@v1
+ name: Restore gradle chache
+ with:
+ path: ~/.gradle/caches
+ key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+ restore-keys: |
+ ${{ runner.OS }}-gradle-${{ env.cache-name }}-
+ ${{ runner.OS }}-gradle-
+ ${{ runner.OS }}-
+ - uses: actions/cache@v1
+ name: Restore gradle wrapper
+ with:
+ path: ~/.gradle/wrapper
+ key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+ - name: Start Oracle XE
+ run: |
+ mkdir ~/oracle-xe || true
+ cd ~/oracle-xe
+ wget -qN https://github.com/deusaquilus/docker-oracle-xe/archive/master.zip
+ unzip master.zip
+ cd docker-oracle-xe-master
+ wget -qN http://ccrypt.sourceforge.net/download/1.11/ccrypt-1.11.linux-x86_64.tar.gz
+ wget -qN -O files/oracle-database-xe-18c-1.0-1.x86_64.rpm.cpt https://files.jabref.org/thing.cpt
+ pwd
+ tar xzf ccrypt-1.11.linux-x86_64.tar.gz
+ ccrypt-1.11.linux-x86_64/ccrypt -d -E CCRYPT files/oracle-database-xe-18c-1.0-1.x86_64.rpm.cpt
+ docker build -t oracle-xe:18c .
+ docker run -d -p 32118:1521 -p 35518:5500 --name=oracle-xe oracle-xe:18c
+ # give oracle some time to start
+ sleep 300
+ docker logs oracle-xe
+ # path `/opt/oracle/product/18c/dbhomeXE` is taken from the `Dockerfile` used to build "oracle-xe"
+ docker exec -i oracle-xe bash -c "source /home/oracle/.bashrc; /bin/bash -c '/opt/oracle/product/18c/dbhomeXE/bin/sqlplus sys/Oracle18@localhost/XE as sysdba'" < $GITHUB_WORKSPACE/buildres/setup-test-oracle.sql
+ env:
+ CCRYPT: ${{ secrets.CCRYPT }}
+ - name: Run database test
+ run: ./gradlew databaseTest --rerun-tasks
+ env:
+ DBMS: "oracle"

.github/workflows/tests.yml

@@ -17,7 +17,7 @@ jobs:
  with:
  java-version: 13
  - uses: actions/cache@v1
- name: Restore gradle chache
+ name: Restore gradle cache
  with:
  path: ~/.gradle/caches
  key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
@@ -67,7 +67,7 @@ jobs:
  if: failure()
  run: |
  sudo apt-get install -qq -y xml-twig-tools xsltproc
- scripts/after-failure.sh 
+ scripts/after-failure.sh
  databasetests:
  name: Database tests
  runs-on: ubuntu-latest
@@ -227,7 +227,7 @@ jobs:
  name: Restore gradle wrapper
  with:
  path: ~/.gradle/wrapper
- key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }} 
+ key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
  - name: Update test coverage metrics
  run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);
  env:

CHANGELOG.md

@@ -24,6 +24,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added support to switch between biblatex and bibtex library types. [#5550](https://github.com/JabRef/jabref/issues/5550)
 - We changed the save action buttons to be easier to understand. [#5565](https://github.com/JabRef/jabref/issues/5565)
 - We made the columns for groups, files and uri in the main table reorderable and merged the clickable icon columns for uri, url, doi and eprint. [#5544](https://github.com/JabRef/jabref/pull/5544)
+- We reduced the number of write actions performed when autosave is enabled [#5679](https://github.com/JabRef/jabref/issues/5679)
 
 ### Fixed
 
@@ -67,6 +68,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the author field was not correctly parsed during bibtex key-generation. [#5551](https://github.com/JabRef/jabref/issues/5551)
 - We fixed an issue where notifications where shown during autosave. [#5555](https://github.com/JabRef/jabref/issues/5555)
 - We fixed an issue where the side pane was not remembering its position. [#5615](https://github.com/JabRef/jabref/issues/5615)
+- We fixed an issue where JabRef could not interact with [Oracle XE](https://www.oracle.com/de/database/technologies/appdev/xe.html) in the [shared SQL database setup](https://docs.jabref.org/collaborative-work/sqldatabase).
+- We fixed an issue where the toolbar icons were hidden on smaller screens.
 
 ### Removed
 

build.gradle

@@ -166,7 +166,7 @@ dependencies {
  compile 'org.fxmisc.richtext:richtextfx:0.10.3'
  compile group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
  compile 'com.jfoenix:jfoenix:9.0.9'
- compile 'org.controlsfx:controlsfx:11.0.0'
+ compile 'org.controlsfx:controlsfx:11.0.1'
 
  compile 'org.jsoup:jsoup:1.12.1'
  compile 'com.konghq:unirest-java:3.2.00'

buildres/setup-test-oracle.sql

@@ -0,0 +1,6 @@
+create pluggable database jabref admin user jabref identified by jabref
+ file_name_convert=('/opt/oracle/oradata/XE/pdbseed','/opt/oracle/oradata/XE/JABREF');
+alter pluggable database jabref open read write;
+alter pluggable database all save state;
+ALTER SESSION SET CONTAINER = jabref;
+grant all privileges to jabref container=current;

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -422,8 +422,6 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
 
  EasyBind.subscribe(sidePane.visibleProperty(), visible -> {
  if (visible) {
- // Run SplitPane.setResizableWithParent later to avoid miscalculation during initial layouting
- Platform.runLater(() -> SplitPane.setResizableWithParent(sidePane, Boolean.FALSE));
  if (!splitPane.getItems().contains(sidePane)) {
  splitPane.getItems().add(0, sidePane);
  setDividerPosition();
@@ -452,6 +450,7 @@ private void setDividerPosition() {
 
  private Node createToolbar() {
  Pane leftSpacer = new Pane();
+ leftSpacer.setMinWidth(50);
  HBox.setHgrow(leftSpacer, Priority.SOMETIMES);
  Pane rightSpacer = new Pane();
  HBox.setHgrow(rightSpacer, Priority.SOMETIMES);
@@ -471,9 +470,6 @@ private Node createToolbar() {
  factory.createIconButton(StandardActions.SAVE_LIBRARY, new OldDatabaseCommandWrapper(Actions.SAVE, this, stateManager)),
  leftSpacer
  );
- leftSide.setMinWidth(100);
- leftSide.prefWidthProperty().bind(sidePane.widthProperty());
- leftSide.maxWidthProperty().bind(sidePane.widthProperty());
 
  final PushToApplicationAction pushToApplicationAction = getPushToApplicationsManager().getPushToApplicationAction();
  final Button pushToApplicationButton = factory.createIconButton(pushToApplicationAction.getActionInformation(), pushToApplicationAction);

src/main/java/org/jabref/logic/autosaveandbackup/AutosaveManager.java

@@ -2,11 +2,9 @@
 
 import java.util.HashSet;
 import java.util.Set;
-import java.util.concurrent.ArrayBlockingQueue;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.RejectedExecutionException;
-import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.Future;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.ScheduledThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 
 import org.jabref.model.database.BibDatabaseContext;
@@ -21,38 +19,40 @@
 
 /**
  * Saves the given {@link BibDatabaseContext} on every {@link BibDatabaseContextChangedEvent} by posting a new {@link AutosaveEvent}.
- * An intelligent {@link ExecutorService} with a {@link BlockingQueue} prevents a high load while saving and rejects all redundant save tasks.
+ * An intelligent {@link ScheduledThreadPoolExecutor} prevents a high load while saving and rejects all redundant save tasks.
+ * The scheduled action is stored and canceled if a newer save action is proposed.
  */
 public class AutosaveManager {
 
  private static final Logger LOGGER = LoggerFactory.getLogger(AutosaveManager.class);
+ private static final int AUTO_SAVE_DELAY = 200;
 
  private static Set<AutosaveManager> runningInstances = new HashSet<>();
 
  private final BibDatabaseContext bibDatabaseContext;
- private final BlockingQueue<Runnable> workerQueue;
- private final ExecutorService executor;
+ private final ScheduledExecutorService executor;
  private final EventBus eventBus;
  private final CoarseChangeFilter changeFilter;
+ private Future<?> scheduledSaveAction;
 
  private AutosaveManager(BibDatabaseContext bibDatabaseContext) {
  this.bibDatabaseContext = bibDatabaseContext;
- this.workerQueue = new ArrayBlockingQueue<>(1);
- this.executor = new ThreadPoolExecutor(1, 1, 0, TimeUnit.SECONDS, workerQueue);
+ ScheduledThreadPoolExecutor executor = new ScheduledThreadPoolExecutor(1);
+ executor.setRemoveOnCancelPolicy(true); // This prevents memory leaks
+ this.executor = executor;
  this.eventBus = new EventBus();
  this.changeFilter = new CoarseChangeFilter(bibDatabaseContext);
  changeFilter.registerListener(this);
  }
 
  @Subscribe
  public synchronized void listen(@SuppressWarnings("unused") BibDatabaseContextChangedEvent event) {
- try {
- executor.submit(() -> {
- eventBus.post(new AutosaveEvent());
- });
- } catch (RejectedExecutionException e) {
- LOGGER.debug("Rejecting autosave while another save process is already running.");
+ if (scheduledSaveAction != null) {
+ scheduledSaveAction.cancel(false);
  }
+ scheduledSaveAction = executor.schedule(() -> {
+ eventBus.post(new AutosaveEvent());
+ }, AUTO_SAVE_DELAY, TimeUnit.MILLISECONDS);
  }
 
  private void shutdown() {

src/main/java/org/jabref/logic/importer/fetcher/SpringerFetcher.java

@@ -38,7 +38,7 @@ public class SpringerFetcher implements SearchBasedParserFetcher {
  private static final Logger LOGGER = LoggerFactory.getLogger(SpringerFetcher.class);
 
  private static final String API_URL = "http://api.springernature.com/meta/v1/json?q=";
- private static final String API_KEY = "b0c7151179b3d9c1119cf325bca8460d";
+ private static final String API_KEY = "a98b4a55181ffcd27259bea45edad12e";
 
  /**
  * Convert a JSONObject obtained from http://api.springer.com/metadata/json to a BibEntry