Merge branch 'master' into batch_DBMSProcessor_fields

JabRef · Jan 2, 2020 · 931ccad · 931ccad
2 parents 8cf40b4 + fab4bdc
commit 931ccad
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diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml
@@ -5,15 +5,14 @@ on:
     types: [closed]
 
 jobs:
-  build:
-
+  cleanup:
     runs-on: ubuntu-latest
 
     steps:
     - name: Extract branch name
       id: extract_branch
       run: |
-        echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
     - name: Delete folder on builds.jabref.org
       uses: appleboy/[email protected]
       with:

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -1,6 +1,10 @@
 name: Refresh Citation Style Language Files
 
 on:
+  push:
+    paths:
+      - '.github/workflows/refresh-csl-subtrees.yml'
+      - 'src/main/resources/csl-locales/**'
   schedule:
     # run on 1st and 15th of each month
     - cron: '1 2 1,15 * *'
@@ -11,28 +15,32 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2-beta
+        uses: actions/checkout@v2
         with:
           ref: master
+          fetch-depth: 0
       - name: Add csl-styles remote
         run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
       - name: Update csl-styles
-        run: | 
+        run: |
           git checkout master
+          git config --local core.editor /usr/bin/cat
+          git config user.name "github actions"
+          git config user.email "[email protected]"
           git subtree pull --prefix src/main/resources/csl-styles csl-styles master --squash
       - name: Add csl-locales remote
         run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
       - name: Update csl-locales
         run: |
-          git checkout master
           git subtree pull --prefix src/main/resources/csl-locales csl-locales master --squash
       - uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: master
       - name: Report issues
         if: failure()
         uses: JasonEtco/create-an-issue@master
-        env: 
+        env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           filename: .github/failure-csl-update.md
diff --git a/.github/workflows/tests-oracle.yml b/.github/workflows/tests-oracle.yml
@@ -2,6 +2,8 @@ name: Oracle Tests
 
 on:
   push:
+    branches:
+      - master
     paths:
       - 'src/test/java/org/jabref/model/database/**'
       - 'src/test/java/org/jabref/logic/shared/**'

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,6 +1,11 @@
 name: Tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    # always run on pull requests
 
 jobs:
   checkstyle:

diff --git a/AUTHORS b/AUTHORS
@@ -151,6 +151,7 @@ Jong-Ho Shinn
 Jorge Tornero
 josephshin93
 Joshua Ramon Enslin
+José Jesús Sinohui Fernández
 Julian Pfeifer
 Jure Slak
 József Pallagi
@@ -182,6 +183,7 @@ Ling Wang
 Linus Dietz
 Lorenzo Genta
 Luciana de Melo e Abud
+Luis Romero
 Mairieli Wessel
 Malik Atalla
 Malte Deiseroth
@@ -196,6 +198,7 @@ Martin Stolle
 Martina Catizone
 Mathias Walter
 Matthias Geiger
+Matthias Mueller
 Mattia Bunel
 Mattias Ulbrich
 mcmoody

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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)
 - We fixed an issue where non-default previews didn't handle unicode characters. [#5779](https://github.com/JabRef/jabref/issues/5779)
+- We fixed an issue where the ampersand character wasn't rendering correctly on previews.[#3840](https://github.com/JabRef/jabref/issues/3840)
 
 
 ### Removed

diff --git a/build.gradle b/build.gradle
@@ -110,9 +110,9 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.17'
-    compile 'org.apache.pdfbox:fontbox:2.0.17'
-    compile 'org.apache.pdfbox:xmpbox:2.0.17'
+    compile 'org.apache.pdfbox:pdfbox:2.0.18'
+    compile 'org.apache.pdfbox:fontbox:2.0.18'
+    compile 'org.apache.pdfbox:xmpbox:2.0.18'
 
     compile group: 'org.apache.commons', name: 'commons-csv', version: '1.7'
 
@@ -149,7 +149,7 @@ dependencies {
         exclude module: 'oraclepki'
     }
 
-    compile ('com.google.guava:guava:28.1-jre') {
+    compile ('com.google.guava:guava:28.2-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -225,7 +225,7 @@ dependencies {
     testCompile "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testCompile "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.27'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.28'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.2'
     jython 'org.python:jython-standalone:2.7.1'
 }
@@ -255,7 +255,9 @@ dependencyUpdates.resolutionStrategy = {
             }
         }
         rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.0.26-9.1.1/ || selection.candidate.version ==~ /2.0.26-9.1.2/) {
+            if (selection.candidate.version ==~ /2.0.26-9.1.2/
+                || selection.candidate.version ==~ /2.0.26-9.1.1/ 
+                || selection.candidate.version ==~ /2.0.26-9.1.0/) {
                 selection.reject('1.7.22-11 is actually newer (strange version system)')
             }
         }

diff --git a/config/checkstyle/checkstyle.xml b/config/checkstyle/checkstyle.xml
@@ -20,11 +20,8 @@
         <!-- Checks for Javadoc comments: https://checkstyle.org/config_javadoc.html -->
         <module name="InvalidJavadocPosition"/>
         <module name="JavadocMethod">
-            <property name="allowUndeclaredRTE" value="true"/>
             <property name="allowMissingParamTags" value="true"/>
-            <property name="allowMissingThrowsTags" value="true"/>
             <property name="allowMissingReturnTag" value="true"/>
-            <property name="validateThrows" value="true"/>
         </module>
 
         <!-- Checks for imports: https://checkstyle.org/config_import.html -->

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -59,7 +59,7 @@
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.worker.SendAsEMailAction;
@@ -80,8 +80,8 @@
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
 import org.jabref.model.database.event.CoarseChangeFilter;
+import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.database.event.EntriesRemovedEvent;
-import org.jabref.model.database.event.EntryAddedEvent;
 import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.database.shared.DatabaseSynchronizer;
 import org.jabref.model.entry.BibEntry;
@@ -168,7 +168,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         setupActions();
 
         this.getDatabase().registerListener(new SearchListener());
-        this.getDatabase().registerListener(new EntryRemovedListener());
+        this.getDatabase().registerListener(new EntriesRemovedListener());
 
         // ensure that at each addition of a new entry, the entry is added to the groups interface
         this.bibDatabaseContext.getDatabase().registerListener(new GroupTreeListener());
@@ -605,29 +605,39 @@ public void registerUndoableChanges(List<FieldChange> changes) {
         }
     }
 
+    public void insertEntry(final BibEntry bibEntry) {
+        if (bibEntry != null) {
+            insertEntries(Collections.singletonList(bibEntry));
+        }
+    }
+
     /**
-     * This method is called from JabRefFrame when the user wants to create a new entry.
+     * This method is called from JabRefFrame when the user wants to create a new entry or entries.
+     * It is necessary when the user would expect the added entry or one of the added entries
+     * to be selected in the entry editor
      *
-     * @param bibEntry The new entry.
+     * @param entries The new entries.
      */
-    public void insertEntry(final BibEntry bibEntry) {
-        if (bibEntry != null) {
+
+    public void insertEntries(final List<BibEntry> entries) {
+        if (!entries.isEmpty()) {
             try {
-                bibDatabaseContext.getDatabase().insertEntry(bibEntry);
+                bibDatabaseContext.getDatabase().insertEntries(entries);
 
                 // Set owner and timestamp
-                UpdateField.setAutomaticFields(bibEntry, true, true, Globals.prefs.getUpdateFieldPreferences());
-
-                // Create an UndoableInsertEntry object.
-                getUndoManager().addEdit(new UndoableInsertEntry(bibDatabaseContext.getDatabase(), bibEntry));
+                for (BibEntry entry : entries) {
+                    UpdateField.setAutomaticFields(entry, true, true, Globals.prefs.getUpdateFieldPreferences());
+                }
+                // Create an UndoableInsertEntries object.
+                getUndoManager().addEdit(new UndoableInsertEntries(bibDatabaseContext.getDatabase(), entries));
 
                 markBaseChanged(); // The database just changed.
                 if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
-                    showAndEdit(bibEntry);
+                    showAndEdit(entries.get(0));
                 }
-                clearAndSelect(bibEntry);
+                clearAndSelect(entries.get(0));
             } catch (KeyCollisionException ex) {
-                LOGGER.info("Collision for bibtex key" + bibEntry.getId(), ex);
+                LOGGER.info("Collision for bibtex key" + ex.getId(), ex);
             }
         }
     }
@@ -1111,22 +1121,21 @@ public void searchAndOpen() {
     private class GroupTreeListener {
 
         @Subscribe
-        public void listen(EntryAddedEvent addedEntryEvent) {
-            // if the added entry is an undo don't add it to the current group
-            if (addedEntryEvent.getEntriesEventSource() == EntriesEventSource.UNDO) {
+        public void listen(EntriesAddedEvent addedEntriesEvent) {
+            // if the event is an undo, don't add it to the current group
+            if (addedEntriesEvent.getEntriesEventSource() == EntriesEventSource.UNDO) {
                 return;
             }
 
-            // Automatically add new entry to the selected group (or set of groups)
+            // Automatically add new entries to the selected group (or set of groups)
             if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_ASSIGN_GROUP)) {
-                final List<BibEntry> entries = Collections.singletonList(addedEntryEvent.getBibEntry());
                 Globals.stateManager.getSelectedGroup(bibDatabaseContext).forEach(
-                        selectedGroup -> selectedGroup.addEntriesToGroup(entries));
+                        selectedGroup -> selectedGroup.addEntriesToGroup(addedEntriesEvent.getBibEntries()));
             }
         }
     }
 
-    private class EntryRemovedListener {
+    private class EntriesRemovedListener {
 
         @Subscribe
         public void listen(EntriesRemovedEvent entriesRemovedEvent) {
@@ -1141,8 +1150,8 @@ public void listen(EntriesRemovedEvent entriesRemovedEvent) {
     private class SearchAutoCompleteListener {
 
         @Subscribe
-        public void listen(EntryAddedEvent addedEntryEvent) {
-            DefaultTaskExecutor.runInJavaFXThread(() -> searchAutoCompleter.indexEntry(addedEntryEvent.getBibEntry()));
+        public void listen(EntriesAddedEvent addedEntriesEvent) {
+            DefaultTaskExecutor.runInJavaFXThread(() -> addedEntriesEvent.getBibEntries().forEach(entry -> searchAutoCompleter.indexEntry(entry)));
         }
 
         @Subscribe
@@ -1158,7 +1167,7 @@ public void listen(EntryChangedEvent entryChangedEvent) {
     private class SearchListener {
 
         @Subscribe
-        public void listen(EntryAddedEvent addedEntryEvent) {
+        public void listen(EntriesAddedEvent addedEntryEvent) {
             DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
         }
 

diff --git a/src/main/java/org/jabref/gui/autocompleter/AutoCompleteUpdater.java b/src/main/java/org/jabref/gui/autocompleter/AutoCompleteUpdater.java
@@ -1,6 +1,9 @@
 package org.jabref.gui.autocompleter;
 
-import org.jabref.model.database.event.EntryAddedEvent;
+import java.util.List;
+
+import org.jabref.model.database.event.EntriesAddedEvent;
+import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.event.EntryChangedEvent;
 
 import com.google.common.eventbus.Subscribe;
@@ -17,8 +20,11 @@ public AutoCompleteUpdater(SuggestionProviders suggestionProviders) {
     }
 
     @Subscribe
-    public void listen(EntryAddedEvent addedEntryEvent) {
-        suggestionProviders.indexEntry(addedEntryEvent.getBibEntry());
+    public void listen(EntriesAddedEvent entryAddedEvent) {
+        List<BibEntry> entries = entryAddedEvent.getBibEntries();
+        for (BibEntry entry : entries) {
+            suggestionProviders.indexEntry(entry);
+        }
     }
 
     @Subscribe

diff --git a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
@@ -6,7 +6,7 @@
 import org.jabref.JabRefGUI;
 import org.jabref.gui.preview.PreviewViewer;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -26,7 +26,7 @@ public EntryAddChangeViewModel(BibEntry entry) {
     @Override
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         database.getDatabase().insertEntry(entry);
-        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), entry));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), entry));
     }
 
     @Override

diff --git a/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java
@@ -8,7 +8,7 @@
 import org.jabref.gui.mergeentries.MergeEntries;
 import org.jabref.gui.mergeentries.MergeEntries.DefaultRadioButtonSelectionMode;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -43,8 +43,8 @@ public EntryChangeViewModel(BibEntry entry, BibEntry newEntry, BibDatabaseContex
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         database.getDatabase().removeEntry(oldEntry);
         database.getDatabase().insertEntry(mergePanel.getMergeEntry());
-        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), oldEntry));
-        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), mergePanel.getMergeEntry()));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), oldEntry));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), mergePanel.getMergeEntry()));
     }
 
     @Override

diff --git a/src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java b/src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java
@@ -21,7 +21,7 @@
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog.DuplicateResolverResult;
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog.DuplicateResolverType;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
@@ -167,10 +167,8 @@ private void handleDuplicates(DuplicateSearchResult result) {
         }
         // and adding merged entries:
         if (!result.getToAdd().isEmpty()) {
-            for (BibEntry entry : result.getToAdd()) {
-                panel.getDatabase().insertEntry(entry);
-                compoundEdit.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry));
-            }
+            compoundEdit.addEdit(new UndoableInsertEntries(panel.getDatabase(), result.getToAdd()));
+            panel.getDatabase().insertEntries(result.getToAdd());
             panel.markBaseChanged();
         }
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,6 +2,8 @@ name: Oracle Tests @@
     on:
       push:
+        branches:
+          - master
         paths:
           - 'src/test/java/org/jabref/model/database/**'
           - 'src/test/java/org/jabref/logic/shared/**'
@@ Expand Down @@