Merge remote-tracking branch 'upstream/master' into jdk9

# By Carl Christian Snethlage (33) and others # Via GitHub (21) and Carl Christian Snethlage (2) * upstream/master: (103 commits) Bump junit-vintage-engine from 5.4.2 to 5.5.0 Bump log4j-api from 2.11.2 to 2.12.0 Bump junit-platform-launcher from 1.4.2 to 1.5.0 Bump log4j-core from 2.11.2 to 2.12.0 Bump log4j-slf4j18-impl from 2.11.2 to 2.12.0 Bump log4j-jul from 2.11.2 to 2.12.0 Bump junit-jupiter from 5.4.2 to 5.5.0 Bump com.github.johnrengelman.shadow from 5.0.0 to 5.1.0 Bump log4j-jcl from 2.11.2 to 2.12.0 Bump fontbox from 2.0.15 to 2.0.16 (#5080) Bump pdfbox from 2.0.15 to 2.0.16 (#5081) Bump xmpbox from 2.0.15 to 2.0.16 (#5082) Update FUNDING.yml Delete autoapproval.yml Bump com.install4j.gradle from 7.0.11 to 7.0.12 (#5077) Configure autoapproval plugin for dependabot Bump xmlunit-matchers from 2.6.2 to 2.6.3 (#5074) Bump checkstyle from 8.21 to 8.22 (#5072) Bump xmlunit-core from 2.6.2 to 2.6.3 (#5073) Refactor for loop to stream in groupTree Close version socket ... # Conflicts: # build.gradle
JabRef · Jul 6, 2019 · 666f1f3 · 666f1f3
2 parents 11039d8 + a50cb34
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diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+patreon: # Patreon user account
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: JabRef
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+custom: https://github.com/JabRef/jabref/wiki/Donations # Replace with a single custom sponsorship URL
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -61,10 +61,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We added a warning for empty BibTeX keys in the entry editor. [#4440](https://github.com/JabRef/jabref/issues/4440)
 - We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 - We added an option on the Linked File Viewer to rename the attached file of an entry directly on the JabRef. [#4844](https://github.com/JabRef/jabref/issues/4844)
 - We added an option in the preference dialog box that allows user to enable helpful tooltips.[#3599](https://github.com/JabRef/jabref/issues/3599)
+- We moved the dropdown menu for selecting the push-application from the toolbar into the external application preferences. [#674](https://github.com/JabRef/jabref/issues/674)
+- We removed the alphabetical ordering of the custom tabs and updated the error message when trying to create a general field with a name containing an illegal character. [#5019](https://github.com/JabRef/jabref/issues/5019)
+- We added a context menu to the bib(la)tex-source-editor to copy'n'paste. [#5007](https://github.com/JabRef/jabref/pull/5007)
 
 
 ### Fixed
@@ -123,7 +127,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the JabRef Icon in the macOS launchpad was not displayed correctly [#5003](https://github.com/JabRef/jabref/issues/5003)
 
 
-
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.

diff --git a/build.gradle b/build.gradle
@@ -21,8 +21,8 @@ buildscript {
 plugins {
     id 'application'
     id 'com.gradle.build-scan' version '2.3'
-    id 'com.install4j.gradle' version '7.0.11'
-    id 'com.github.johnrengelman.shadow' version '5.0.0'
+    id 'com.install4j.gradle' version '7.0.12'
+    id 'com.github.johnrengelman.shadow' version '5.1.0'
     // TODO: Modernizer does not yet work with Java 11
     //id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
@@ -118,14 +118,14 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.15'
-    compile 'org.apache.pdfbox:fontbox:2.0.15'
-    compile 'org.apache.pdfbox:xmpbox:2.0.15'
+    compile 'org.apache.pdfbox:pdfbox:2.0.16'
+    compile 'org.apache.pdfbox:fontbox:2.0.16'
+    compile 'org.apache.pdfbox:xmpbox:2.0.16'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.21'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.61'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.62'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -147,11 +147,11 @@ dependencies {
 
     compile 'mysql:mysql-connector-java:8.0.16'
 
-    compile 'org.postgresql:postgresql:42.2.5'
+    compile 'org.postgresql:postgresql:42.2.6'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:27.1-jre'
+    compile 'com.google.guava:guava:28.0-jre'
 
     compile group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
 
@@ -170,11 +170,12 @@ dependencies {
     compile 'org.jsoup:jsoup:1.12.1'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
-    compile 'org.slf4j:slf4j-api:1.8.0-beta4'
-    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-api:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-core:2.11.2'
+    // >1.8.0-beta is required for java 9 compatibility
+    compile 'org.slf4j:slf4j-api:2.0.0-alpha0'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.12.0'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.12.0'
+    compile 'org.apache.logging.log4j:log4j-api:2.12.0'
+    compile 'org.apache.logging.log4j:log4j-core:2.12.0'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
@@ -189,25 +190,24 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testCompile 'junit:junit:4.12'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.5.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.5.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.5.0'
 
-    testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
+    testRuntime 'org.apache.logging.log4j:log4j-core:2.12.0'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.12.0'
     testCompile 'net.bytebuddy:byte-buddy-parent:1.9.13'
     testCompile 'org.mockito:mockito-core:2.28.2'
     //testCompile 'com.github.tomakehurst:wiremock:2.23.2'
     testCompile 'org.reflections:reflections:0.9.11'
-    testCompile 'org.xmlunit:xmlunit-core:2.6.2'
-    testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    //testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
+    testCompile 'org.xmlunit:xmlunit-core:2.6.3'
+    testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
+    //testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.21'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.22'
     xjc 'com.sun.xml.bind:jaxb-xjc:2.2.4-1'
     jython 'org.python:jython-standalone:2.7.1'
 }

diff --git a/src/main/java/org/jabref/Globals.java b/src/main/java/org/jabref/Globals.java
@@ -1,6 +1,7 @@
 package org.jabref;
 
 import java.awt.GraphicsEnvironment;
+import java.io.IOException;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -24,6 +25,7 @@
 import org.jabref.preferences.JabRefPreferences;
 
 import com.google.common.base.StandardSystemProperty;
+import com.mashape.unirest.http.Unirest;
 import com.microsoft.applicationinsights.TelemetryClient;
 import com.microsoft.applicationinsights.TelemetryConfiguration;
 import com.microsoft.applicationinsights.internal.shutdown.SDKShutdownActivity;
@@ -125,6 +127,9 @@ public static void shutdownThreadPools() {
 
     public static void stopBackgroundTasks() {
         stopTelemetryClient();
+        try {
+            Unirest.shutdown();
+        } catch (IOException ignore) { }
     }
 
     public static Optional<TelemetryClient> getTelemetryClient() {

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
@@ -1028,11 +1028,20 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-background-color: -jr-error;
 }
 
+.titleHeader {
+    -fx-font-size: 150%;
+    -fx-padding: 0em 0em 0.5em 0em;
+}
+
 .sectionHeader {
-    -fx-font-size: 1.5em;
-    -fx-padding: 1em 0em 1em 0em;
+    -fx-font-size: 130%;
+    -fx-padding: 1em 0em 0.2em 0em;
 }
 
 .dialog-pane {
     -fx-background-color: -fx-control-inner-background;
 }
+
+.preference-sidepane {
+    -fx-background-color: -jr-sidepane-background;
+}
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -182,10 +182,9 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
 
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
 
-        this.entryEditor = new EntryEditor(this, preferences.getEntryEditorPreferences(), Globals.getFileUpdateMonitor(), dialogService, externalFileTypes, Globals.TASK_EXECUTOR);
+        this.entryEditor = new EntryEditor(this, preferences.getEntryEditorPreferences(), Globals.getFileUpdateMonitor(), dialogService, externalFileTypes, Globals.TASK_EXECUTOR, Globals.stateManager);
 
         this.preview = new PreviewPanel(getBibDatabaseContext(), this, dialogService, externalFileTypes, Globals.getKeyPrefs(), preferences.getPreviewPreferences());
-        frame().getGlobalSearchBar().getSearchQueryHighlightObservable().addSearchListener(preview);
     }
 
     @Subscribe

diff --git a/src/main/java/org/jabref/gui/ClipBoardManager.java b/src/main/java/org/jabref/gui/ClipBoardManager.java
@@ -1,6 +1,8 @@
 package org.jabref.gui;
 
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
@@ -28,13 +30,11 @@
 import org.slf4j.LoggerFactory;
 
 public class ClipBoardManager {
-
     public static final DataFormat XML = new DataFormat("application/xml");
-    
+
     private static final Logger LOGGER = LoggerFactory.getLogger(ClipBoardManager.class);
 
     private final Clipboard clipboard;
-
     private final ImportFormatReader importFormatReader;
 
     public ClipBoardManager() {
@@ -63,9 +63,8 @@ public String getContents() {
         String result = clipboard.getString();
         if (result == null) {
             return "";
-        } else {
-            return result;
         }
+        return result;
     }
 
     public void setHtmlContent(String html) {
@@ -89,40 +88,55 @@ public void setContent(List<BibEntry> entries) throws IOException {
         clipboard.setContent(content);
     }
 
-    public List<BibEntry> extractEntries() {
+    public List<BibEntry> extractData() {
         Object entries = clipboard.getContent(DragAndDropDataFormats.ENTRIES);
 
+        if (entries == null) {
+            return handleStringData(clipboard.getString());
+        }
+        return handleBibTeXData((String) entries);
+    }
+
+    private List<BibEntry> handleBibTeXData(String entries) {
         BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
-        if (entries != null) {
-            // We have determined that the clipboard data is a set of entries (serialized as a string).
-            try {
-                return parser.parseEntries((String) entries);
-            } catch (ParseException ex) {
-                LOGGER.error("Could not paste", ex);
-            }
-        } else {
-            String data = clipboard.getString();
-            if (data != null) {
-                try {
-                    // fetch from doi
-                    Optional<DOI> doi = DOI.parse(data);
-                    if (doi.isPresent()) {
-                        LOGGER.info("Found DOI in clipboard");
-                        Optional<BibEntry> entry = new DoiFetcher(Globals.prefs.getImportFormatPreferences()).performSearchById(doi.get().getDOI());
-                        return OptionalUtil.toList(entry);
-                    } else {
-                        try {
-                            UnknownFormatImport unknownFormatImport = importFormatReader.importUnknownFormat(data);
-                            return unknownFormatImport.parserResult.getDatabase().getEntries();
-                        } catch (ImportException e) {
-                            // import failed and result will be empty
-                        }
-                    }
-                } catch (FetcherException ex) {
-                    LOGGER.error("Error while fetching", ex);
-                }
-            }
+        try {
+            return parser.parseEntries(new ByteArrayInputStream(entries.getBytes(StandardCharsets.UTF_8)));
+        } catch (ParseException ex) {
+            LOGGER.error("Could not paste", ex);
+            return Collections.emptyList();
+        }
+    }
+
+    private List<BibEntry> handleStringData(String data) {
+        if (data == null || data.isEmpty()) {
+            return Collections.emptyList();
+        }
+
+        Optional<DOI> doi = DOI.parse(data);
+        if (doi.isPresent()) {
+            return fetchByDOI(doi.get());
+        }
+
+        return tryImportFormats(data);
+    }
+
+    private List<BibEntry> tryImportFormats(String data) {
+        try {
+            UnknownFormatImport unknownFormatImport = importFormatReader.importUnknownFormat(data);
+            return unknownFormatImport.parserResult.getDatabase().getEntries();
+        } catch (ImportException ignored) {
+            return Collections.emptyList();
+        }
+    }
+
+    private List<BibEntry> fetchByDOI(DOI doi) {
+        LOGGER.info("Found DOI in clipboard");
+        try {
+            Optional<BibEntry> entry = new DoiFetcher(Globals.prefs.getImportFormatPreferences()).performSearchById(doi.getDOI());
+            return OptionalUtil.toList(entry);
+        } catch (FetcherException ex) {
+            LOGGER.error("Error while fetching", ex);
+            return Collections.emptyList();
         }
-        return Collections.emptyList();
     }
 }