Merge remote-tracking branch 'upstream/master' into copyLinkedFilesIn…

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* upstream/master: (21 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
  ...

.github/FUNDING.yml

@@ -1,12 +1,12 @@
 # These are supported funding model platforms
 
 github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
-patreon: koppor
+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: koppor
+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

build.gradle

@@ -17,8 +17,8 @@ buildscript {
 
 plugins {
     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'
     id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
     id 'net.ltgt.errorprone' version '0.8.1'
@@ -90,9 +90,9 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.15'
-    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'
 
@@ -143,10 +143,10 @@ dependencies {
 
     // >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:2.11.2'
-    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'
+    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'
 
@@ -157,23 +157,23 @@ 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'
 
-    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 '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'
+    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'
 }

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();
     }
 }

src/main/java/org/jabref/gui/groups/GroupTreeView.java

@@ -7,6 +7,7 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Consumer;
+import java.util.stream.Collectors;
 
 import javax.inject.Inject;
 
@@ -280,12 +281,7 @@ private void updateSelection(List<TreeItem<GroupNodeViewModel>> newSelectedGroup
         if ((newSelectedGroups == null) || newSelectedGroups.isEmpty()) {
             viewModel.selectedGroupsProperty().clear();
         } else {
-            List<GroupNodeViewModel> list = new ArrayList<>();
-            for (TreeItem<GroupNodeViewModel> model : newSelectedGroups) {
-                if ((model != null) && (model.getValue() != null) && !(model.getValue().getGroupNode().getGroup() instanceof AllEntriesGroup)) {
-                    list.add(model.getValue());
-                }
-            }
+            List<GroupNodeViewModel> list = newSelectedGroups.stream().filter(model -> model != null && !(model.getValue().getGroupNode().getGroup() instanceof AllEntriesGroup)).map(TreeItem<GroupNodeViewModel>::getValue).collect(Collectors.toList());
             viewModel.selectedGroupsProperty().setAll(list);
         }
     }
@@ -304,15 +300,7 @@ private Optional<TreeItem<GroupNodeViewModel>> getTreeItemByValue(TreeItem<Group
         if (root.getValue().equals(value)) {
             return Optional.of(root);
         }
-
-        for (TreeItem<GroupNodeViewModel> child : root.getChildren()) {
-            Optional<TreeItem<GroupNodeViewModel>> treeItemByValue = getTreeItemByValue(child, value);
-            if (treeItemByValue.isPresent()) {
-                return treeItemByValue;
-            }
-        }
-
-        return Optional.empty();
+        return root.getChildren().stream().filter(child -> getTreeItemByValue(child, value).isPresent()).findFirst();
     }
 
     private ContextMenu createContextMenuForGroup(GroupNodeViewModel group) {

src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -209,7 +209,7 @@ private void clearAndSelectLast() {
 
     public void paste() {
         // Find entries in clipboard
-        List<BibEntry> entriesToAdd = Globals.clipboardManager.extractEntries();
+        List<BibEntry> entriesToAdd = Globals.clipboardManager.extractData();
 
         if (!entriesToAdd.isEmpty()) {
             // Add new entries

src/main/java/org/jabref/logic/util/Version.java

@@ -3,8 +3,8 @@
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
 import java.net.URL;
-import java.net.URLConnection;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
@@ -91,7 +91,7 @@ public static Version parse(String version) {
      * Grabs all the available releases from the GitHub repository
      */
     public static List<Version> getAllAvailableVersions() throws IOException {
-        URLConnection connection = new URL(JABREF_GITHUB_RELEASES).openConnection();
+        HttpURLConnection connection = (HttpURLConnection) new URL(JABREF_GITHUB_RELEASES).openConnection();
         connection.setRequestProperty("Accept-Charset", "UTF-8");
         try (BufferedReader rd = new BufferedReader(new InputStreamReader(connection.getInputStream()))) {
 
@@ -102,6 +102,7 @@ public static List<Version> getAllAvailableVersions() throws IOException {
                 Version version = Version.parse(jsonObject.getString("tag_name").replaceFirst("v", ""));
                 versions.add(version);
             }
+            connection.disconnect();
             return versions;
         }
     }