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

* upstream/master: (21 commits) Squashed 'src/main/resources/csl-locales/' changes from 4fa753374e..d73af4a3fe Squashed 'src/main/resources/csl-styles/' changes from 9e81857..f03dece Add deep link to uni Basel Refine information on codacy New Crowdin translations (#6020) Fix l10n New Crowdin translations (#6016) Fix teamscale link - and sort list alphabetically Update code-quality.md Update link to codacy/JabRef Integrate gradle validation in normal test workflow (#6001) Update CleanupUrlFormatter.java Update URLUtil.java Fix modernizer warnings Remove unused error prone Use Java version class Remove commented out code Upgrade deprecated gradle API Add plugin scope New menu "Lookup" ...
JabRef · Feb 26, 2020 · 0898e53 · 0898e53
2 parents 07868ff + 74667e9
commit 0898e53
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diff --git a/.github/workflows/gradle-wrapper-validation.yml b/.github/workflows/gradle-wrapper-validation.yml
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -208,3 +208,11 @@ jobs:
           CI: "false" # we pretend to run locally - even if tests fail on the CI, they count towards test coverage
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
+  # This is https://github.com/marketplace/actions/gradle-wrapper-validation
+  # It ensures that the jar file is from gradle and not by a strange third party.
+  gradlevalidation:
+    name: "Validate Gradle Wrapper"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: gradle/wrapper-validation-action@v1
diff --git a/build.gradle b/build.gradle
@@ -19,7 +19,6 @@ plugins {
     id 'application'
     id "com.simonharrer.modernizer" version '1.8.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.0'
-    //id 'net.ltgt.errorprone' version '0.8.1'
     id 'com.github.ben-manes.versions' version '0.28.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
@@ -46,10 +45,14 @@ apply from: 'eclipse.gradle'
 group = "org.jabref"
 version = project.findProperty('projVersion') ?: '100.0.0'
 
-sourceCompatibility = 13
-targetCompatibility = 13
+java {
+    sourceCompatibility = JavaVersion.VERSION_13
+    targetCompatibility = JavaVersion.VERSION_13
+}
 
-mainClassName = "$moduleName/org.jabref.JabRefLauncher"
+application {
+    mainClassName = "$moduleName/org.jabref.JabRefLauncher"
+}
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
 // These should be removed, as well as the files in the lib folder, as soon as they have valid module names
@@ -91,7 +94,6 @@ repositories {
 }
 
 configurations {
-    //errorprone
     libreoffice
 
     // TODO: Remove the following workaround for split error messages such as
@@ -108,121 +110,108 @@ javafx {
 
 dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
-    compile fileTree(dir: 'lib', includes: ['*.jar'])
+    implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.18'
-    compile 'org.apache.pdfbox:fontbox:2.0.18'
-    compile 'org.apache.pdfbox:xmpbox:2.0.18'
+    implementation 'org.apache.pdfbox:pdfbox:2.0.18'
+    implementation 'org.apache.pdfbox:fontbox:2.0.18'
+    implementation 'org.apache.pdfbox:xmpbox:2.0.18'
 
-    compile group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
+    implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
 
-    compile group: 'org.apache.tika', name: 'tika-core', version: '1.23'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '1.23'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.64'
+    implementation 'org.bouncycastle:bcprov-jdk15on:1.64'
 
-    compile 'commons-cli:commons-cli:1.4'
+    implementation 'commons-cli:commons-cli:1.4'
 
     // For Java 9+ compatibility, we include a bundled version of the libreoffice libraries
     // See https://bugs.documentfoundation.org/show_bug.cgi?id=117331#c8 for background information
     // Use the task bundleLibreOffice to update the bundled jar
-    //compile "org.libreoffice:juh:6.2.3"
-    //compile "org.libreoffice:jurt:6.2.3"
-    //compile "org.libreoffice:ridl:6.2.3"
-    //compile "org.libreoffice:unoil:6.2.3"
+    //implementation "org.libreoffice:juh:6.2.3"
+    //implementation "org.libreoffice:jurt:6.2.3"
+    //implementation "org.libreoffice:ridl:6.2.3"
+    //implementation "org.libreoffice:unoil:6.2.3"
 
-    compile 'io.github.java-diff-utils:java-diff-utils:4.5'
-    compile 'info.debatty:java-string-similarity:1.2.1'
+    implementation 'io.github.java-diff-utils:java-diff-utils:4.5'
+    implementation 'info.debatty:java-string-similarity:1.2.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
-    compile 'org.antlr:antlr-runtime:3.5.2'
+    implementation 'org.antlr:antlr-runtime:3.5.2'
 
     antlr4 'org.antlr:antlr4:4.8-1'
-    compile 'org.antlr:antlr4-runtime:4.8-1'
+    implementation 'org.antlr:antlr4-runtime:4.8-1'
 
-    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.4'
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.4'
 
-    compile 'org.postgresql:postgresql:42.2.10'
+    implementation 'org.postgresql:postgresql:42.2.10'
 
-    compile ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
+    implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
         exclude module: 'oraclepki'
     }
 
-    compile ('com.google.guava:guava:28.2-jre') {
+    implementation ('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"
     }
 
-    compile group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '1.3.5'
+    implementation group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '1.3.5'
 
     // JavaFX stuff
-    compile 'de.jensd:fontawesomefx-commons:11.0'
-    compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-11'
-    compile 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
-    compile 'de.saxsys:mvvmfx:1.8.0'
-    compile 'org.fxmisc.easybind:easybind:1.0.3'
-    compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.10.4'
-    compile group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
-    compile 'com.jfoenix:jfoenix:9.0.9'
-    compile 'org.controlsfx:controlsfx:11.0.1'
-
-    compile 'org.jsoup:jsoup:1.12.2'
-    compile 'com.konghq:unirest-java:3.6.00'
-
-    compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-SNAPSHOT'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-SNAPSHOT'
+    implementation 'de.jensd:fontawesomefx-commons:11.0'
+    implementation 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-11'
+    implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
+    implementation 'de.saxsys:mvvmfx:1.8.0'
+    implementation 'org.fxmisc.easybind:easybind:1.0.3'
+    implementation 'org.fxmisc.flowless:flowless:0.6.1'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.4'
+    implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
+    implementation 'com.jfoenix:jfoenix:9.0.9'
+    implementation 'org.controlsfx:controlsfx:11.0.1'
+
+    implementation 'org.jsoup:jsoup:1.12.2'
+    implementation 'com.konghq:unirest-java:3.6.00'
+
+    implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-SNAPSHOT'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-SNAPSHOT'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '3.0.0-SNAPSHOT'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
 
-    compile 'de.undercouch:citeproc-java:2.0.0'
+    implementation 'de.undercouch:citeproc-java:2.0.0'
 
-    compile group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
-    compile group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
-    compile group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
+    implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
+    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
+    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
 
-    compile ('com.github.tomtung:latex2unicode_2.12:0.2.6') {
+    implementation ('com.github.tomtung:latex2unicode_2.12:0.2.6') {
         exclude module: 'fastparse_2.12'
     }
 
-    /*
-    TODO: Reenable error prone as soon as https://github.com/google/error-prone/issues/1210 is fixed
-    errorprone ('com.google.errorprone:error_prone_core:2.3.2') {
-        exclude module: "jsr305"
-        exclude group: 'org.checkerframework', module: 'checker-qual'
-        exclude group: 'com.google.errorprone', module: 'error_prone_annotation'
-        exclude group: 'com.google.errorprone', module: 'error_prone_annotations'
-        exclude group: 'com.google.errorprone', module: 'error_prone_check_api'
-    }
-    */
-
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.4.1'
-    compile (group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.4.1') {
+    implementation group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.4.1'
+    implementation (group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.4.1') {
         exclude module: "log4j-core"
     }
 
 
-    testCompile 'io.github.classgraph:classgraph:4.8.65'
+    testImplementation 'io.github.classgraph:classgraph:4.8.65'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.6.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.6.0'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.6.0'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.6.0'
 
-    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.8'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.8'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testCompile 'org.mockito:mockito-core:3.3.0'
-    //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
-    testCompile 'org.xmlunit:xmlunit-core:2.6.3'
-    testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.13.1'
-    //testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.13.0'
-    testCompile "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
-    testCompile "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
-    testCompile "org.hamcrest:hamcrest-library:2.2"
+    testImplementation 'org.mockito:mockito-core:3.3.0'
+    testImplementation 'org.xmlunit:xmlunit-core:2.6.3'
+    testImplementation 'org.xmlunit:xmlunit-matchers:2.6.3'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.13.1'
+    testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
+    testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
+    testImplementation "org.hamcrest:hamcrest-library:2.2"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:8.29'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.2'
@@ -310,7 +299,6 @@ processResources {
     }
 }
 
-
 task generateSource(dependsOn: ["generateBstGrammarSource",
                                 "generateSearchGrammarSource",
                                 "generateMedlineSource",
@@ -379,7 +367,6 @@ task generateModsSource(type: XjcTask) {
 }
 
 tasks.withType(JavaCompile) {
-    // use UTF-8
     options.encoding = 'UTF-8'
 }
 
@@ -552,12 +539,6 @@ checkstyle {
     sourceSets = []
 }
 
-modernizer {
-    // We have more than 20 issues, which are not fixed yet. Nevertheless, we produce the modernizer output.
-    // See https://github.com/andrewgaul/modernizer-maven-plugin for more information on modernizer
-    failOnViolations = false
-}
-
 // Release tasks
 task deleteInstallerTemp(type: Delete) {
     delete "$buildDir/installer"

diff --git a/docs/README.md b/docs/README.md
@@ -2,9 +2,15 @@
 
 This page presents all development informatation around JabRef. For users documentation see <https://docs.jabref.org>.
 
+## Excersises
+
+Uni Basel offers a German (🇩🇪) Software Engineering course which uses JabRef as one example.
+Look at [Exercise 5](https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week5/exercises/practical-exercises.md) for an exercise where some important points of JabRef are touched.
+
 ## How tos
 
-- [Sync your fork with the JabRef repository](https://help.github.com/articles/syncing-a-fork/)
+- External: [Sync your fork with the JabRef repository](https://help.github.com/articles/syncing-a-fork/)
+- External (🇩🇪): Branches and pull requests: <https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week2/exercises/practical-exercises.md>
 
 ## Command Line
 

diff --git a/docs/code-quality.md b/docs/code-quality.md
@@ -2,9 +2,9 @@
 
 We monitor the general source code quality at three places:
 
-* [Teamscale](https://www.cqse.eu/de/produkte/teamscale/landing/) is a popular German product analyzing code quality. The analysis results are available at <https://demo.teamscale.com/dashboard.html#show//?id=kinnen%2FJabref%20Overview>.
-* [codacy](https://www.codacy.com/) is a hosted service to monitor code quality. The code quality analysis for JabRef is available at <https://www.codacy.com/app/simonharrer/jabref/dashboard>.
+* [codacy](https://www.codacy.com/) is a hosted service to monitor code quality. It thereby combines the results of available open source code quality checkers such as [Checkstyle](https://checkstyle.sourceforge.io/) or [PMD](https://pmd.github.io/). The code quality analysis for JabRef is available at <https://app.codacy.com/gh/JabRef/jabref/dashboard>, especially the [list of open issues](https://app.codacy.com/gh/JabRef/jabref/issues/index). In case a rule feels wrong, it is most likely a PMD rule. The JabRef team can change the configuration at <https://app.codacy.com/p/306789/patterns/list?engine=9ed24812-b6ee-4a58-9004-0ed183c45b8f>.
 * [codecov](https://codecov.io/) is a solution to check code coverage of test cases. The code coverage metrics for JabRef are available at <https://codecov.io/github/JabRef/jabref>.
+* [Teamscale](https://www.cqse.eu/de/produkte/teamscale/landing/) is a popular German product analyzing code quality. The analysis results are available at <https://demo.teamscale.com/findings.html#/jabref/?>.
 
 We strongly recommend to read following two books on code quality:
 

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -653,6 +653,7 @@ private MenuBar createMenu() {
         Menu edit = new Menu(Localization.lang("Edit"));
         Menu library = new Menu(Localization.lang("Library"));
         Menu quality = new Menu(Localization.lang("Quality"));
+        Menu lookup = new Menu(Localization.lang("Lookup"));
         Menu view = new Menu(Localization.lang("View"));
         Menu tools = new Menu(Localization.lang("Tools"));
         Menu options = new Menu(Localization.lang("Options"));
@@ -764,6 +765,10 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager, Globals.TASK_EXECUTOR))
         );
 
+        lookup.getItems().addAll(
+                factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService, stateManager))
+        );
+
         // PushToApplication
         final PushToApplicationAction pushToApplicationAction = pushToApplicationsManager.getPushToApplicationAction();
         final MenuItem pushToApplicationMenuItem = factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction);

diff --git a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
@@ -65,7 +65,7 @@ public LatexCitationsTabViewModel(BibDatabaseContext databaseContext, Preference
         this.preferencesService = preferencesService;
         this.taskExecutor = taskExecutor;
         this.dialogService = dialogService;
-        this.directory = new SimpleObjectProperty<>(databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
+        this.directory = new SimpleObjectProperty<>(databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
                                                                    .orElseGet(preferencesService::getWorkingDir));
         this.citationList = FXCollections.observableArrayList();
         this.status = new SimpleObjectProperty<>(Status.IN_PROGRESS);
@@ -126,7 +126,7 @@ private void cancelSearch() {
     }
 
     private Collection<Citation> searchAndParse(String citeKey) throws IOException {
-        Path newDirectory = databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
+        Path newDirectory = databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
                                            .orElseGet(preferencesService::getWorkingDir);
 
         if (texParserResult == null || !newDirectory.equals(directory.get())) {
@@ -168,7 +168,7 @@ public void setLatexDirectory() {
                 .withInitialDirectory(directory.get()).build();
 
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
-                databaseContext.getMetaData().setLaTexFileDirectory(preferencesService.getUser(), selectedDirectory.toAbsolutePath()));
+                databaseContext.getMetaData().setLatexFileDirectory(preferencesService.getUser(), selectedDirectory.toAbsolutePath()));
 
         init(currentEntry);
     }

diff --git a/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java b/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.fieldeditors;
 
-import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLDecoder;
@@ -53,15 +52,15 @@ public static String cleanGoogleSearchURL(String url) {
                 if (pair.startsWith("url=")) {
                     String value = pair.substring(pair.indexOf('=') + 1);
 
-                    String decode = URLDecoder.decode(value, StandardCharsets.UTF_8.name());
+                    String decode = URLDecoder.decode(value, StandardCharsets.UTF_8);
                     // url?
                     if (decode.matches(URL_EXP)) {
                         return decode;
                     }
                 }
             }
             return url;
-        } catch (UnsupportedEncodingException | MalformedURLException e) {
+        } catch (MalformedURLException e) {
             return url;
         }
     }

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java b/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java
@@ -392,7 +392,7 @@ public void openHelpPage() {
     private List<Path> getFileDirectoriesAsPaths() {
         List<Path> fileDirs = new ArrayList<>();
         MetaData metaData = currentDatabase.getMetaData();
-        metaData.getLaTexFileDirectory(preferencesService.getFilePreferences().getUser()).ifPresent(fileDirs::add);
+        metaData.getLatexFileDirectory(preferencesService.getFilePreferences().getUser()).ifPresent(fileDirs::add);
 
         return fileDirs;
     }

diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -65,9 +65,9 @@
                     <Button text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="5"
                             onAction="#browseUserSpecificFileDirectory"/>
 
-                    <Label text="%LaTex file directory" GridPane.columnIndex="0" GridPane.rowIndex="6"/>
+                    <Label text="%LaTeX file directory" GridPane.columnIndex="0" GridPane.rowIndex="6"/>
                     <TextField fx:id="laTexFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="6"/>
-                    <Button text="%Browse" onAction="#browseLaTexFileDirectory" GridPane.columnIndex="2"
+                    <Button text="%Browse" onAction="#browseLatexFileDirectory" GridPane.columnIndex="2"
                             GridPane.rowIndex="6"/>
                 </GridPane>