[WIP] Modularize JabRef with JPMS

.gitignore

@@ -1,5 +1,5 @@
 # no generated files in version control
-src/main/gen/
+**/src/main/gen/
 
 # private data
 /buildres/jabref-cert-2016.p12
@@ -348,3 +348,6 @@ gradle-app.setting
 
 # do not distribute Oracle's JDBC driver
 lib/ojdbc.jar
+
+# do not ignore the source of the build
+!/buildSrc/src/

CHANGELOG.md

@@ -25,13 +25,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀<kbd>alt</kbd> + <kbd>up/down</kbd>.
 - Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file.
 - Window state is saved on close and restored on start.
+- Files without a defined external file type are now directly opened with the default aplication of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
 
 
 
 
 
 
+
 ### Fixed
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
@@ -58,7 +60,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
 - We fixed an issue where the preview pane in entry preview in preferences wasn't showing the citation style selected [#3849](https://github.com/JabRef/jabref/issues/3849)
 - We fixed an issue where the default entry preview style still contained the field `review`. The field `review` in the style is now replaced with comment to be consistent with the entry editor [#4098](https://github.com/JabRef/jabref/issues/4098)
-
+- We fixed an issue where users were vulnerable to XXE attacks during parsing [#4229](https://github.com/JabRef/jabref/issues/4229)
+- We fixed an issue where files added via the "Attach file" contextmenu of an entry were not made relative. [#4201](https://github.com/JabRef/jabref/issues/4201)
 
 
 

build.gradle

@@ -19,10 +19,10 @@ plugins {
     id 'com.install4j.gradle' version '7.0.6'
     id 'com.github.johnrengelman.shadow' version '2.0.4'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
-    id "com.simonharrer.modernizer" version '1.6.0-1'
+//    id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.7'
     id 'com.zyxist.chainsaw' version '0.3.1'
-    //id 'net.ltgt.errorprone' version '0.0.14'
+    //id 'net.ltgt.errorprone' version '0.0.15'
     id 'com.github.ben-manes.versions' version '0.20.0'
 }
 
@@ -38,20 +38,36 @@ apply plugin: 'project-report'
 apply plugin: 'jacoco'
 apply plugin: 'install4j'
 apply plugin: 'me.champeau.gradle.jmh'
-apply plugin: 'checkstyle'
+//apply plugin: 'checkstyle'
+apply plugin: org.jabref.build.antlr.AntlrPlugin
 
 apply from: 'eclipse.gradle'
 apply from: 'localization.gradle'
-apply from: 'xjc.gradle'
 
-group = "org.jabref"
-version = "5.0-dev"
-project.ext.threeDotVersion = "5.0.0.0"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j7' : 'install4j7')
-sourceCompatibility = 9
-targetCompatibility = 9
 mainClassName = "org.jabref.JabRefMain"
 
+allprojects {
+    group = "org.jabref"
+    version = "5.0-dev"
+    project.ext.threeDotVersion = "5.0.0.0"
+
+    sourceCompatibility = 9
+    targetCompatibility = 9
+
+    repositories {
+        mavenLocal()
+        jcenter()
+        maven {
+            url 'https://oss.sonatype.org/content/groups/public'
+        }
+    }
+
+    tasks.withType(JavaCompile) {
+        options.encoding = 'UTF-8'
+    }
+}
+
 javaModule {
     name = "org.jabref"
     hacks {
@@ -69,36 +85,25 @@ ext.allowJava9 = true
 
 sourceSets {
     main {
-        java {
-            srcDirs = ["src/main/java", "src/main/gen"]
-        }
-
         resources {
             srcDirs = ["src/main/java", "src/main/resources"]
         }
     }
 }
 
-repositories {
-    mavenLocal()
-    jcenter()
-    maven {
-        url 'https://oss.sonatype.org/content/groups/public'
-    }
-}
-
 configurations {
-    antlr3
-    antlr4
-
     compile {
         exclude group: 'com.google.code.findbugs', module: 'jsr305'
     }
 }
 
+// FIXME: bug in chainsaw does not build multi module projects in right order
+compileJava.dependsOn ":jabref-model:assemble"
+compileJava.dependsOn ":jabref-logic:assemble"
+
 dependencies {
-    // Include all jar-files in the 'lib' folder as dependencies
-    compile fileTree(dir: 'lib', includes: ['*.jar'])
+    compile project(':jabref-model')
+    compile project(':jabref-logic')
 
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
@@ -118,43 +123,24 @@ dependencies {
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"*/
 
-    compile 'io.github.java-diff-utils:java-diff-utils:2.2.0'
-    compile 'info.debatty:java-string-similarity:1.1.0'
-
-    antlr3 'org.antlr:antlr:3.5.2'
-    compile 'org.antlr:antlr-runtime:3.5.2'
-
-    antlr4 'org.antlr:antlr4:4.7.1'
-    compile 'org.antlr:antlr4-runtime:4.7.1'
-
-    // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
-    compile 'mysql:mysql-connector-java:5.1.46'
-
-    compile 'org.postgresql:postgresql:42.2.4'
-
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
     compile 'com.google.guava:guava:25.1-jre'
 
     compile group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
 
     // JavaFX stuff
-    compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
-    compile 'de.jensd:fontawesomefx-commons:9.1.2'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.0'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.1'
 //    compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
 
     // Cannot be updated to 9.*.* until Jabref works with Java 9
     compile 'org.controlsfx:controlsfx:9.0.0'
 
-    compile 'org.jsoup:jsoup:1.11.3'
-    compile 'com.mashape.unirest:unirest-java:1.4.9'
-
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta2'
     compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.11.0'
@@ -165,11 +151,6 @@ dependencies {
     // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
     compile 'org.citationstyles:locales:1.0.1-SNAPSHOT'
-    compile 'de.undercouch:citeproc-java:1.0.1'
-
-    // JAX-B is considered JavaEE API and is no longer part of JavaSE (JDK 9)
-    compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
-    compile group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0'
 
 // TODO: recognized as 'latex2unicode.2.12', which is an invalid module name, temporarily removed
 //    compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
@@ -186,17 +167,17 @@ dependencies {
     testCompile 'org.junit-pioneer:junit-pioneer:0.1.2'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
-    testCompile 'org.mockito:mockito-core:2.19.1'
+    testCompile 'org.mockito:mockito-core:2.20.0'
     testCompile 'com.github.tomakehurst:wiremock:2.18.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.0'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
-    testCompile 'com.tngtech.archunit:archunit-junit:0.8.2'
+    testCompile 'com.tngtech.archunit:archunit-junit:0.8.3'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.11'
+//    checkstyle 'com.puppycrawl.tools:checkstyle:8.11'
 }
 
 jacoco {
@@ -256,80 +237,18 @@ clean {
 processResources {
     filteringCharset = 'UTF-8'
 
-    filesMatching("build.properties") {
-        expand(version: project.version,
-                "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
-                "authors": new File('AUTHORS').readLines().findAll { !it.startsWith("#") }.join(", "),
-                "developers": new File('DEVELOPERS').readLines().findAll { !it.startsWith("#") }.join(", "),
-                "azureInstrumentationKey": System.getenv('AzureInstrumentationKey'),
-                "minRequiredJavaVersion": minRequiredJavaVersion,
-                "allowJava9": allowJava9
-
-        )
-        filteringCharset = 'UTF-8'
-    }
-
     filesMatching("resource/**/meta.xml") {
         expand version: project.version
     }
 }
 
-
-task generateSource(dependsOn: ["generateBstGrammarSource", "generateSearchGrammarSource"]) {
-    group = 'JabRef'
-    description 'Generates all Java source files.'
-}
-
-task generateBstGrammarSource(type: JavaExec) {
-    group 'JabRef'
-    description 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.'
-
-    File antlrSource = file('src/main/antlr3/org/jabref/bst/Bst.g')
-
-    inputs.file antlrSource
-    outputs.file file('src/main/gen/org/jabref/logic/bst/BstLexer.java')
-    outputs.file file('src/main/gen/org/jabref/logic/bst/BstParser.java')
-
-    main = 'org.antlr.Tool'
-    classpath = configurations.antlr3
-    args = ["-o", file('src/main/gen/org/jabref/logic/bst/'), antlrSource]
-}
-
-task generateSearchGrammarSource(type: JavaExec) {
-    String grammarFile = "Search"
-
-    group 'JabRef'
-    description "Generates java files for ${grammarFile}.g antlr4."
-
-    String packagePath = "org/jabref/search"
-    File antlrPath = file("src/main/antlr4")
-    File genPath = file("src/main/gen")
-
-    File antlrSource = file("$antlrPath/$packagePath/${grammarFile}.g4")
-    File destinationDir = file("$genPath/$packagePath")
-
-    inputs.file antlrSource
-    outputs.file file("$destinationDir/${grammarFile}Parser.java")
-    outputs.file file("$destinationDir/${grammarFile}Lexer.java")
-    outputs.file file("$destinationDir/${grammarFile}Visitor.java")
-    outputs.file file("$destinationDir/${grammarFile}BaseVisitor.java")
-    outputs.file file("$destinationDir/${grammarFile}.tokens")
-    outputs.file file("$destinationDir/${grammarFile}Lexer.tokens")
-
-    main = 'org.antlr.v4.Tool'
-    classpath = configurations.antlr4
-    args = ["-o", destinationDir, "-visitor", "-no-listener", "-package", "org.jabref.search", antlrSource]
+tasks.withType(JavaCompile) {
+    options.encoding = 'UTF-8' // use UTF-8 for regular and test compilation
 }
 
 compileJava {
-    options.encoding = 'UTF-8'
     options.compilerArgs << "-Xlint:none"
 }
-compileJava.dependsOn "generateSource"
-
-compileTestJava {
-    options.encoding = 'UTF-8'
-}
 
 javadoc {
     options {
@@ -401,20 +320,20 @@ jacocoTestReport {
 }
 
 // Code quality tasks
-checkstyle {
-    // do not use other packages for checkstyle, excluding gen(erated) sources
-    checkstyleMain.source = "src/main/java"
-    toolVersion = '8.5'
-
-    // do not perform checkstyle checks by default
-    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
-}
+//checkstyle {
+//    // do not use other packages for checkstyle, excluding gen(erated) sources
+//    checkstyleMain.source = "src/main/java"
+//    toolVersion = '8.5'
+//
+//    // do not perform checkstyle checks by default
+//    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
 shadowJar {

buildSrc/src/main/groovy/org/jabref/build/antlr/Antlr3CommandLine.groovy

@@ -0,0 +1,27 @@
+package org.jabref.build.antlr
+
+import org.gradle.api.file.FileCollection
+
+class Antlr3CommandLine implements AntlrCommandLine {
+
+    private final task
+
+    Antlr3CommandLine(AntlrTask task) {
+        this.task = task
+    }
+
+    @Override
+    String getMain() {
+        return "org.antlr.Tool"
+    }
+
+    @Override
+    FileCollection getClasspath() {
+        return task.project.configurations.antlr3
+    }
+
+    @Override
+    List<String> getArguments() {
+        return ["-o", task.project.file(task.outputDir).toString(), task.project.file(task.inputFile).toString()]
+    }
+}

buildSrc/src/main/groovy/org/jabref/build/antlr/Antlr4CommandLine.groovy

@@ -0,0 +1,31 @@
+package org.jabref.build.antlr
+
+import org.gradle.api.file.FileCollection
+
+class Antlr4CommandLine implements AntlrCommandLine {
+
+    private final AntlrTask task
+
+    Antlr4CommandLine(AntlrTask task) {
+        this.task = task
+    }
+
+    @Override
+    String getMain() {
+        return "org.antlr.v4.Tool"
+    }
+
+    @Override
+    FileCollection getClasspath() {
+        return task.project.configurations.antlr4
+    }
+
+    @Override
+    List<String> getArguments() {
+        return ["-o", file(task.outputDir), "-visitor", "-no-listener", "-package", task.javaPackage, file(task.inputFile)]
+    }
+
+    private String file(String path) {
+        return task.project.file(path).toString()
+    }
+}