Programming exercises: Add R programming language template

build.gradle

@@ -246,14 +246,15 @@ dependencies {
     implementation "org.gitlab4j:gitlab4j-api:6.0.0-rc.5"
 
     implementation "de.jplag:jplag:${jplag_version}"
-    implementation "de.jplag:java:${jplag_version}"
-    implementation "de.jplag:kotlin:${jplag_version}"
+
     implementation "de.jplag:c:${jplag_version}"
-    implementation "de.jplag:swift:${jplag_version}"
     implementation "de.jplag:java:${jplag_version}"
+    implementation "de.jplag:javascript:${jplag_version}"
+    implementation "de.jplag:kotlin:${jplag_version}"
     implementation "de.jplag:python-3:${jplag_version}"
+    implementation "de.jplag:rlang:${jplag_version}"
     implementation "de.jplag:rust:${jplag_version}"
-    implementation "de.jplag:javascript:${jplag_version}"
+    implementation "de.jplag:swift:${jplag_version}"
     implementation "de.jplag:text:${jplag_version}"
 
     // those are transitive dependencies of JPlag Text --> Stanford NLP

docs/user/exercises/programming-exercise-features.inc

@@ -37,6 +37,8 @@ Instructors can still use those templates to generate programming exercises and
   +----------------------+----------+---------+
   | JavaScript           | yes      | yes     |
   +----------------------+----------+---------+
+  | R                    | yes      | yes     |
+  +----------------------+----------+---------+
 
 - Not all ``templates`` support the same feature set and supported features can also change depending on the continuous integration system setup.
   Depending on the feature set, some options might not be available during the creation of the programming exercise.
@@ -71,6 +73,8 @@ Instructors can still use those templates to generate programming exercises and
   +----------------------+----------------------+----------------------+---------------------+--------------+------------------------------------------+------------------------------+----------------------------+------------------------+
   | JavaScript           | no                   | no                   | yes                 | no           | n/a                                      | no                           | no                         | L: yes, J: no          |
   +----------------------+----------------------+----------------------+---------------------+--------------+------------------------------------------+------------------------------+----------------------------+------------------------+
+  | R                    | no                   | no                   | yes                 | no           | n/a                                      | no                           | no                         | L: yes, J: no          |
+  +----------------------+----------------------+----------------------+---------------------+--------------+------------------------------------------+------------------------------+----------------------------+------------------------+
 
   - *Sequential Test Runs*: ``Artemis`` can generate a build plan which first executes structural and then behavioral tests. This feature can help students to better concentrate on the immediate challenge at hand.
   - *Static Code Analysis*: ``Artemis`` can generate a build plan which additionally executes static code analysis tools.

src/main/java/de/tum/cit/aet/artemis/plagiarism/service/ProgrammingPlagiarismDetectionService.java

@@ -37,6 +37,7 @@
 import de.jplag.options.JPlagOptions;
 import de.jplag.python3.PythonLanguage;
 import de.jplag.reporting.reportobject.ReportObjectFactory;
+import de.jplag.rlang.RLanguage;
 import de.jplag.rust.RustLanguage;
 import de.jplag.swift.SwiftLanguage;
 import de.tum.cit.aet.artemis.core.exception.BadRequestAlertException;
@@ -310,14 +311,15 @@ public void deleteTempLocalRepository(Repository repository) {
 
     private Language getJPlagProgrammingLanguage(ProgrammingExercise programmingExercise) {
         return switch (programmingExercise.getProgrammingLanguage()) {
-            case JAVA -> new JavaLanguage();
             case C -> new CLanguage();
-            case PYTHON -> new PythonLanguage();
-            case SWIFT -> new SwiftLanguage();
+            case JAVA -> new JavaLanguage();
+            case JAVASCRIPT -> new JavaScriptLanguage();
             case KOTLIN -> new KotlinLanguage();
+            case PYTHON -> new PythonLanguage();
+            case R -> new RLanguage();
             case RUST -> new RustLanguage();
-            case JAVASCRIPT -> new JavaScriptLanguage();
-            case EMPTY, PHP, DART, HASKELL, ASSEMBLER, OCAML, C_SHARP, C_PLUS_PLUS, SQL, R, TYPESCRIPT, GO, MATLAB, BASH, VHDL, RUBY, POWERSHELL, ADA ->
+            case SWIFT -> new SwiftLanguage();
+            case EMPTY, PHP, DART, HASKELL, ASSEMBLER, OCAML, C_SHARP, C_PLUS_PLUS, SQL, TYPESCRIPT, GO, MATLAB, BASH, VHDL, RUBY, POWERSHELL, ADA ->
                 throw new BadRequestAlertException("Programming language " + programmingExercise.getProgrammingLanguage() + " not supported for plagiarism check.",
                         "ProgrammingExercise", "notSupported");
         };

src/main/java/de/tum/cit/aet/artemis/programming/domain/ProgrammingLanguage.java

@@ -38,18 +38,19 @@ public enum ProgrammingLanguage {
     PHP("php");
 
     private static final Set<ProgrammingLanguage> ENABLED_LANGUAGES = Set.of(
-        EMPTY,
-        JAVA,
-        PYTHON,
+        ASSEMBLER,
         C,
         HASKELL,
+        JAVA,
+        JAVASCRIPT,
         KOTLIN,
-        VHDL,
-        ASSEMBLER,
-        SWIFT,
         OCAML,
+        PYTHON,
+        R,
         RUST,
-        JAVASCRIPT
+        SWIFT,
+        VHDL,
+        EMPTY
     );
     // @formatter:on
 

src/main/java/de/tum/cit/aet/artemis/programming/service/TemplateUpgradePolicyService.java

@@ -32,8 +32,8 @@ public TemplateUpgradePolicyService(JavaTemplateUpgradeService javaRepositoryUpg
     public TemplateUpgradeService getUpgradeService(ProgrammingLanguage programmingLanguage) {
         return switch (programmingLanguage) {
             case JAVA -> javaRepositoryUpgradeService;
-            case KOTLIN, PYTHON, C, HASKELL, VHDL, ASSEMBLER, SWIFT, OCAML, EMPTY, RUST, JAVASCRIPT -> defaultRepositoryUpgradeService;
-            case C_SHARP, C_PLUS_PLUS, SQL, R, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
+            case KOTLIN, PYTHON, C, HASKELL, VHDL, ASSEMBLER, SWIFT, OCAML, EMPTY, RUST, JAVASCRIPT, R -> defaultRepositoryUpgradeService;
+            case C_SHARP, C_PLUS_PLUS, SQL, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
                 throw new UnsupportedOperationException("Unsupported programming language: " + programmingLanguage);
         };
     }

src/main/java/de/tum/cit/aet/artemis/programming/service/ci/ContinuousIntegrationService.java

@@ -219,8 +219,8 @@ enum RepositoryCheckoutPath implements CustomizableCheckoutPath {
             @Override
             public String forProgrammingLanguage(ProgrammingLanguage language) {
                 return switch (language) {
-                    case JAVA, PYTHON, C, HASKELL, KOTLIN, VHDL, ASSEMBLER, SWIFT, OCAML, EMPTY, RUST, JAVASCRIPT -> "assignment";
-                    case C_SHARP, C_PLUS_PLUS, SQL, R, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
+                    case JAVA, PYTHON, C, HASKELL, KOTLIN, VHDL, ASSEMBLER, SWIFT, OCAML, EMPTY, RUST, JAVASCRIPT, R -> "assignment";
+                    case C_SHARP, C_PLUS_PLUS, SQL, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
                         throw new UnsupportedOperationException("Unsupported programming language: " + language);
                 };
             }
@@ -230,9 +230,9 @@ public String forProgrammingLanguage(ProgrammingLanguage language) {
             @Override
             public String forProgrammingLanguage(ProgrammingLanguage language) {
                 return switch (language) {
-                    case JAVA, PYTHON, HASKELL, KOTLIN, SWIFT, EMPTY, RUST, JAVASCRIPT -> "";
+                    case JAVA, PYTHON, HASKELL, KOTLIN, SWIFT, EMPTY, RUST, JAVASCRIPT, R -> "";
                     case C, VHDL, ASSEMBLER, OCAML -> "tests";
-                    case C_SHARP, C_PLUS_PLUS, SQL, R, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
+                    case C_SHARP, C_PLUS_PLUS, SQL, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
                         throw new UnsupportedOperationException("Unsupported programming language: " + language);
                 };
             }

src/main/java/de/tum/cit/aet/artemis/programming/service/gitlabci/GitLabCIProgrammingLanguageFeatureService.java

@@ -25,7 +25,7 @@ public class GitLabCIProgrammingLanguageFeatureService extends ProgrammingLangua
     public GitLabCIProgrammingLanguageFeatureService() {
         programmingLanguageFeatures.put(EMPTY, new ProgrammingLanguageFeature(EMPTY, false, false, false, false, false, List.of(), false, false));
         programmingLanguageFeatures.put(JAVA, new ProgrammingLanguageFeature(JAVA, false, false, false, true, false, List.of(PLAIN_MAVEN, MAVEN_MAVEN), false, false));
-        programmingLanguageFeatures.put(RUST, new ProgrammingLanguageFeature(RUST, false, false, true, false, false, List.of(), false, false));
         programmingLanguageFeatures.put(JAVASCRIPT, new ProgrammingLanguageFeature(JAVASCRIPT, false, false, true, false, false, List.of(), false, false));
+        programmingLanguageFeatures.put(RUST, new ProgrammingLanguageFeature(RUST, false, false, true, false, false, List.of(), false, false));
     }
 }

src/main/java/de/tum/cit/aet/artemis/programming/service/jenkins/JenkinsProgrammingLanguageFeatureService.java

@@ -7,6 +7,7 @@
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.JAVASCRIPT;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.KOTLIN;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.PYTHON;
+import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.R;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.RUST;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.SWIFT;
 import static de.tum.cit.aet.artemis.programming.domain.ProjectType.FACT;
@@ -33,15 +34,16 @@ public class JenkinsProgrammingLanguageFeatureService extends ProgrammingLanguag
     public JenkinsProgrammingLanguageFeatureService() {
         // Must be extended once a new programming language is added
         programmingLanguageFeatures.put(EMPTY, new ProgrammingLanguageFeature(EMPTY, false, false, false, false, false, List.of(), false, false));
+        programmingLanguageFeatures.put(C, new ProgrammingLanguageFeature(C, false, false, true, false, false, List.of(FACT, GCC), false, false));
+        programmingLanguageFeatures.put(HASKELL, new ProgrammingLanguageFeature(HASKELL, false, false, false, false, true, List.of(), false, false));
         programmingLanguageFeatures.put(JAVA,
                 new ProgrammingLanguageFeature(JAVA, true, true, true, true, false, List.of(PLAIN_GRADLE, GRADLE_GRADLE, PLAIN_MAVEN, MAVEN_MAVEN, MAVEN_BLACKBOX), true, false));
+        programmingLanguageFeatures.put(JAVASCRIPT, new ProgrammingLanguageFeature(JAVASCRIPT, false, false, true, false, false, List.of(), false, false));
         programmingLanguageFeatures.put(KOTLIN, new ProgrammingLanguageFeature(KOTLIN, true, false, true, true, false, List.of(), true, false));
         programmingLanguageFeatures.put(PYTHON, new ProgrammingLanguageFeature(PYTHON, false, false, true, false, false, List.of(), false, false));
+        programmingLanguageFeatures.put(R, new ProgrammingLanguageFeature(R, false, false, true, false, false, List.of(), false, false));
+        programmingLanguageFeatures.put(RUST, new ProgrammingLanguageFeature(RUST, false, false, true, false, false, List.of(), false, false));
         // Jenkins is not supporting XCODE at the moment
         programmingLanguageFeatures.put(SWIFT, new ProgrammingLanguageFeature(SWIFT, false, true, true, true, false, List.of(PLAIN), false, false));
-        programmingLanguageFeatures.put(C, new ProgrammingLanguageFeature(C, false, false, true, false, false, List.of(FACT, GCC), false, false));
-        programmingLanguageFeatures.put(HASKELL, new ProgrammingLanguageFeature(HASKELL, false, false, false, false, true, List.of(), false, false));
-        programmingLanguageFeatures.put(RUST, new ProgrammingLanguageFeature(RUST, false, false, true, false, false, List.of(), false, false));
-        programmingLanguageFeatures.put(JAVASCRIPT, new ProgrammingLanguageFeature(JAVASCRIPT, false, false, true, false, false, List.of(), false, false));
     }
 }

src/main/java/de/tum/cit/aet/artemis/programming/service/jenkins/build_plan/JenkinsBuildPlanService.java

@@ -184,8 +184,8 @@ private JenkinsXmlConfigBuilder builderFor(ProgrammingLanguage programmingLangua
             throw new UnsupportedOperationException("Xcode templates are not available for Jenkins.");
         }
         return switch (programmingLanguage) {
-            case JAVA, KOTLIN, PYTHON, C, HASKELL, SWIFT, EMPTY, RUST, JAVASCRIPT -> jenkinsBuildPlanCreator;
-            case VHDL, ASSEMBLER, OCAML, C_SHARP, C_PLUS_PLUS, SQL, R, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
+            case JAVA, KOTLIN, PYTHON, C, HASKELL, SWIFT, EMPTY, RUST, JAVASCRIPT, R -> jenkinsBuildPlanCreator;
+            case VHDL, ASSEMBLER, OCAML, C_SHARP, C_PLUS_PLUS, SQL, TYPESCRIPT, GO, MATLAB, BASH, RUBY, POWERSHELL, ADA, DART, PHP ->
                 throw new UnsupportedOperationException(programmingLanguage + " templates are not available for Jenkins.");
         };
     }

src/main/java/de/tum/cit/aet/artemis/programming/service/localci/LocalCIProgrammingLanguageFeatureService.java

@@ -10,6 +10,7 @@
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.KOTLIN;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.OCAML;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.PYTHON;
+import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.R;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.RUST;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.SWIFT;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.VHDL;
@@ -39,17 +40,18 @@ public class LocalCIProgrammingLanguageFeatureService extends ProgrammingLanguag
     public LocalCIProgrammingLanguageFeatureService() {
         // Must be extended once a new programming language is added
         programmingLanguageFeatures.put(EMPTY, new ProgrammingLanguageFeature(EMPTY, false, false, false, false, false, List.of(), false, true));
+        programmingLanguageFeatures.put(ASSEMBLER, new ProgrammingLanguageFeature(ASSEMBLER, false, false, false, false, false, List.of(), false, true));
+        programmingLanguageFeatures.put(C, new ProgrammingLanguageFeature(C, false, true, true, false, false, List.of(FACT, GCC), false, true));
+        programmingLanguageFeatures.put(HASKELL, new ProgrammingLanguageFeature(HASKELL, true, false, false, false, true, List.of(), false, true));
         programmingLanguageFeatures.put(JAVA,
                 new ProgrammingLanguageFeature(JAVA, true, true, true, true, false, List.of(PLAIN_GRADLE, GRADLE_GRADLE, PLAIN_MAVEN, MAVEN_MAVEN), false, true));
-        programmingLanguageFeatures.put(PYTHON, new ProgrammingLanguageFeature(PYTHON, false, false, true, false, false, List.of(), false, true));
-        programmingLanguageFeatures.put(C, new ProgrammingLanguageFeature(C, false, true, true, false, false, List.of(FACT, GCC), false, true));
-        programmingLanguageFeatures.put(ASSEMBLER, new ProgrammingLanguageFeature(ASSEMBLER, false, false, false, false, false, List.of(), false, true));
+        programmingLanguageFeatures.put(JAVASCRIPT, new ProgrammingLanguageFeature(JAVASCRIPT, false, false, true, false, false, List.of(), false, true));
         programmingLanguageFeatures.put(KOTLIN, new ProgrammingLanguageFeature(KOTLIN, false, false, true, true, false, List.of(), false, true));
-        programmingLanguageFeatures.put(VHDL, new ProgrammingLanguageFeature(VHDL, false, false, false, false, false, List.of(), false, true));
-        programmingLanguageFeatures.put(HASKELL, new ProgrammingLanguageFeature(HASKELL, true, false, false, false, true, List.of(), false, true));
         programmingLanguageFeatures.put(OCAML, new ProgrammingLanguageFeature(OCAML, false, false, false, false, true, List.of(), false, true));
-        programmingLanguageFeatures.put(SWIFT, new ProgrammingLanguageFeature(SWIFT, false, false, true, true, false, List.of(PLAIN), false, true));
+        programmingLanguageFeatures.put(PYTHON, new ProgrammingLanguageFeature(PYTHON, false, false, true, false, false, List.of(), false, true));
+        programmingLanguageFeatures.put(R, new ProgrammingLanguageFeature(R, false, false, true, false, false, List.of(), false, true));
         programmingLanguageFeatures.put(RUST, new ProgrammingLanguageFeature(RUST, false, false, true, false, false, List.of(), false, true));
-        programmingLanguageFeatures.put(JAVASCRIPT, new ProgrammingLanguageFeature(JAVASCRIPT, false, false, true, false, false, List.of(), false, true));
+        programmingLanguageFeatures.put(SWIFT, new ProgrammingLanguageFeature(SWIFT, false, false, true, true, false, List.of(PLAIN), false, true));
+        programmingLanguageFeatures.put(VHDL, new ProgrammingLanguageFeature(VHDL, false, false, false, false, false, List.of(), false, true));
     }
 }

src/main/resources/config/application.yml

@@ -91,6 +91,8 @@ artemis:
                     default: "ghcr.io/ls1intum/artemis-rust-docker:v0.9.70"
                 javascript:
                     default: "ghcr.io/ls1intum/artemis-javascript-docker:v1.0.0"
+                r:
+                    default: "ghcr.io/ls1intum/artemis-r-docker:v1.0.0"
 
 management:
     endpoints:

src/main/resources/templates/aeolus/r/default.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+set -e
+export AEOLUS_INITIAL_DIRECTORY=${PWD}
+install () {
+  echo '⚙️ executing install'
+  R CMD INSTALL assignment
+}
+
+run_all_tests () {
+  echo '⚙️ executing run_all_tests'
+  Rscript -e 'library("testthat"); options(testthat.output_file = "junit.xml"); test_local(".", reporter = "junit")'
+}
+
+main () {
+  if [[ "${1}" == "aeolus_sourcing" ]]; then
+    return 0 # just source to use the methods in the subshell, no execution
+  fi
+  local _script_name
+  _script_name=${BASH_SOURCE[0]:-$0}
+  cd "${AEOLUS_INITIAL_DIRECTORY}"
+  bash -c "source ${_script_name} aeolus_sourcing; install"
+  cd "${AEOLUS_INITIAL_DIRECTORY}"
+  bash -c "source ${_script_name} aeolus_sourcing; run_all_tests"
+}
+
+main "${@}"

src/main/resources/templates/aeolus/r/default.yaml

@@ -0,0 +1,14 @@
+api: v0.0.1
+metadata:
+  name: R
+  id: r
+  description: Test package using testthat
+actions:
+  - name: install
+    script: R CMD INSTALL assignment
+  - name: run_all_tests
+    script: Rscript -e 'library("testthat"); options(testthat.output_file = "junit.xml"); test_local(".", reporter = "junit")'
+    results:
+      - name: junit
+        path: tests/testthat/junit.xml
+        type: junit

src/main/resources/templates/jenkins/r/regularRuns/pipeline.groovy

@@ -0,0 +1,59 @@
+/*
+ * This file configures the actual build steps for the automatic grading.
+ *
+ * !!!
+ * For regular exercises, there is no need to make changes to this file.
+ * Only this base configuration is actively supported by the Artemis maintainers
+ * and/or your Artemis instance administrators.
+ * !!!
+ */
+
+dockerImage = '#dockerImage'
+dockerFlags = '#dockerArgs'
+
+/**
+ * Main function called by Jenkins.
+ */
+void testRunner() {
+    docker.image(dockerImage).inside(dockerFlags) { c ->
+        runTestSteps()
+    }
+}
+
+private void runTestSteps() {
+    test()
+}
+
+/**
+ * Run unit tests
+ */
+private void test() {
+    stage('Test') {
+        sh '''
+        R CMD INSTALL assignment
+        Rscript -e 'library("testthat"); options(testthat.output_file = "junit.xml"); test_local(".", reporter = "junit")'
+        '''
+    }
+}
+
+/**
+ * Script of the post build tasks aggregating all JUnit files in $WORKSPACE/results.
+ *
+ * Called by Jenkins.
+ */
+void postBuildTasks() {
+    sh '''
+    rm -rf results
+    mkdir results
+    if [ -e tests/testthat/junit.xml ]
+    then
+        sed -i 's/<testsuites[^>]*>/<testsuite>/g ; s/<\\/testsuites>/<\\/testsuite>/g' tests/testthat/junit.xml
+    fi
+    cp tests/testthat/junit.xml $WORKSPACE/results/ || true
+    sed -i 's/[^[:print:]\t]/�/g' $WORKSPACE/results/*.xml || true
+    '''
+}
+
+// very important, do not remove
+// required so that Jenkins finds the methods defined in this script
+return this

src/main/resources/templates/r/exercise/DESCRIPTION

@@ -0,0 +1,7 @@
+Package: assignment
+Title: Artemis R Student Assignment
+Version: 0.0.0.9000
+Author: Artemis
+Description: This is an assignment to be solved by students.
+License: MIT
+Encoding: UTF-8

src/main/resources/templates/r/exercise/NAMESPACE

@@ -0,0 +1 @@
+exportPattern("^[^\\.]")

src/main/resources/templates/r/exercise/R/convert.R

@@ -0,0 +1,3 @@
+matrix_to_column_list <- function(mat) {
+  # TODO: implement
+}