Programming exercises: Add R programming language template

build.gradle

@@ -254,6 +254,7 @@ dependencies {
     implementation "de.jplag:python-3:${jplag_version}"
     implementation "de.jplag:rust:${jplag_version}"
     implementation "de.jplag:javascript:${jplag_version}"
+    implementation "de.jplag:rlang:${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;
@@ -317,7 +318,8 @@ private Language getJPlagProgrammingLanguage(ProgrammingExercise programmingExer
             case KOTLIN -> new KotlinLanguage();
             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 R -> new RLanguage();
+            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

@@ -49,7 +49,8 @@ public enum ProgrammingLanguage {
         SWIFT,
         OCAML,
         RUST,
-        JAVASCRIPT
+        JAVASCRIPT,
+        R
     );
     // @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

@@ -3,6 +3,7 @@
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.EMPTY;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.JAVA;
 import static de.tum.cit.aet.artemis.programming.domain.ProgrammingLanguage.JAVASCRIPT;
+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.ProjectType.MAVEN_MAVEN;
 import static de.tum.cit.aet.artemis.programming.domain.ProjectType.PLAIN_MAVEN;
@@ -27,5 +28,6 @@ public GitLabCIProgrammingLanguageFeatureService() {
         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(R, new ProgrammingLanguageFeature(R, 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;
@@ -43,5 +44,6 @@ public JenkinsProgrammingLanguageFeatureService() {
         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));
+        programmingLanguageFeatures.put(R, new ProgrammingLanguageFeature(R, 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;
@@ -51,5 +52,6 @@ public LocalCIProgrammingLanguageFeatureService() {
         programmingLanguageFeatures.put(SWIFT, new ProgrammingLanguageFeature(SWIFT, false, false, true, true, false, List.of(PLAIN), 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(R, new ProgrammingLanguageFeature(R, false, false, true, 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/gitlabci/r/regularRuns/.gitlab-ci.yml

@@ -0,0 +1,48 @@
+stages:
+    - test
+    - upload
+
+
+test-job:
+    image: ${ARTEMIS_BUILD_DOCKER_IMAGE}
+    stage: test
+    only:
+        variables:
+            - $CI_COMMIT_BRANCH == $ARTEMIS_SUBMISSION_GIT_BRANCH
+    allow_failure: true
+    variables:
+        GIT_STRATEGY: none
+    script:
+        - git clone --branch ${ARTEMIS_TEST_GIT_BRANCH} ${CI_SERVER_PROTOCOL}://${ARTEMIS_TEST_GIT_USER}:${ARTEMIS_TEST_GIT_TOKEN}@${CI_SERVER_HOST}:${CI_SERVER_PORT}/${CI_PROJECT_NAMESPACE}/${ARTEMIS_TEST_GIT_REPOSITORY_SLUG} .
+        - git clone --branch ${ARTEMIS_SUBMISSION_GIT_BRANCH} ${CI_SERVER_PROTOCOL}://${ARTEMIS_TEST_GIT_USER}:${ARTEMIS_TEST_GIT_TOKEN}@${CI_SERVER_HOST}:${CI_SERVER_PORT}/${CI_PROJECT_NAMESPACE}/${CI_PROJECT_NAME} assignment
+        - export ARTEMIS_NOTIFICATION_SECRET=[hidden] # Workaround for overwriting the secret
+        - export ARTEMIS_TEST_GIT_TOKEN=[hidden]
+        - R CMD INSTALL assignment | tee -a "${ARTEMIS_BUILD_LOGS_FILE}" && echo "ARTEMIS_BUILD_STATUS=success" > .env || echo "ARTEMIS_BUILD_STATUS=failed" > .env
+        - Rscript -e 'library("testthat"); options(testthat.output_file = "junit.xml"); test_local(".", reporter = "junit")' | tee -a "${ARTEMIS_BUILD_LOGS_FILE}"
+        - test -e tests/testthat/junit.xml && sed -i 's/<testsuites[^>]*>/<testsuite>/g ; s/<\/testsuites>/<\/testsuite>/g' tests/testthat/junit.xml  # <testsuites> not supported by notification plugin
+    after_script:
+        - echo "ARTEMIS_TEST_GIT_HASH=$(git rev-parse HEAD)" >> .env
+        - echo "ARTEMIS_SUBMISSION_GIT_HASH=${CI_COMMIT_SHA}" >> .env
+        - echo "ARTEMIS_SUBMISSION_GIT_REPOSITORY_SLUG=${CI_PROJECT_NAME}" >> .env
+    artifacts:
+        paths:
+            - ${ARTEMIS_BUILD_LOGS_FILE}
+            - tests/testthat/*.xml
+        reports:
+            dotenv: .env
+
+
+upload-job:
+    image: ${ARTEMIS_NOTIFICATION_PLUGIN_DOCKER_IMAGE}
+    stage: upload
+    dependencies:
+        - test-job
+    only:
+        variables:
+            - $CI_COMMIT_BRANCH == $ARTEMIS_SUBMISSION_GIT_BRANCH
+    variables:
+        GIT_STRATEGY: none
+    script:
+        - cp -r /notification-plugin/* .
+        - export ARTEMIS_TEST_RESULTS_DIR="tests/testthat"  # override project variable
+        - gradle run

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
+}

src/main/resources/templates/r/readme

@@ -0,0 +1,6 @@
+# Matrix Columns
+
+Write a function `matrix_to_column_list` in R that takes a matrix of any shape and converts it into a list of
+column-vectors. Each element of the list should represent a column of the matrix.
+
+1. [task][Convert to column-vectors](converts_3x3_matrix_to_vectors,converts_4x2_matrix_to_vectors,converts_1x5_matrix_to_scalars,converts_5x1_matrix_to_vector)

src/main/resources/templates/r/solution/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/solution/NAMESPACE

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

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

@@ -0,0 +1,17 @@
+matrix_to_column_list <- function(mat) {
+  if (!is.matrix(mat)) {
+    stop("Input must be a matrix")
+  }
+
+  n_cols <- ncol(mat)
+
+  # Initialize an empty list to store column-vectors
+  column_list <- vector("list", length = n_cols)
+
+  # Loop through each column and store it in the list
+  for (i in 1:n_cols) {
+    column_list[[i]] <- mat[, i]
+  }
+
+  return(column_list)
+}

src/main/resources/templates/r/test/DESCRIPTION

@@ -0,0 +1,14 @@
+Package: test
+Title: Artemis R Tests
+Version: 0.0.0.9000
+Author: Artemis
+Description: This package tests the student assignment.
+License: MIT
+Encoding: UTF-8
+Imports:
+    assignment
+Remotes:
+    local::./assignment
+Suggests:
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

src/main/resources/templates/r/test/tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(tests)
+
+test_check("tests")