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nygrenhnygrenh
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Merge pull request #86 from RTMC/master
Added R support to tmc-langs.
2 parents 55e4dfb + 59a58a5 commit 76dfbc6

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‎.travis.yml

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before_install:
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- curl -L https://static.rust-lang.org/rustup.sh | sh -s -- --channel=stable --yes --prefix=$PWD --disable-sudo
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- sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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- echo "deb https://cloud.r-project.org/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
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- sudo apt-get update -qq
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- sudo apt-get install r-base -y
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- sudo chmod 277 /usr/local/lib/R/site-library
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- Rscript -e 'install.packages(c("devtools","testthat"),repos="http://cran.us.r-project.org")'
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- Rscript -e 'devtools::install_github("RTMC/tmc-r-tester/tmcRtestrunner")'
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- export PATH=$PATH:$PWD/bin
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- export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib
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- mkdir -p $HOME/bin && ln -s $(which python3.4) $HOME/bin/python3 && export PATH="$HOME/bin:$PATH"
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- mvn install -Dmaven.test.skip=true
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script:
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- mvn clean test
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- mvn checkstyle:check

‎pom.xml

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<module>tmc-langs-util</module>
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<module>tmc-langs-cli</module>
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<module>tmc-langs-r</module>
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</modules>
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<profiles>

‎tmc-langs-r/pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>fi.helsinki.cs.tmc</groupId>
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<artifactId>tmc-langs</artifactId>
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<version>0.7.7-SNAPSHOT</version>
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</parent>
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<artifactId>tmc-langs-r</artifactId>
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<packaging>jar</packaging>
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<dependencies>
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<dependency>
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<groupId>fi.helsinki.cs.tmc</groupId>
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<artifactId>tmc-langs-framework</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>fi.helsinki.cs.tmc</groupId>
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<artifactId>tmc-langs-util</artifactId>
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<version>${project.version}</version>
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</dependency>
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</dependencies>
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</project>

‎tmc-langs-r/src/main/java/fi/helsinki/cs/tmc/langs/r/RExerciseDescParser.java

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package fi.helsinki.cs.tmc.langs.r;
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import fi.helsinki.cs.tmc.langs.domain.TestDesc;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.ImmutableList;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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public class RExerciseDescParser {
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private static final Path RESULT_FILE = Paths.get(".available_points.json");
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private static final TypeReference<Map<String, List<String>>> MAP_TYPE_REFERENCE =
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new TypeReference<Map<String, List<String>>>() {};
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private final Path path;
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private final ObjectMapper mapper;
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public RExerciseDescParser(Path path) {
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this.path = path;
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this.mapper = new ObjectMapper();
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}
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public ImmutableList<TestDesc> parse() throws IOException {
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List<TestDesc> testDescs = new ArrayList<>();
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byte[] json = Files.readAllBytes(path.resolve(RESULT_FILE));
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Map<String, List<String>> parse = mapper.readValue(json, MAP_TYPE_REFERENCE);
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for (String name : parse.keySet()) {
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ImmutableList<String> points = ImmutableList.copyOf(parse.get(name));
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testDescs.add(new TestDesc(name, points));
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}
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return ImmutableList.copyOf(testDescs);
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}
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}

‎tmc-langs-r/src/main/java/fi/helsinki/cs/tmc/langs/r/RPlugin.java

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package fi.helsinki.cs.tmc.langs.r;
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import fi.helsinki.cs.tmc.langs.AbstractLanguagePlugin;
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import fi.helsinki.cs.tmc.langs.abstraction.Strategy;
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import fi.helsinki.cs.tmc.langs.abstraction.ValidationError;
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import fi.helsinki.cs.tmc.langs.abstraction.ValidationResult;
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import fi.helsinki.cs.tmc.langs.domain.ExerciseBuilder;
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import fi.helsinki.cs.tmc.langs.domain.ExerciseDesc;
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import fi.helsinki.cs.tmc.langs.domain.RunResult;
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import fi.helsinki.cs.tmc.langs.domain.SpecialLogs;
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import fi.helsinki.cs.tmc.langs.domain.TestDesc;
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import fi.helsinki.cs.tmc.langs.domain.TestResult;
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import fi.helsinki.cs.tmc.langs.io.StudentFilePolicy;
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import fi.helsinki.cs.tmc.langs.io.sandbox.StudentFileAwareSubmissionProcessor;
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import fi.helsinki.cs.tmc.langs.io.zip.StudentFileAwareUnzipper;
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import fi.helsinki.cs.tmc.langs.io.zip.StudentFileAwareZipper;
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import fi.helsinki.cs.tmc.langs.utils.ProcessRunner;
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import com.google.common.base.Optional;
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import com.google.common.collect.ImmutableList;
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import com.google.common.collect.ImmutableMap;
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import com.google.common.collect.Maps;
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import org.apache.commons.lang3.ArrayUtils;
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import org.apache.commons.lang3.SystemUtils;
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import org.apache.commons.lang3.exception.ExceptionUtils;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.File;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Locale;
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import java.util.Map;
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public final class RPlugin extends AbstractLanguagePlugin {
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/**
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* R folder contains the actual R files used in the
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* project/package. It is automatically included when creating a
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* R package but now when making a regular project in RStudio.
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*/
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private static final Path R_FOLDER_PATH = Paths.get("R");
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/**
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* test/testthat folder contains the unit testing
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* files which use the testThat library for the R project.
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*/
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private static final Path TEST_FOLDER_PATH = Paths.get("tests");
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private static final Path TESTTHAT_FOLDER_PATH = Paths.get("testthat");
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private static final String CANNOT_RUN_TESTS_MESSAGE = "Failed to run tests.";
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private static final String CANNOT_PARSE_TEST_RESULTS_MESSAGE = "Failed to read test results.";
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private static final String CANNOT_SCAN_EXERCISE_MESSAGE = "Failed to scan exercise.";
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private static final String CANNOT_PARSE_EXERCISE_DESCRIPTION_MESSAGE =
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"Failed to parse exercise description.";
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private static Logger log = LoggerFactory.getLogger(RPlugin.class);
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public RPlugin() {
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super(
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new ExerciseBuilder(),
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new StudentFileAwareSubmissionProcessor(),
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new StudentFileAwareZipper(),
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new StudentFileAwareUnzipper());
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}
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/**
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* NOTE: Files.exists does not seem to be able to verify the R and
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* testthat folder's existence if they are empty.
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*/
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@Override
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public boolean isExerciseTypeCorrect(Path path) {
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return Files.exists(path.resolve(R_FOLDER_PATH))
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|| Files.exists(path.resolve(TEST_FOLDER_PATH).resolve(TESTTHAT_FOLDER_PATH));
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}
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@Override
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protected StudentFilePolicy getStudentFilePolicy(Path projectPath) {
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return new RStudentFilePolicy(projectPath);
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}
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@Override
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public String getPluginName() {
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return "r";
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}
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@Override
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public Optional<ExerciseDesc> scanExercise(Path path, String exerciseName) {
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ProcessRunner runner = new ProcessRunner(this.getAvailablePointsCommand(), path);
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try {
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runner.call();
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} catch (Exception e) {
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log.error(CANNOT_SCAN_EXERCISE_MESSAGE, e);
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return Optional.absent();
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}
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try {
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ImmutableList<TestDesc> testDescs = new RExerciseDescParser(path).parse();
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return Optional.of(new ExerciseDesc(exerciseName, testDescs));
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} catch (IOException e) {
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log.error(CANNOT_PARSE_EXERCISE_DESCRIPTION_MESSAGE, e);
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}
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return Optional.absent();
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}
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@Override
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public RunResult runTests(Path path) {
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ProcessRunner runner = new ProcessRunner(getTestCommand(), path);
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try {
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runner.call();
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} catch (Exception e) {
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log.error(CANNOT_RUN_TESTS_MESSAGE, e);
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return getGenericErrorRunResult(e);
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}
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try {
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return new RTestResultParser(path).parse();
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} catch (IOException e) {
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log.error(CANNOT_PARSE_TEST_RESULTS_MESSAGE, e);
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return getGenericErrorRunResult(e);
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}
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}
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private RunResult getGenericErrorRunResult(Throwable exception) {
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Map<String, byte[]> logMap = new HashMap<>();
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byte[] stackTraceAsByteArray = ExceptionUtils.getStackTrace(exception).getBytes();
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logMap.put(SpecialLogs.GENERIC_ERROR_MESSAGE, stackTraceAsByteArray);
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ImmutableMap<String, byte[]> logs = ImmutableMap.copyOf(logMap);
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return new RunResult(RunResult.Status.GENERIC_ERROR,
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ImmutableList.copyOf(new ArrayList<TestResult>()), logs);
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}
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@Override
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public ValidationResult checkCodeStyle(Path path, Locale messageLocale) {
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return new ValidationResult() {
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@Override
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public Strategy getStrategy() {
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return Strategy.DISABLED;
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}
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@Override
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public Map<File, List<ValidationError>> getValidationErrors() {
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return Maps.newHashMap();
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}
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};
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}
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public String[] getTestCommand() {
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String[] command = new String[]{"Rscript"};
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String[] args;
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if (SystemUtils.IS_OS_WINDOWS) {
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args = new String[]{"-e", "\"library('tmcRtestrunner');run_tests()\""};
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} else {
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args = new String[]{"-e", "library(tmcRtestrunner);run_tests()"};
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}
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return ArrayUtils.addAll(command, args);
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}
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public String[] getAvailablePointsCommand() {
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String[] command = new String[]{"Rscript"};
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String[] args;
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if (SystemUtils.IS_OS_WINDOWS) {
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args = new String[]{"-e", "\"library('tmcRtestrunner');run_available_points()\""};
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} else {
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args = new String[]{"-e", "library(tmcRtestrunner);run_available_points()"};
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}
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return ArrayUtils.addAll(command, args);
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}
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/**
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* No operation for now. To be possibly implemented later: remove .Rdata, .Rhistory etc
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*/
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@Override
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public void clean(Path path) {
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}
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}

‎tmc-langs-r/src/main/java/fi/helsinki/cs/tmc/langs/r/RStudentFilePolicy.java

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package fi.helsinki.cs.tmc.langs.r;
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import fi.helsinki.cs.tmc.langs.io.ConfigurableStudentFilePolicy;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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public class RStudentFilePolicy extends ConfigurableStudentFilePolicy {
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public RStudentFilePolicy(Path configFileParent) {
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super(configFileParent);
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}
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/**
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* Returns {@code True} for all files in the <tt>projectRoot/R/</tt> directory and other
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* files required for building the project.
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*
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* <p>Will NOT return {@code True} for any test files. If test file modification are part
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* of the exercise, those test files are whitelisted as <tt>ExtraStudentFiles</tt> and the
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* decision to include them is made by {@link ConfigurableStudentFilePolicy}.
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*/
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@Override
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public boolean isStudentSourceFile(Path path, Path projectRootPath) {
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return path.startsWith(Paths.get("R"));
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}
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}

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