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Library allowing generation of plots and data from proteomics and metabolomics mass spectrometry data through the use of R and java methods.
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package uk.ac.liv.pgb.analytica.lib.wrappedr;

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
 * Manages execution of an executable/command.
 * @author sperkins
 */
public final class CommandExecutor {

    /**
     * The executable/command to be executed.
     */
    private final File executable;

    /**
     * The error message produced by the executable/command.
     */
    private String errorMessage;

    /**
     * The standard output of the executable/command.
     */
    private List standardOutput = new ArrayList<>();

    /**
     * The standard error of the executable/command.
     */
    private List standardError = new ArrayList<>();

    /**
     * Creates an instance of this class using the given executable/command.
     * @param executable The executable/command to execute.
     */
    public CommandExecutor(final File executable) {
        this.executable = executable;
        if (this.executable == null) {
            throw new RuntimeException("No executable command provided.");
        }
    }

    /**
     * Executes an executable/command given some arguments.
     * @param arguments The arguments to the executable/command.
     * @return True if no exception occurred and the return value was normal.
     * @throws InterruptedException Thrown if there was an error waiting for the executable/command to finish.
     */
    public boolean execute(final List arguments) throws InterruptedException {
        // Put the path to the executable at the front of the list of arguments.
        arguments.add(0, executable.getAbsolutePath());

        // Create the process builder with the list.
        ProcessBuilder processBuilder = new ProcessBuilder(arguments);
        Process process = null;
        try {
            process = processBuilder.start();
            InputStream outputStream = process.getInputStream();
            readStream(outputStream, standardOutput);

            InputStream errorStream = process.getErrorStream();
            readStream(errorStream, standardError);

            process.waitFor();
        } catch (IOException e) {
            return false;
        }

        int exitValue = process.exitValue();

        return exitValue == 0;
    }

    /**
     * Reads an input stream into a list.
     * @param stream The input stream.
     * @param streamOutput The list to read the stream into.
     * @throws IOException Thrown if there is an error reading the stream.
     */
    private static void readStream(final InputStream stream, final List streamOutput) throws IOException {
        BufferedReader reader = new BufferedReader(new InputStreamReader(stream, StandardCharsets.UTF_8));
        String line;
        while ((line = reader.readLine()) != null) {
            streamOutput.add(line);
        }
    }

    /**
     * Executes an executable/command with no arguments.
     * @return True if no exception occurred.
     * @throws InterruptedException Thrown if there was an error waiting for the executable/command to finish.
     * @deprecated This method should not be used anymore, developers should instead provide an empty list to execute().
     */
    @Deprecated
    public boolean callExe() throws InterruptedException {
        return execute(Collections.emptyList());
    }

    /**
     * Gets the standard error reported by the executable/command.
     * @return The standard error.
     */
    public List getError() {
        return standardError;
    }

    /**
     * Gets the standard output reported by the command/executable.
     * @return The standard output.
     */
    public List getOutput() {
        return standardOutput;
    }
}