IMI-Application/src/main/java/de/vanitasvitae/imi/codes/persistence/FileRepository.java

package de.vanitasvitae.imi.codes.persistence;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.util.HashMap;

import de.vanitasvitae.imi.codes.input.InvalidOptionException;
import de.vanitasvitae.imi.codes.types.StudyNumber;

/**
 * Repository, that stores generated sample codes per study to files on disk.
 * The repository stores the next sample code which would be generated for any {@link StudyNumber} {@code stn} to
 * the directory {@code <base>/stn}.
 * If no sample number record has been found for a {@link StudyNumber}, 0 is returned.
 *
 * Additionally, the repository is initialized with some hard-coded values for studies "AAA" and "BBB".
 * If the user tries to generate codes for those studies, the generated codes start at the hard coded values instead
 * of 0.
 */
public class FileRepository implements Repository {

    private final File base;
    private final HashMap<StudyNumber, Integer> hardCoded = new HashMap<>();

    /**
     * Create a new file-based repository which stores files in the given directory {@code base}.
     *
     * @param base base directory.
     */
    public FileRepository(File base) {
        this.base = base;

        // Populate the repository with some hard coded values
        try {
            hardCoded.put(new StudyNumber("AAA"), 35);
            hardCoded.put(new StudyNumber("BBB"), 42);
        } catch (InvalidOptionException e) {
            // It should never happen here, that the hard coded study numbers are invalid.
            throw new AssertionError(e);
        }
    }

    /**
     * Return the base directory of the repository.
     * @return base directory
     */
    public File getBaseDirectory() {
        return base;
    }

    // Returns a hard coded value, or 0 if absent.
    private int getHardCodedOrZero(StudyNumber studyNumber) {
        Integer i = hardCoded.get(studyNumber);
        return (i != null ? i : 0);
    }

    /**
     * Return the sample number of the next code which will be generated for the given {@link StudyNumber}.
     *
     * @param study code for the study
     * @return sample number
     */
    @Override
    public int getNextSampleCode(StudyNumber study) {
        File studyNumberFile = new File(base, study.toString());
        int next;
        // Check, if we have hard-coded values available
        if (!studyNumberFile.exists()) {
            next = getHardCodedOrZero(study);
        } // Otherwise read from file
        else {
            next = readInt(studyNumberFile);
        }

        return next;
    }

    /**
     * Write the next sample code number, which should be generated to file.
     * The next sample code number should be the last generated sample code number + 1.
     *
     * @param study study number
     * @param nextSampleCode next sample code to be generated.
     *
     * @throws IOException in case the file cannot be written
     */
    @Override
    public void setNextSampleCode(StudyNumber study, int nextSampleCode) throws IOException {
        writeInt(new File(base, study.toString()), nextSampleCode);
    }

    /**
     * Reads an integer from the first line inside a file. If the file does not exist or is not readable, 0 is returned.
     *
     * @param file file to read from
     * @return integer or 0
     */
    private int readInt(File file) {
        try(BufferedReader in = new BufferedReader(new FileReader(file))) {
            return Integer.parseInt(in.readLine());
        } catch (FileNotFoundException e) {
            System.out.println("File " + file.getAbsolutePath() + " does not exist.");
            return 0;
        } catch (IOException e) {
            e.printStackTrace();
            return 0;
        }
    }

    /**
     * Write an integer to a destination file.
     * This method throws an {@link IOException} in case the parent directories or the file
     * cannot be created or written to.
     *
     * @param file destination
     * @param integer integer to be written
     */
    private void writeInt(File file, int integer) throws IOException {
        // Check if destination is directory, which would be illegal
        if (file.isDirectory()) {
            throw new IOException("Provided output directory points to a directory, which is not allowed.");
        }

        // Make sure, the parent folder exists
        File parent = file.getParentFile();
        if (!parent.exists() && !parent.mkdirs()) {
            throw new IOException("Cannot create parent directory " + parent.getAbsolutePath());
        }

        // Check if destination file exists and if not, try to create it
        if (!file.exists()) {
            try {
                if (!file.createNewFile()) {
                    throw new IOException("Output file " +file.getAbsolutePath() + " cannot be created.");
                }
            } catch (IOException e) {
                throw new IOException("Output file " + file.getAbsolutePath() + " cannot be created." , e);
            }
        }

        try(Writer wr = new FileWriter(file)) {
            wr.write(Integer.toString(integer));
        } catch (FileNotFoundException e) {
            // Must not happen
            throw new AssertionError(e);
        } catch (IOException e) {
            throw new IOException("Cannot write to output file " + file.getAbsolutePath(), e);
        }
    }
}