Implement file-based repository and persist number of generated codes per study
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62BEE9264BF17311
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@ -1,7 +1,15 @@
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package de.vanitasvitae.imi.codes;
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import java.io.File;
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import java.io.IOException;
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import de.vanitasvitae.imi.codes.input.Arguments;
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import de.vanitasvitae.imi.codes.input.InputValidator;
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import de.vanitasvitae.imi.codes.input.InvalidOptionException;
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import de.vanitasvitae.imi.codes.persistence.FileRepository;
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import de.vanitasvitae.imi.codes.types.SampleTubeCode;
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import de.vanitasvitae.imi.codes.types.SampleType;
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import de.vanitasvitae.imi.codes.types.StudyNumber;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.CommandLineParser;
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import org.apache.commons.cli.DefaultParser;
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@ -53,12 +61,32 @@ public class Main {
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return;
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}
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// Debug. TODO: Remove
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System.out.println("StudyNr: " + studyNumber + " sampleType: " + sampleType + " #codes: " + numberOfCodes
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+ " output: " + outputPath + " browser: " + externalBrowser);
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FileRepository repository = new FileRepository(new File(".imicodes"));
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// Read the next sample code from file
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int nextSampleCode = repository.nextSampleCode(studyNumber);
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int nextTotal = nextSampleCode + numberOfCodes;
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// Check, if we'd have an overflow of sample numbers
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// We check like this to prevent integer overflows
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if (nextSampleCode > 9999 || numberOfCodes > 9999 || nextTotal - 1 > 9999) {
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System.out.println("Study " + studyNumber + "would have too many sample tubes" +
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" (" + (nextTotal - 1) + "). Aborting.");
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return;
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}
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// Write back the number of the next sample number that should be generated next time
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try {
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repository.writeNextSampleCode(studyNumber, nextSampleCode + numberOfCodes);
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} catch (IOException e) {
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e.printStackTrace();
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return;
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}
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// Now we are finished with dangerous IO...
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// Generate codes
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for (int i = 0; i < numberOfCodes; i++) {
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System.out.format("%s%04d%n", studyNumber.toString() + sampleType, i);
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System.out.println(new SampleTubeCode(studyNumber, sampleType, nextSampleCode + i));
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}
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}
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@ -72,6 +100,4 @@ public class Main {
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formatter.printHelp(NAME_JAR, HELP_HEADER, options, HELP_FOOTER, true);
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}
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}
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@ -1,11 +1,11 @@
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package de.vanitasvitae.imi.codes;
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package de.vanitasvitae.imi.codes.input;
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import org.apache.commons.cli.Option;
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import org.apache.commons.cli.Options;
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class Arguments {
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public class Arguments {
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static final Option STUDY_NUMBER = Option.builder("s")
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public static final Option STUDY_NUMBER = Option.builder("s")
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.longOpt("study")
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.desc("Three-letter code of the associated study")
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.required()
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@ -13,7 +13,7 @@ class Arguments {
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.argName("SNR")
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.build();
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static final Option SAMPLE_TYPE = Option.builder("t")
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public static final Option SAMPLE_TYPE = Option.builder("t")
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.longOpt("type")
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.desc("Type of the sample (b = blood, u = urine)")
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.required()
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@ -21,7 +21,7 @@ class Arguments {
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.argName("sample type")
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.build();
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static final Option NUMBER_CODES = Option.builder("n")
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public static final Option NUMBER_CODES = Option.builder("n")
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.longOpt("number")
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.desc("Number of codes to be generated")
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.required()
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@ -29,19 +29,19 @@ class Arguments {
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.argName("n")
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.build();
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static final Option OUTPUT_DESTINATION = Option.builder("o")
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public static final Option OUTPUT_DESTINATION = Option.builder("o")
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.longOpt("output")
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.desc("Filename for the generated html output")
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.hasArg()
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.argName("file name")
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.build();
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static final Option EXTERNAL_BROWSER = Option.builder("b")
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public static final Option EXTERNAL_BROWSER = Option.builder("b")
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.longOpt("browser")
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.desc("Open the generated HTML output in a an external browser")
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.build();
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static final Option HELP = Option.builder("h")
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public static final Option HELP = Option.builder("h")
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.longOpt("help")
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.desc("Print this help text")
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.build();
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@ -1,7 +1,9 @@
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package de.vanitasvitae.imi.codes;
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package de.vanitasvitae.imi.codes.input;
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import java.io.File;
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import java.util.regex.Pattern;
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import de.vanitasvitae.imi.codes.types.SampleType;
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import de.vanitasvitae.imi.codes.types.StudyNumber;
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public class InputValidator {
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@ -1,4 +1,4 @@
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package de.vanitasvitae.imi.codes;
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package de.vanitasvitae.imi.codes.input;
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/**
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* Exception which gets thrown when the user-provided input arguments are not valid.
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@ -0,0 +1,133 @@
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package de.vanitasvitae.imi.codes.persistence;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileReader;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.Writer;
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import java.util.HashMap;
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import de.vanitasvitae.imi.codes.input.InvalidOptionException;
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import de.vanitasvitae.imi.codes.types.StudyNumber;
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public class FileRepository {
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private final File base;
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private final HashMap<StudyNumber, Integer> hardCoded = new HashMap<>();
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/**
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* Create a new file-based repository which stores files in the given directory {@code base}.
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*
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* @param base base directory.
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*/
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public FileRepository(File base) {
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this.base = base;
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// Populate the repository with some hard coded values
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try {
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hardCoded.put(new StudyNumber("AAA"), 35);
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hardCoded.put(new StudyNumber("BBB"), 42);
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} catch (InvalidOptionException e) {
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throw new AssertionError(e);
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}
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}
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private int getHardCodedOrZero(StudyNumber studyNumber) {
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Integer i = hardCoded.get(studyNumber);
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return (i != null ? i : 0);
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}
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/**
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* Return the sample number of the next code which will be generated for the given {@link StudyNumber}.
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*
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* @param study code for the study
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* @return sample number
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*/
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public int nextSampleCode(StudyNumber study) {
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File studyNumberFile = new File(base, study.toString());
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int next;
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// Check, if we have hard-coded values available
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if (!studyNumberFile.exists()) {
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next = getHardCodedOrZero(study);
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} // Otherwise read from file
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else {
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next = readInt(studyNumberFile);
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}
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return next;
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}
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/**
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* Write the next sample code number, which should be generated to file.
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* The next sample code number should be the last generated sample code number + 1.
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*
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* @param study study number
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* @param nextSampleCode next sample code to be generated.
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*
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* @throws IOException in case the file cannot be written
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*/
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public void writeNextSampleCode(StudyNumber study, int nextSampleCode) throws IOException {
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writeInt(new File(base, study.toString()), nextSampleCode);
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}
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/**
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* Reads an integer from the first line inside a file. If the file does not exist or is not readable, 0 is returned.
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*
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* @param file file to read from
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* @return integer or 0
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*/
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private int readInt(File file) {
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try(BufferedReader in = new BufferedReader(new FileReader(file))) {
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return Integer.parseInt(in.readLine());
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} catch (FileNotFoundException e) {
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System.out.println("File " + file.getAbsolutePath() + " does not exist.");
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return 0;
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} catch (IOException e) {
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e.printStackTrace();
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return 0;
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}
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}
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/**
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* Write an integer to a destination file.
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* This method throws an {@link IOException} in case the parent directories or the file
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* cannot be created or written to.
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*
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* @param file destination
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* @param integer integer to be written
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*/
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private void writeInt(File file, int integer) throws IOException {
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// Check if destination is directory, which would be illegal
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if (file.isDirectory()) {
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throw new IOException("Provided output directory points to a directory, which is not allowed.");
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}
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// Make sure, the parent folder exists
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File parent = file.getParentFile();
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if (!parent.exists() && !parent.mkdirs()) {
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throw new IOException("Cannot create parent directory " + parent.getAbsolutePath());
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}
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// Check if destination file exists and if not, try to create it
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if (!file.exists()) {
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try {
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if (!file.createNewFile()) {
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throw new IOException("Output file " +file.getAbsolutePath() + " cannot be created.");
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}
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} catch (IOException e) {
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throw new IOException("Output file " + file.getAbsolutePath() + " cannot be created." , e);
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}
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}
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try(Writer wr = new FileWriter(file)) {
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wr.write(Integer.toString(integer));
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} catch (FileNotFoundException e) {
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// Must not happen
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throw new AssertionError(e);
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} catch (IOException e) {
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throw new IOException("Cannot write to output file " + file.getAbsolutePath(), e);
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}
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}
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}
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@ -1,8 +1,10 @@
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package de.vanitasvitae.imi.codes;
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package de.vanitasvitae.imi.codes.types;
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import java.util.regex.Pattern;
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import java.util.stream.IntStream;
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import de.vanitasvitae.imi.codes.input.InvalidOptionException;
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public abstract class BoundedCharSequence implements CharSequence {
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private final Pattern regex;
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@ -0,0 +1,67 @@
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package de.vanitasvitae.imi.codes.types;
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import java.util.stream.IntStream;
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public class SampleTubeCode implements CharSequence {
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private final StudyNumber studyNumber;
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private final SampleType sampleType;
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private final int sampleNumber;
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public SampleTubeCode(StudyNumber studyNumber, SampleType sampleType, int sampleNumber) {
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if (studyNumber == null) {
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throw new IllegalArgumentException("StudyNumber MUST NOT be null.");
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}
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if (sampleType == null) {
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throw new IllegalArgumentException("SampleType MUST NOT be null.");
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}
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if (sampleNumber < 0 || sampleNumber > 9999) {
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throw new IllegalArgumentException("SampleNumber MUST BE an integer between 0 and 9999 (inclusive).");
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}
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this.studyNumber = studyNumber;
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this.sampleType = sampleType;
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this.sampleNumber = sampleNumber;
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}
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@Override
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public int length() {
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return toString().length();
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}
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@Override
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public char charAt(int i) {
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return toString().charAt(i);
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}
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@Override
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public CharSequence subSequence(int a, int b) {
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return toString().subSequence(a, b);
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}
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@Override
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public IntStream chars() {
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return toString().chars();
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}
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@Override
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public IntStream codePoints() {
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return toString().codePoints();
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}
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@Override
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public int hashCode() {
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return toString().hashCode();
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}
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@Override
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public boolean equals(Object o) {
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return toString().equals(o.toString());
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}
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@Override
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public String toString() {
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String number = String.format("%04d", sampleNumber);
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return studyNumber.toString() + sampleType.toString() + number;
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}
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}
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@ -1,7 +1,10 @@
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package de.vanitasvitae.imi.codes;
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package de.vanitasvitae.imi.codes.types;
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import java.util.regex.Pattern;
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import de.vanitasvitae.imi.codes.input.InputValidator;
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import de.vanitasvitae.imi.codes.input.InvalidOptionException;
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/**
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* Sub-class of {@link CharSequence}, which can only represent char sequences of length 1 from the alphabet [a-zA-Z0-9].
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*/
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@ -0,0 +1,13 @@
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package de.vanitasvitae.imi.codes.types;
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import java.util.ArrayList;
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import java.util.List;
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public class Study {
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private final StudyNumber number;
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private final List<SampleTubeCode> codes = new ArrayList<>();
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public Study(StudyNumber number) {
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this.number = number;
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}
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}
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@ -1,7 +1,10 @@
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package de.vanitasvitae.imi.codes;
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package de.vanitasvitae.imi.codes.types;
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import java.util.regex.Pattern;
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import de.vanitasvitae.imi.codes.input.InputValidator;
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import de.vanitasvitae.imi.codes.input.InvalidOptionException;
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/**
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* Sub-class of {@link CharSequence}, which can only represent char sequences of length 3 from the alphabet [a-zA-Z0-9].
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*/
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@ -16,7 +19,7 @@ public class StudyNumber extends BoundedCharSequence {
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* @param value input string
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* @throws InvalidOptionException if the input doesn't match the regex
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*/
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protected StudyNumber(String value) throws InvalidOptionException {
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public StudyNumber(String value) throws InvalidOptionException {
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super(REGEX, value);
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}
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}
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@ -6,6 +6,10 @@ import java.util.ArrayList;
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import java.util.List;
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import java.util.Random;
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import de.vanitasvitae.imi.codes.input.InputValidator;
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import de.vanitasvitae.imi.codes.input.InvalidOptionException;
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import de.vanitasvitae.imi.codes.types.SampleType;
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import de.vanitasvitae.imi.codes.types.StudyNumber;
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import org.junit.Test;
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public class InputValidatorTest {
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