Add command line option parsing

src/main/java/de/vanitasvitae/imi/codes/Arguments.java

@@ -0,0 +1,56 @@
+package de.vanitasvitae.imi.codes;
+
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+
+public class Arguments {
+
+    static final Option STUDY_NUMBER = Option.builder("s")
+            .longOpt("study")
+            .desc("Three-letter code of the associated study")
+            .required()
+            .hasArg()
+            .argName("SNR")
+            .build();
+
+    static final Option SAMPLE_TYPE = Option.builder("t")
+            .longOpt("type")
+            .desc("Type of the sample (b = blood, u = urine)")
+            .required(true)
+            .hasArg()
+            .argName("sample type")
+            .build();
+
+    static final Option OUTPUT_DESTINATION = Option.builder("o")
+            .longOpt("OUTPUT_DESTINATION")
+            .desc("Filename for the generated html output")
+            .hasArg()
+            .argName("file name")
+            .build();
+
+    static final Option EXTERNAL_BROWSER = Option.builder("b")
+            .longOpt("EXTERNAL_BROWSER")
+            .desc("Open the generated HTML output in a an external browser")
+            .build();
+
+    static final Option HELP = Option.builder("h")
+            .longOpt("help")
+            .desc("Print this help text")
+            .build();
+    /**
+     * Assemble and return the available command line options.
+     *
+     * @return command line options.
+     */
+    public static Options getCommandLineOptions() {
+        Options options = new Options();
+
+        options.addOption(STUDY_NUMBER);
+        options.addOption(SAMPLE_TYPE);
+        options.addOption(OUTPUT_DESTINATION);
+        options.addOption(EXTERNAL_BROWSER);
+        options.addOption(HELP);
+
+        return options;
+    }
+}

src/main/java/de/vanitasvitae/imi/codes/InputValidator.java

@@ -0,0 +1,47 @@
+package de.vanitasvitae.imi.codes;
+
+import java.util.regex.Pattern;
+
+public class InputValidator {
+
+    // Allowed characters
+    private static final String ALPHABET = "[a-zA-Z0-9]";
+
+    /*
+    REGEX pattern for study numbers. Allowed are all 3-letter numbers from the alphabet [a-zA-Z0-9].
+     */
+    private static final Pattern STUDY_NUMBER_MATCHER = Pattern.compile(ALPHABET+"{3}");
+
+    /*
+    REGEX pattern for sample numbers. Allowed are four-letter numbers from the alphabet [a-zA-Z0-9].
+     */
+    private static final Pattern SAMPLE_NUMBER_MATCHER = Pattern.compile(ALPHABET+"{4}");
+
+    /**
+     * Validate a given study number. Valid study numbers are 3-letter codes from the alphabet [a-zA-Z0-9].
+     *
+     * @param in input String
+     * @return unmodified input String if it matches.
+     * @throws IllegalArgumentException if the input String doesn't match the regex.
+     */
+    public static String validateStudyNumber(String in) {
+        if (!STUDY_NUMBER_MATCHER.matcher(in).matches()) {
+            throw new IllegalArgumentException("Study number does not match REGEX.");
+        }
+
+        return in;
+    }
+
+    /**
+     * Validate a given sample type. Valid types are found in {@link SampleType}.#
+     *
+     * @param in input String
+     * @return parsed {@link SampleType}.
+     *
+     * @throws IllegalArgumentException if the given String doesn't match a {@link SampleType}.
+     * @throws NullPointerException in case the given String is {@code null}.
+     */
+    public static SampleType validateSampleType(String in) {
+        return SampleType.valueOf(in);
+    }
+}

src/main/java/de/vanitasvitae/imi/codes/Main.java

@@ -0,0 +1,48 @@
+package de.vanitasvitae.imi.codes;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+public class Main {
+
+    private static final String NAME_JAR = "imicodes";
+    private static final String HELP_HEADER = "Generate ID codes for sample tubes.";
+    private static final String HELP_FOOTER = "\nAuthor: Paul Schaub <paul.schaub@wwu.de>";
+
+    public static void main(String[] args) {
+
+        Options options = Arguments.getCommandLineOptions();
+        CommandLineParser parser = new DefaultParser();
+
+        CommandLine arguments;
+        try {
+            arguments = parser.parse(options, args);
+        } catch (ParseException e) {
+            System.out.println(e.getMessage());
+            printHelp(options);
+            return;
+        }
+
+        if (arguments.hasOption(Arguments.HELP)) {
+            printHelp(options);
+            return;
+        }
+    }
+
+    /**
+     * Print a descriptive help text to the console.
+     *
+     * @param options {@link Options} for which we want to print a help text.
+     */
+    private static void printHelp(Options options) {
+        HelpFormatter formatter = new HelpFormatter();
+
+        formatter.printHelp(NAME_JAR, HELP_HEADER, options, HELP_FOOTER, true);
+    }
+
+
+}

src/main/java/de/vanitasvitae/imi/codes/SampleType.java

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+package de.vanitasvitae.imi.codes;
+
+public enum SampleType {
+
+    b("Blood"),
+    u("Urine"),
+    ;
+
+    // Members of the enum
+
+    private final String name;
+
+    SampleType(String name) {
+        this.name = name;
+    }
+
+    public String getName() {
+        return name;
+    }
+}