Implement HTML table renderer and export
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parent
dd1336beb5
commit
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4 changed files with 149 additions and 25 deletions
47
src/main/java/de/vanitasvitae/imi/codes/CodeGenerator.java
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47
src/main/java/de/vanitasvitae/imi/codes/CodeGenerator.java
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@ -0,0 +1,47 @@
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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 java.util.ArrayList;
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import java.util.List;
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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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public class CodeGenerator {
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private final FileRepository repository = new FileRepository(new File(".imicodes"));
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public CodeGenerator() {
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}
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public List<SampleTubeCode> generateCodes(StudyNumber studyNumber, SampleType sampleType, int numberOfCodes)
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throws InvalidOptionException, IOException {
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List<SampleTubeCode> codes = new ArrayList<>();
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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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throw new InvalidOptionException("Study " + studyNumber + "would have too many sample tubes" +
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" (" + (nextTotal - 1) + "). Aborting.");
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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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repository.writeNextSampleCode(studyNumber, nextSampleCode + numberOfCodes);
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// Generate codes
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for (int i = 0; i < numberOfCodes; i++) {
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codes.add(new SampleTubeCode(studyNumber, sampleType, nextSampleCode + i));
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}
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return codes;
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}
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}
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@ -0,0 +1,52 @@
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package de.vanitasvitae.imi.codes;
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import java.util.List;
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import de.vanitasvitae.imi.codes.types.SampleTubeCode;
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public class HtmlTableStringBuilder {
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private StringBuilder html;
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public HtmlTableStringBuilder(String title, List<SampleTubeCode> codes) {
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html = new StringBuilder("<!DOCTYPE html>\n")
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.append("<html>\n")
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.append("<head>\n")
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.append("<style>\n")
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.append("table, th, td {\n")
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.append(" border: 1px solid black;\n")
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.append("}\n")
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.append("</style>\n")
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.append("</head>")
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.append("<body>")
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.append("\n");
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// Add title
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html.append("<h2>").append(title).append("</h2>\n");
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// Open table
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html.append("<table>\n")
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.append("<tr>\n")
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.append("<th>Code</th>\n")
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.append("</tr>\n");
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// Append table entries
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for (SampleTubeCode c : codes) {
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html.append("<tr>\n")
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.append("<td>").append(c.toString()).append("</td>\n")
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.append("</tr>\n");
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}
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// Close table
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html.append("</table>\n");
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// Close body and html
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html.append("</body>\n");
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html.append("</html>");
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}
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@Override
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public String toString() {
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return html.toString();
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}
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}
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@ -1,12 +1,14 @@
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package de.vanitasvitae.imi.codes;
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import java.io.File;
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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.List;
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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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@ -19,10 +21,17 @@ import org.apache.commons.cli.ParseException;
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public class Main {
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private static final String NAME_JAR = "imicodes";
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private static final String NAME_JAR = "java -jar imicodes.jar";
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private static final String HELP_HEADER = "Generate ID codes for sample tubes.";
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private static final String HELP_FOOTER = "\nAuthor: Paul Schaub <paul.schaub@wwu.de>";
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/**
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* Entry point to the program.
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* Any provided arguments are parsed and the behaviour of the program is modified respectively.
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* A list of available options can be displayed using "-h".
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*
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* @param args arguments
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*/
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public static void main(String[] args) {
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Options options = Arguments.getCommandLineOptions();
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CommandLineParser parser = new DefaultParser();
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return;
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}
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// Parse arguments
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StudyNumber studyNumber;
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SampleType sampleType;
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int numberOfCodes;
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File outputPath;
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boolean externalBrowser;
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// Parse arguments
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try {
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studyNumber = InputValidator.validateStudyNumber(arguments.getOptionValue(Arguments.STUDY_NUMBER));
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sampleType = InputValidator.validateSampleType(arguments.getOptionValue(Arguments.SAMPLE_TYPE));
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numberOfCodes = InputValidator.validateNumberOfCodes(arguments.getOptionValue(Arguments.NUMBER_CODES));
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if (arguments.hasOption(Arguments.OUTPUT_DESTINATION)) {
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outputPath = InputValidator.validateOutputPath(arguments.getOptionValue(Arguments.OUTPUT_DESTINATION));
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} else {
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outputPath = InputValidator.validateOutputPath("./out.html");
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}
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externalBrowser = arguments.hasOption(Arguments.EXTERNAL_BROWSER);
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} catch (InvalidOptionException e) {
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// Something is wrong with the users input, so exit.
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@ -61,32 +76,28 @@ public class Main {
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return;
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}
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FileRepository repository = new FileRepository(new File(".imicodes"));
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CodeGenerator generator = new CodeGenerator();
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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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List<SampleTubeCode> codes;
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try {
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repository.writeNextSampleCode(studyNumber, nextSampleCode + numberOfCodes);
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codes = generator.generateCodes(studyNumber, sampleType, numberOfCodes);
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} catch (InvalidOptionException e) {
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System.out.println(e.getMessage());
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return;
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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.println(new SampleTubeCode(studyNumber, sampleType, nextSampleCode + i));
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String html = new HtmlTableStringBuilder("IMI Sample Tube Code Generator", codes).toString();
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writeHtml(html, outputPath);
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}
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private static void writeHtml(String html, File destination) {
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try(Writer writer = new FileWriter(destination)) {
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writer.write(html);
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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@ -1,6 +1,7 @@
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package de.vanitasvitae.imi.codes.input;
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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.types.SampleType;
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import de.vanitasvitae.imi.codes.types.StudyNumber;
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* destination is not writable.
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*/
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public static File validateOutputPath(String path) throws InvalidOptionException {
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// TODO
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return null;
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File file = new File(path);
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File parent = file.getParentFile();
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if (!parent.exists() || parent.isFile()) {
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throw new InvalidOptionException("Invalid directory " + parent.getAbsolutePath());
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}
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if (!file.exists()) {
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try {
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file.createNewFile();
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} catch (IOException e) {
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throw new InvalidOptionException("Cannot write file " + file.getAbsolutePath(), e);
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}
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}
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return file;
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}
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}
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