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IMI-Application
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Clean up code and comment

This commit is contained in:
Paul Schaub 2018-11-17 15:39:58 +01:00
parent 3c9344dcef
commit 32c1bb2999
Signed by: vanitasvitae
GPG Key ID: 62BEE9264BF17311
7 changed files with 82 additions and 27 deletions
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4
build.gradle
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@ -1,11 +1,13 @@
plugins { plugins {
id 'java' id 'java'
id 'application'
} }
group 'de.vanitasvitae' group 'de.vanitasvitae'
version '1.0-SNAPSHOT' version '1.0-SNAPSHOT'
sourceCompatibility = 1.8 sourceCompatibility = 1.8
mainClassName = "de.vanitasvitae.imi.codes.Main"
repositories { repositories {
mavenCentral() mavenCentral()
@ -19,4 +21,4 @@ dependencies {
// Testing // Testing
testCompile group: 'junit', name: 'junit', version: '4.12' testCompile group: 'junit', name: 'junit', version: '4.12'
} }

25
src/main/java/de/vanitasvitae/imi/codes/CodeGenerator.java
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@ -1,6 +1,5 @@
package de.vanitasvitae.imi.codes; package de.vanitasvitae.imi.codes;
import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
@ -11,15 +10,31 @@ import de.vanitasvitae.imi.codes.types.SampleTubeCode;
import de.vanitasvitae.imi.codes.types.SampleType; import de.vanitasvitae.imi.codes.types.SampleType;
import de.vanitasvitae.imi.codes.types.StudyNumber; import de.vanitasvitae.imi.codes.types.StudyNumber;
/**
* Class that generates {@link SampleTubeCode SampleTubeCodes}.
*/
public class CodeGenerator { public class CodeGenerator {
private final FileRepository repository = new FileRepository(new File(".imicodes")); // Pls do not instantiate.
private CodeGenerator() {
public CodeGenerator() {
} }
public List<SampleTubeCode> generateCodes(StudyNumber studyNumber, SampleType sampleType, int numberOfCodes) /**
* Generate {@code numberOfCodes} new codes for samples of type {@code sampleType}, which are associated to study
* {@code studyNumber}.
*
* @param repository provides access to records of existing codes
* @param studyNumber number of the study
* @param sampleType type of the samples
* @param numberOfCodes number of codes to be generated
*
* @return list of {@link SampleTubeCode SampleTubeCodes}
*
* @throws InvalidOptionException if too many codes would be generated.
* @throws IOException if IO goes wrong reading or writing sample code records.
*/
public static List<SampleTubeCode> generateCodes(FileRepository repository, StudyNumber studyNumber, SampleType sampleType, int numberOfCodes)
throws InvalidOptionException, IOException { throws InvalidOptionException, IOException {
List<SampleTubeCode> codes = new ArrayList<>(); List<SampleTubeCode> codes = new ArrayList<>();

6
src/main/java/de/vanitasvitae/imi/codes/HtmlTableStringBuilder.java
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@ -8,6 +8,12 @@ public class HtmlTableStringBuilder {
private StringBuilder html; private StringBuilder html;
/**
* Generated a HTML String which contains a table of {@link SampleTubeCode SampleTubeCodes}.
*
* @param title Title which gets inserted as level 2 header.
* @param codes list of codes
*/
public HtmlTableStringBuilder(String title, List<SampleTubeCode> codes) { public HtmlTableStringBuilder(String title, List<SampleTubeCode> codes) {
html = new StringBuilder("<!DOCTYPE html>\n") html = new StringBuilder("<!DOCTYPE html>\n")
.append("<html>\n") .append("<html>\n")

36
src/main/java/de/vanitasvitae/imi/codes/Main.java
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@ -7,11 +7,13 @@ import java.io.IOException;
import java.io.Writer; import java.io.Writer;
import java.net.URI; import java.net.URI;
import java.net.URISyntaxException; import java.net.URISyntaxException;
import java.sql.SQLOutput;
import java.util.List; import java.util.List;
import de.vanitasvitae.imi.codes.input.Arguments; import de.vanitasvitae.imi.codes.input.Arguments;
import de.vanitasvitae.imi.codes.input.InputValidator; import de.vanitasvitae.imi.codes.input.InputValidator;
import de.vanitasvitae.imi.codes.input.InvalidOptionException; import de.vanitasvitae.imi.codes.input.InvalidOptionException;
import de.vanitasvitae.imi.codes.persistence.FileRepository;
import de.vanitasvitae.imi.codes.types.SampleTubeCode; import de.vanitasvitae.imi.codes.types.SampleTubeCode;
import de.vanitasvitae.imi.codes.types.SampleType; import de.vanitasvitae.imi.codes.types.SampleType;
import de.vanitasvitae.imi.codes.types.StudyNumber; import de.vanitasvitae.imi.codes.types.StudyNumber;
@ -24,9 +26,10 @@ import org.apache.commons.cli.ParseException;
public class Main { public class Main {
private static final String NAME_JAR = "java -jar imicodes.jar"; private static final String NAME_JAR = "imi.codes";
private static final String HELP_HEADER = "Generate ID codes for sample tubes."; 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>"; private static final String HELP_FOOTER = "\nAuthor: Paul Schaub <paul.schaub@wwu.de>";
private static final File RECORD_DIR = new File(".imicodes");
/** /**
* Entry point to the program. * Entry point to the program.
@ -39,6 +42,7 @@ public class Main {
Options options = Arguments.getCommandLineOptions(); Options options = Arguments.getCommandLineOptions();
CommandLineParser parser = new DefaultParser(); CommandLineParser parser = new DefaultParser();
// Parse command line arguments
CommandLine arguments; CommandLine arguments;
try { try {
arguments = parser.parse(options, args); arguments = parser.parse(options, args);
@ -60,7 +64,7 @@ public class Main {
File outputPath; File outputPath;
boolean externalBrowser; boolean externalBrowser;
// Parse arguments // Validate command line arguments
try { try {
studyNumber = InputValidator.validateStudyNumber(arguments.getOptionValue(Arguments.STUDY_NUMBER)); studyNumber = InputValidator.validateStudyNumber(arguments.getOptionValue(Arguments.STUDY_NUMBER));
sampleType = InputValidator.validateSampleType(arguments.getOptionValue(Arguments.SAMPLE_TYPE)); sampleType = InputValidator.validateSampleType(arguments.getOptionValue(Arguments.SAMPLE_TYPE));
@ -76,39 +80,55 @@ public class Main {
} catch (InvalidOptionException e) { } catch (InvalidOptionException e) {
// Something is wrong with the users input, so exit. // Something is wrong with the users input, so exit.
System.out.println(e.getMessage()); System.out.println(e.getMessage());
printHelp(options);
return; return;
} }
CodeGenerator generator = new CodeGenerator(); // Store/read number of generated codes to file
FileRepository repository = new FileRepository(RECORD_DIR);
// Generate codes
List<SampleTubeCode> codes; List<SampleTubeCode> codes;
try { try {
codes = generator.generateCodes(studyNumber, sampleType, numberOfCodes); codes = CodeGenerator.generateCodes(repository, studyNumber, sampleType, numberOfCodes);
} catch (InvalidOptionException e) { } catch (InvalidOptionException e) {
System.out.println(e.getMessage()); System.out.println(e.getMessage());
return; return;
} catch (IOException e) { } catch (IOException e) {
System.out.println("Could not store records about already generated codes.");
e.printStackTrace(); e.printStackTrace();
return; return;
} }
// Build HTML
String html = new HtmlTableStringBuilder("IMI Sample Tube Code Generator", codes).toString(); String html = new HtmlTableStringBuilder("IMI Sample Tube Code Generator", codes).toString();
writeHtml(html, outputPath);
// Write HTML to output path
try {
writeHtml(html, outputPath);
} catch (IOException e) {
System.out.println("Could not write HTML to file " + outputPath.getAbsolutePath());
e.printStackTrace();
return;
}
// Upon users wish, open generated HTML in a browser.
if (externalBrowser && Desktop.isDesktopSupported()) { if (externalBrowser && Desktop.isDesktopSupported()) {
try { try {
Desktop.getDesktop().browse(new URI("file://" + outputPath.getAbsolutePath())); Desktop.getDesktop().browse(new URI("file://" + outputPath.getAbsolutePath()));
} catch (IOException | URISyntaxException e) { } catch (IOException | URISyntaxException e) {
System.out.println("Could not open generated HTML in a browser.");
e.printStackTrace(); e.printStackTrace();
} }
} }
} }
private static void writeHtml(String html, File destination) { /*
Write HTML to a file.
*/
private static void writeHtml(String html, File destination) throws IOException {
try(Writer writer = new FileWriter(destination)) { try(Writer writer = new FileWriter(destination)) {
writer.write(html); writer.write(html);
} catch (IOException e) {
e.printStackTrace();
} }
} }

11
src/main/java/de/vanitasvitae/imi/codes/types/BoundedCharSequence.java
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@ -5,11 +5,22 @@ import java.util.stream.IntStream;
import de.vanitasvitae.imi.codes.input.InvalidOptionException; import de.vanitasvitae.imi.codes.input.InvalidOptionException;
/**
* Abstract class, that represents a {@link CharSequence} which MUST match a given REGEX.
*/
public abstract class BoundedCharSequence implements CharSequence { public abstract class BoundedCharSequence implements CharSequence {
private final Pattern regex; private final Pattern regex;
private final String value; private final String value;
/**
* Create a {@link BoundedCharSequence}. If the {@code value} doesn't match the {@code regex},
* a {@link InvalidOptionException} is thrown.
*
* @param regex regular expression
* @param value value of the {@link BoundedCharSequence}.
* @throws InvalidOptionException thrown when the value doesn't match the regex.
*/
protected BoundedCharSequence(Pattern regex, String value) throws InvalidOptionException { protected BoundedCharSequence(Pattern regex, String value) throws InvalidOptionException {
this.regex = regex; this.regex = regex;
if (!matchPattern(value)) { if (!matchPattern(value)) {

14
src/main/java/de/vanitasvitae/imi/codes/types/SampleTubeCode.java
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@ -2,12 +2,26 @@ package de.vanitasvitae.imi.codes.types;
import java.util.stream.IntStream; import java.util.stream.IntStream;
/**
* Identification Code for Sample Tubes.
*/
public class SampleTubeCode implements CharSequence { public class SampleTubeCode implements CharSequence {
private final StudyNumber studyNumber; private final StudyNumber studyNumber;
private final SampleType sampleType; private final SampleType sampleType;
private final int sampleNumber; private final int sampleNumber;
/**
* Create a new {@link SampleTubeCode} object.
* This constructor throws an {@link IllegalArgumentException}, if one of the following cases is happening:
* - {@code studyNumber} is null
* - {@code sampleType} is null
* - {@code sampleNumber is negative or greater than 9999}
*
* @param studyNumber code that identifies the associated study
* @param sampleType type of the sample
* @param sampleNumber number of the sample
*/
public SampleTubeCode(StudyNumber studyNumber, SampleType sampleType, int sampleNumber) { public SampleTubeCode(StudyNumber studyNumber, SampleType sampleType, int sampleNumber) {
if (studyNumber == null) { if (studyNumber == null) {
throw new IllegalArgumentException("StudyNumber MUST NOT be null."); throw new IllegalArgumentException("StudyNumber MUST NOT be null.");

13
src/main/java/de/vanitasvitae/imi/codes/types/Study.java
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@ -1,13 +0,0 @@
package de.vanitasvitae.imi.codes.types;
import java.util.ArrayList;
import java.util.List;
public class Study {
private final StudyNumber number;
private final List<SampleTubeCode> codes = new ArrayList<>();
public Study(StudyNumber number) {
this.number = number;
}
}