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IMI-Application
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Implement HTML table renderer and export

This commit is contained in:
Paul Schaub 2018-11-15 21:04:25 +01:00
parent dd1336beb5
commit fa95d578f5
Signed by: vanitasvitae
GPG Key ID: 62BEE9264BF17311
4 changed files with 149 additions and 25 deletions
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47
src/main/java/de/vanitasvitae/imi/codes/CodeGenerator.java Normal file
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@ -0,0 +1,47 @@
package de.vanitasvitae.imi.codes;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
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.SampleType;
import de.vanitasvitae.imi.codes.types.StudyNumber;
public class CodeGenerator {
private final FileRepository repository = new FileRepository(new File(".imicodes"));
public CodeGenerator() {
}
public List<SampleTubeCode> generateCodes(StudyNumber studyNumber, SampleType sampleType, int numberOfCodes)
throws InvalidOptionException, IOException {
List<SampleTubeCode> codes = new ArrayList<>();
// Read the next sample code from file
int nextSampleCode = repository.nextSampleCode(studyNumber);
int nextTotal = nextSampleCode + numberOfCodes;
// Check, if we'd have an overflow of sample numbers
// We check like this to prevent integer overflows
if (nextSampleCode > 9999 || numberOfCodes > 9999 || nextTotal - 1 > 9999) {
throw new InvalidOptionException("Study " + studyNumber + "would have too many sample tubes" +
" (" + (nextTotal - 1) + "). Aborting.");
}
// Write back the number of the next sample number that should be generated next time
repository.writeNextSampleCode(studyNumber, nextSampleCode + numberOfCodes);
// Generate codes
for (int i = 0; i < numberOfCodes; i++) {
codes.add(new SampleTubeCode(studyNumber, sampleType, nextSampleCode + i));
}
return codes;
}
}

52
src/main/java/de/vanitasvitae/imi/codes/HtmlTableStringBuilder.java Normal file
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@ -0,0 +1,52 @@
package de.vanitasvitae.imi.codes;
import java.util.List;
import de.vanitasvitae.imi.codes.types.SampleTubeCode;
public class HtmlTableStringBuilder {
private StringBuilder html;
public HtmlTableStringBuilder(String title, List<SampleTubeCode> codes) {
html = new StringBuilder("<!DOCTYPE html>\n")
.append("<html>\n")
.append("<head>\n")
.append("<style>\n")
.append("table, th, td {\n")
.append(" border: 1px solid black;\n")
.append("}\n")
.append("</style>\n")
.append("</head>")
.append("<body>")
.append("\n");
// Add title
html.append("<h2>").append(title).append("</h2>\n");
// Open table
html.append("<table>\n")
.append("<tr>\n")
.append("<th>Code</th>\n")
.append("</tr>\n");
// Append table entries
for (SampleTubeCode c : codes) {
html.append("<tr>\n")
.append("<td>").append(c.toString()).append("</td>\n")
.append("</tr>\n");
}
// Close table
html.append("</table>\n");
// Close body and html
html.append("</body>\n");
html.append("</html>");
}
@Override
public String toString() {
return html.toString();
}
}

57
src/main/java/de/vanitasvitae/imi/codes/Main.java
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@ -1,12 +1,14 @@
package de.vanitasvitae.imi.codes;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.util.List;
import de.vanitasvitae.imi.codes.input.Arguments;
import de.vanitasvitae.imi.codes.input.InputValidator;
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.SampleType;
import de.vanitasvitae.imi.codes.types.StudyNumber;
@ -19,10 +21,17 @@ import org.apache.commons.cli.ParseException;
public class Main {
private static final String NAME_JAR = "imicodes";
private static final String NAME_JAR = "java -jar imicodes.jar";
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>";
/**
* Entry point to the program.
* Any provided arguments are parsed and the behaviour of the program is modified respectively.
* A list of available options can be displayed using "-h".
*
* @param args arguments
*/
public static void main(String[] args) {
Options options = Arguments.getCommandLineOptions();
CommandLineParser parser = new DefaultParser();
@ -42,18 +51,24 @@ public class Main {
return;
}
// Parse arguments
StudyNumber studyNumber;
SampleType sampleType;
int numberOfCodes;
File outputPath;
boolean externalBrowser;
// Parse arguments
try {
studyNumber = InputValidator.validateStudyNumber(arguments.getOptionValue(Arguments.STUDY_NUMBER));
sampleType = InputValidator.validateSampleType(arguments.getOptionValue(Arguments.SAMPLE_TYPE));
numberOfCodes = InputValidator.validateNumberOfCodes(arguments.getOptionValue(Arguments.NUMBER_CODES));
outputPath = InputValidator.validateOutputPath(arguments.getOptionValue(Arguments.OUTPUT_DESTINATION));
if (arguments.hasOption(Arguments.OUTPUT_DESTINATION)) {
outputPath = InputValidator.validateOutputPath(arguments.getOptionValue(Arguments.OUTPUT_DESTINATION));
} else {
outputPath = InputValidator.validateOutputPath("./out.html");
}
externalBrowser = arguments.hasOption(Arguments.EXTERNAL_BROWSER);
} catch (InvalidOptionException e) {
// Something is wrong with the users input, so exit.
@ -61,32 +76,28 @@ public class Main {
return;
}
FileRepository repository = new FileRepository(new File(".imicodes"));
CodeGenerator generator = new CodeGenerator();
// Read the next sample code from file
int nextSampleCode = repository.nextSampleCode(studyNumber);
int nextTotal = nextSampleCode + numberOfCodes;
// Check, if we'd have an overflow of sample numbers
// We check like this to prevent integer overflows
if (nextSampleCode > 9999 || numberOfCodes > 9999 || nextTotal - 1 > 9999) {
System.out.println("Study " + studyNumber + "would have too many sample tubes" +
" (" + (nextTotal - 1) + "). Aborting.");
return;
}
// Write back the number of the next sample number that should be generated next time
List<SampleTubeCode> codes;
try {
repository.writeNextSampleCode(studyNumber, nextSampleCode + numberOfCodes);
codes = generator.generateCodes(studyNumber, sampleType, numberOfCodes);
} catch (InvalidOptionException e) {
System.out.println(e.getMessage());
return;
} catch (IOException e) {
e.printStackTrace();
return;
}
// Now we are finished with dangerous IO...
// Generate codes
for (int i = 0; i < numberOfCodes; i++) {
System.out.println(new SampleTubeCode(studyNumber, sampleType, nextSampleCode + i));
String html = new HtmlTableStringBuilder("IMI Sample Tube Code Generator", codes).toString();
writeHtml(html, outputPath);
}
private static void writeHtml(String html, File destination) {
try(Writer writer = new FileWriter(destination)) {
writer.write(html);
} catch (IOException e) {
e.printStackTrace();
}
}

18
src/main/java/de/vanitasvitae/imi/codes/input/InputValidator.java
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@ -1,6 +1,7 @@
package de.vanitasvitae.imi.codes.input;
import java.io.File;
import java.io.IOException;
import de.vanitasvitae.imi.codes.types.SampleType;
import de.vanitasvitae.imi.codes.types.StudyNumber;
@ -70,7 +71,20 @@ public class InputValidator {
* destination is not writable.
*/
public static File validateOutputPath(String path) throws InvalidOptionException {
// TODO
return null;
File file = new File(path);
File parent = file.getParentFile();
if (!parent.exists() || parent.isFile()) {
throw new InvalidOptionException("Invalid directory " + parent.getAbsolutePath());
}
if (!file.exists()) {
try {
file.createNewFile();
} catch (IOException e) {
throw new InvalidOptionException("Cannot write file " + file.getAbsolutePath(), e);
}
}
return file;
}
}