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Fixes #19 - Multiple column information per line in acq.txt files (#23)
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@kevin-belellou
kevin-belellou authored Nov 14, 2024
1 parent 7361c60 commit bc73837
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Showing 3 changed files with 87 additions and 45 deletions.
92 changes: 66 additions & 26 deletions src/main/java/fr/ifpen/allotropeconverters/gc/chemstation/ColumnInformationMapper.java
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import fr.ifpen.allotropeconverters.gc.schema.ChromatographyColumnLength;
import fr.ifpen.allotropeconverters.gc.schema.ColumnInnerDiameter;

import java.io.*;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.InputMismatchException;
import java.util.LinkedHashMap;
import java.util.Locale;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Scanner;
import java.util.regex.MatchResult;
import java.util.regex.Pattern;

import static java.nio.charset.StandardCharsets.UTF_16;

public final class ColumnInformationMapper {

private static final Pattern COLUMN_NAME_PATTERN = Pattern.compile(".*:");

private static final String COLON_REGEX = "\\s*:\\s*";
private static final String SEPARATOR_REGEX = "\\s*";
private static final String TEXT_REGEX = "(\\S+)";
private static final String NUMBER_REGEX = "([\\d.]+)";
private static final String COLUMN_SEPARATOR_REGEX = "(?>\\s+|\\n+)";

private static final Map<String, Boolean> COLUMN_NAMES_MAP = new LinkedHashMap<>();

static {
COLUMN_NAMES_MAP.put("Model#", true);
COLUMN_NAMES_MAP.put("Manufacturer", true);
COLUMN_NAMES_MAP.put("Diameter", false);
COLUMN_NAMES_MAP.put("Length", false);
COLUMN_NAMES_MAP.put("Film thickness", false);
}

private static final Pattern COLUMN_PATTERN;

static {
StringBuilder pattern = new StringBuilder();

COLUMN_NAMES_MAP.forEach((columnName, isOnlyText) -> {
pattern.append(columnName).append(COLON_REGEX);

if (!isOnlyText) {
pattern.append(NUMBER_REGEX).append(SEPARATOR_REGEX);
}

pattern.append(TEXT_REGEX).append(COLUMN_SEPARATOR_REGEX);
});

COLUMN_PATTERN = Pattern.compile(pattern.toString(), Pattern.MULTILINE);
}

public ChromatographyColumnDocument readColumnDocumentFromFile(String folderPath) throws IOException {
ChromatographyColumnDocument columnDocument = new ChromatographyColumnDocument();

File file = new File(folderPath,"acq.txt");
File file = new File(folderPath, "acq.txt");
try (FileInputStream fileInputStream = new FileInputStream(file);
InputStreamReader inputStreamReader = new InputStreamReader(fileInputStream, UTF_16);
Scanner acquisitionScanner = new Scanner(inputStreamReader)){
InputStreamReader inputStreamReader = new InputStreamReader(fileInputStream, UTF_16);
Scanner acquisitionScanner = new Scanner(inputStreamReader)) {

acquisitionScanner.useLocale(Locale.US); //Agilent files are US formatted.

skipToColumnInformation(acquisitionScanner);

acquisitionScanner.skip(COLUMN_NAME_PATTERN);
columnDocument.setChromatographyColumnPartNumber(acquisitionScanner.next()); //Model
acquisitionScanner.nextLine();
MatchResult columnInformation = acquisitionScanner.findAll(COLUMN_PATTERN).findFirst().orElseThrow(() -> new NoSuchElementException("Incorrect column information"));

int groupIndex = 1;

acquisitionScanner.skip(COLUMN_NAME_PATTERN);
columnDocument.setProductManufacturer(acquisitionScanner.next()); //Manufacturer
acquisitionScanner.nextLine();
columnDocument.setChromatographyColumnPartNumber(columnInformation.group(groupIndex++)); //Model
columnDocument.setProductManufacturer(columnInformation.group(groupIndex++)); //Manufacturer

ColumnInnerDiameter columnInnerDiameter = new ColumnInnerDiameter();
acquisitionScanner.skip(COLUMN_NAME_PATTERN);
double value = acquisitionScanner.nextDouble();
String unit = acquisitionScanner.next();
double value = Double.parseDouble(columnInformation.group(groupIndex++));
String unit = columnInformation.group(groupIndex++);

if(unit.equals("µm")){ //Allotrope format forces mm.
if (unit.equals("µm")) { //Allotrope format forces mm.
unit = "mm";
value = value / 1000;
}

columnInnerDiameter.setValue(value);
columnInnerDiameter.setUnit(unit);
columnDocument.setColumnInnerDiameter(columnInnerDiameter);
acquisitionScanner.nextLine();

ChromatographyColumnLength chromatographyColumnLength = new ChromatographyColumnLength();
acquisitionScanner.skip(COLUMN_NAME_PATTERN);
chromatographyColumnLength.setValue(acquisitionScanner.nextDouble());
chromatographyColumnLength.setUnit(acquisitionScanner.next());
chromatographyColumnLength.setValue(Double.parseDouble(columnInformation.group(groupIndex++)));
chromatographyColumnLength.setUnit(columnInformation.group(groupIndex++));
columnDocument.setChromatographyColumnLength(chromatographyColumnLength);
acquisitionScanner.nextLine();

ChromatographyColumnFilmThickness columnFilmThickness = new ChromatographyColumnFilmThickness();
acquisitionScanner.skip(COLUMN_NAME_PATTERN);
columnFilmThickness.setValue(acquisitionScanner.nextDouble());
columnFilmThickness.setUnit(acquisitionScanner.next());
columnFilmThickness.setValue(Double.parseDouble(columnInformation.group(groupIndex++)));
columnFilmThickness.setUnit(columnInformation.group(groupIndex++));
columnDocument.setChromatographyColumnFilmThickness(columnFilmThickness);

columnDocument.setChromatographyColumnSerialNumber("N/A");

return columnDocument;
} catch (InputMismatchException e){
} catch (InputMismatchException e) {
return new ChromatographyColumnDocument();
}
}

private void skipToColumnInformation(Scanner acquisitionScanner){
private void skipToColumnInformation(Scanner acquisitionScanner) {
/* Looking for pattern
=====================================================================
Column(s)
=====================================================================
Column Description : HP-PONA
*/
boolean columnSectionFound = false;
String line;
while ((line = acquisitionScanner.nextLine()) != null) {
if (line.contains("======")) {
line = acquisitionScanner.nextLine();
if (line.contains("Column(s)")) {
acquisitionScanner.nextLine();// === line
acquisitionScanner.nextLine();// empty line
columnSectionFound = true;
break;
}
}
}

if (!columnSectionFound) {
throw new NoSuchElementException("No column information found");
}

acquisitionScanner.nextLine(); //Column Description - Not in model
acquisitionScanner.nextLine(); //Inventory # - Not in model
}
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40 changes: 21 additions & 19 deletions src/test/java/fr/ifpen/allotropeconverters/gc/chemstation/ColumnInformationMapperTests.java
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package fr.ifpen.allotropeconverters.gc.chemstation;

import fr.ifpen.allotropeconverters.gc.chemstation.ColumnInformationMapper;
import java.io.IOException;

import fr.ifpen.allotropeconverters.gc.schema.ChromatographyColumnDocument;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;

import java.io.File;
import java.net.URI;
import java.nio.file.Paths;

class ColumnInformationMapperTests {

@Test
void MapperCI() throws Exception {
URI uri;
uri = new File("src/test/resources/V179.D").toURI();
void mapperCI() throws IOException {
readAndAssertColumnInformation("src/test/resources/V179.D");
}

ColumnInformationMapper columnInformationMapper = new ColumnInformationMapper();
@Test
void mapperCI_withMultipleColumnInformationPerLine() throws IOException {
readAndAssertColumnInformation("src/test/resources/V179_2.D");
}

ChromatographyColumnDocument chromatographyColumnDocument = columnInformationMapper.readColumnDocumentFromFile(
Paths.get(uri).toString());
private static void readAndAssertColumnInformation(String folderPath) throws IOException {
ColumnInformationMapper columnInformationMapper = new ColumnInformationMapper();

Assertions.assertEquals("19091S-001", chromatographyColumnDocument.getChromatographyColumnPartNumber());
Assertions.assertEquals("Agilent",chromatographyColumnDocument.getProductManufacturer());
Assertions.assertEquals(0.2,chromatographyColumnDocument.getColumnInnerDiameter().getValue());
Assertions.assertEquals("mm",chromatographyColumnDocument.getColumnInnerDiameter().getUnit());
Assertions.assertEquals(50,chromatographyColumnDocument.getChromatographyColumnLength().getValue());
Assertions.assertEquals("m",chromatographyColumnDocument.getChromatographyColumnLength().getUnit());
Assertions.assertEquals(0.50,chromatographyColumnDocument.getChromatographyColumnFilmThickness().getValue());
Assertions.assertEquals("µm",chromatographyColumnDocument.getChromatographyColumnFilmThickness().getUnit());
ChromatographyColumnDocument chromatographyColumnDocument = columnInformationMapper.readColumnDocumentFromFile(
folderPath);

Assertions.assertEquals("19091S-001", chromatographyColumnDocument.getChromatographyColumnPartNumber());
Assertions.assertEquals("Agilent", chromatographyColumnDocument.getProductManufacturer());
Assertions.assertEquals(0.2, chromatographyColumnDocument.getColumnInnerDiameter().getValue());
Assertions.assertEquals("mm", chromatographyColumnDocument.getColumnInnerDiameter().getUnit());
Assertions.assertEquals(50, chromatographyColumnDocument.getChromatographyColumnLength().getValue());
Assertions.assertEquals("m", chromatographyColumnDocument.getChromatographyColumnLength().getUnit());
Assertions.assertEquals(0.50, chromatographyColumnDocument.getChromatographyColumnFilmThickness().getValue());
Assertions.assertEquals("µm", chromatographyColumnDocument.getChromatographyColumnFilmThickness().getUnit());
}
}
Binary file added src/test/resources/V179_2.D/acq.txt
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