Update Apache Commons.

eclipse · Oct 26, 2023 · 024c2c7 · 024c2c7
1 parent 8e4342d
commit 024c2c7
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Showing 6 changed files with 16 additions and 11 deletions.
diff --git a/...sv/src/org/eclipse/chemclipse/msd/converter/supplier/csv/core/FileContentMatcherPeak.java b/...sv/src/org/eclipse/chemclipse/msd/converter/supplier/csv/core/FileContentMatcherPeak.java
@@ -28,7 +28,8 @@ public class FileContentMatcherPeak extends AbstractFileContentMatcher implement
  public boolean checkFileFormat(File file) {
 
  try {
- try (CSVParser parser = new CSVParser(new FileReader(file), CSVFormat.EXCEL.withHeader())) {
+ CSVFormat csvFormat = CSVFormat.EXCEL.builder().setHeader().build();
+ try (CSVParser parser = new CSVParser(new FileReader(file), csvFormat)) {
  String[] array = parser.getHeaderMap().keySet().toArray(new String[0]);
  return Arrays.equals(array, CSVPeakConverter.HEADERS);
  }

diff --git a/...r.csv/src/org/eclipse/chemclipse/msd/converter/supplier/csv/io/core/CSVPeakConverter.java b/...r.csv/src/org/eclipse/chemclipse/msd/converter/supplier/csv/io/core/CSVPeakConverter.java
@@ -168,7 +168,8 @@ public IProcessingInfo<IPeaks<?>> convert(File file, IProgressMonitor monitor) {
 
  public static void writePeaks(IPeaks<? extends IPeak> peaks, Writer writer, boolean writeHeader) throws IOException {
 
- try (CSVPrinter csv = new CSVPrinter(writer, CSVFormat.EXCEL.withNullString("").withQuoteMode(QuoteMode.ALL))) {
+ CSVFormat csvFormat = CSVFormat.EXCEL.builder().setNullString("").setQuoteMode(QuoteMode.ALL).build();
+ try (CSVPrinter csv = new CSVPrinter(writer, csvFormat)) {
  if(writeHeader) {
  csv.printRecord(Arrays.asList(HEADERS));
  }
@@ -214,7 +215,8 @@ public static void writePeaks(IPeaks<? extends IPeak> peaks, Writer writer, bool
  public static IPeaks<IPeak> readPeaks(Reader reader) throws IOException, ParseException {
 
  Peaks result = new Peaks();
- try (CSVParser parser = new CSVParser(reader, CSVFormat.EXCEL.withHeader(HEADERS).withSkipHeaderRecord())) {
+ CSVFormat csvFormat = CSVFormat.EXCEL.builder().setHeader(HEADERS).setSkipHeaderRecord(true).build();
+ try (CSVParser parser = new CSVParser(reader, csvFormat)) {
  NumberFormat nf;
  synchronized(NUMBER_FORMAT) {
  nf = (NumberFormat)NUMBER_FORMAT.clone();

diff --git a/...csv/src/org/eclipse/chemclipse/msd/converter/supplier/csv/io/core/ChromatogramReader.java b/...csv/src/org/eclipse/chemclipse/msd/converter/supplier/csv/io/core/ChromatogramReader.java
@@ -84,7 +84,7 @@ private IChromatogramMSD readChromatogram(File file, boolean overview) throws IO
  String zeroMarker = PreferenceSupplier.getImportZeroMarker();
  zeroMarker = zeroMarker.startsWith(ZERO_VALUE) ? zeroMarker : ZERO_VALUE;
  char delimiter = PreferenceSupplier.getImportDelimiter().getCharacter();
- CSVParser csvParser = new CSVParser(fileReader, CSVFormat.newFormat(delimiter).withHeader());
+ CSVParser csvParser = new CSVParser(fileReader, CSVFormat.newFormat(delimiter).builder().setHeader().build());
  chromatogram = new VendorChromatogram();
  if(!overview) {
  /*

diff --git a/...v/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java b/...v/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/csv/core/PCRExportConverter.java
@@ -60,14 +60,15 @@ public class PCRExportConverter extends AbstractPlateExportConverter implements
  private static final Logger logger = Logger.getLogger(PCRExportConverter.class);
  //
  private static final String DESCRIPTION = "PCR CSV Export";
- private static final CSVFormat csvFormat = CSVFormat.RFC4180.withDelimiter(PreferenceSupplier.getDelimiter().getCharacter());
  //
  private DecimalFormat decimalFormat = new DecimalFormat("00" + PreferenceSupplier.getDecimalSeparator().getCharacter() + "00");
 
  @Override
  public IProcessingInfo<File> convert(File file, IPlate plate, IProgressMonitor monitor) {
 
  decimalFormat.applyPattern("#,##0.00");
+ CSVFormat csvFormat = CSVFormat.RFC4180.builder() //
+ .setDelimiter(PreferenceSupplier.getDelimiter().getCharacter()).build();
  IProcessingInfo<File> processingInfo = new ProcessingInfo<>();
  if(plate != null) {
  try (CSVPrinter csvPrinter = new CSVPrinter(new FileWriter(file, false), csvFormat)) {

diff --git a/...r.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java b/...r.pca/src/org/eclipse/chemclipse/xxd/process/supplier/pca/core/PcaExtractionFileText.java
@@ -118,7 +118,8 @@ private Samples extract() {
  /*
  * Data
  */
- CSVParser parser = new CSVParser(reader, CSVFormat.TDF.withHeader());
+ CSVFormat csvFormat = CSVFormat.TDF.builder().setHeader().build();
+ CSVParser parser = new CSVParser(reader, csvFormat);
  Map<Integer, String> indexMap = extractIndexMap(parser);
  for(CSVRecord record : parser.getRecords()) {
  /*

diff --git a/...releng/org.eclipse.chemclipse.targetplatform/org.eclipse.chemclipse.targetplatform.target b/...releng/org.eclipse.chemclipse.targetplatform/org.eclipse.chemclipse.targetplatform.target
@@ -38,13 +38,13 @@
  <dependency>
  <groupId>commons-codec</groupId>
  <artifactId>commons-codec</artifactId>
- <version>1.15</version>
+ <version>1.16.0</version>
  <type>jar</type>
  </dependency>
  <dependency>
  <groupId>commons-io</groupId>
  <artifactId>commons-io</artifactId>
- <version>2.11.0</version>
+ <version>2.14.0</version>
  <type>jar</type>
  </dependency>
  <dependency>
@@ -56,19 +56,19 @@
  <dependency>
  <groupId>org.apache.commons</groupId>
  <artifactId>commons-compress</artifactId>
- <version>1.22</version>
+ <version>1.24.0</version>
  <type>jar</type>
  </dependency>
  <dependency>
  <groupId>org.apache.commons</groupId>
  <artifactId>commons-csv</artifactId>
- <version>1.8</version>
+ <version>1.10.0</version>
  <type>jar</type>
  </dependency>
  <dependency>
  <groupId>org.apache.commons</groupId>
  <artifactId>commons-lang3</artifactId>
- <version>3.12.0</version>
+ <version>3.13.0</version>
  <type>jar</type>
  </dependency>
  <dependency>