Make sample name API.

eclipse · Nov 16, 2023 · 4b5863c · 4b5863c
1 parent ccf1ea3
commit 4b5863c
Show file tree

Hide file tree

Showing 18 changed files with 65 additions and 38 deletions.
diff --git a/...lipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/AbstractMeasurementInfo.java b/...lipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/AbstractMeasurementInfo.java
@@ -27,7 +27,7 @@
 
 public abstract class AbstractMeasurementInfo implements IMeasurementInfo {
 
- private static final long serialVersionUID = 4247159773898302230L;
+ private static final long serialVersionUID = 4247159773898302231L;
  private static final Logger logger = Logger.getLogger(AbstractMeasurementInfo.class);
  //
  private static final String OPERATOR = "Operator";
@@ -36,6 +36,7 @@ public abstract class AbstractMeasurementInfo implements IMeasurementInfo {
  private static final String MISC_INFO_SEPARATED = "Misc Info Separated";
  private static final String SHORT_INFO = "Short Info";
  private static final String DETAILED_INFO = "Detailed Info";
+ private static final String SAMPLE_NAME = "Sample Name";
  private static final String SAMPLE_GROUP = "Sample Group";
  private static final String BARCODE = "Barcode";
  private static final String BARCODE_TYPE = "Barcode Type";
@@ -56,6 +57,7 @@ public AbstractMeasurementInfo() {
  headerMap.put(MISC_INFO_SEPARATED, "");
  headerMap.put(SHORT_INFO, "");
  headerMap.put(DETAILED_INFO, "");
+ headerMap.put(SAMPLE_NAME, "");
  headerMap.put(SAMPLE_GROUP, "");
  headerMap.put(BARCODE, "");
  headerMap.put(BARCODE_TYPE, "");
@@ -231,6 +233,22 @@ public void setDetailedInfo(String detailedInfo) {
  }
  }
 
+ @Override
+ public String getSampleName() {
+
+ return getHeaderData(SAMPLE_NAME);
+ }
+
+ @Override
+ public void setSampleName(String sampleName) {
+
+ if(sampleName != null) {
+ putHeaderData(SAMPLE_NAME, sampleName);
+ } else {
+ putHeaderData(SAMPLE_NAME, "");
+ }
+ }
+
  @Override
  public String getSampleGroup() {
 

diff --git a/...g.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/FilteredMeasurement.java b/...g.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/FilteredMeasurement.java
@@ -56,6 +56,7 @@ public class FilteredMeasurement<FilteredType extends IMeasurement, ConfigType>
  private String sampleWeightUnit;
  private String barcodeType;
  private String barcode;
+ private String sampleName;
  private String sampleGroup;
  private String shortInfo;
  private String miscInfoSeparated;
@@ -296,6 +297,21 @@ public void setDetailedInfo(String detailedInfo) {
  this.detailedInfo = detailedInfo;
  }
 
+ @Override
+ public String getSampleName() {
+
+ if(sampleName != null) {
+ return sampleName;
+ }
+ return measurement.getSampleName();
+ }
+
+ @Override
+ public void setSampleName(String sampleName) {
+
+ this.sampleName = sampleName;
+ }
+
  @Override
  public String getSampleGroup() {
 

diff --git a/.../org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/IMeasurementInfo.java b/.../org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/IMeasurementInfo.java
@@ -74,6 +74,10 @@ public interface IMeasurementInfo extends Serializable {
 
  void setDetailedInfo(String detailedInfo);
 
+ String getSampleName();
+
+ void setSampleName(String sampleName);
+
  String getSampleGroup();
 
  void setSampleGroup(String sampleGroup);

diff --git a/...se/chemclipse/msd/converter/supplier/mzdata/internal/io/ChromatogramReaderVersion104.java b/...se/chemclipse/msd/converter/supplier/mzdata/internal/io/ChromatogramReaderVersion104.java
@@ -72,7 +72,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
  chromatogram = new VendorChromatogram();
  //
  AdminType admin = mzData.getDescription().getAdmin();
- chromatogram.setDataName(admin.getSampleName());
+ chromatogram.setSampleName(admin.getSampleName());
  for(PersonType contact : admin.getContact()) {
  String contactDetails = String.join(", ", contact.getName(), contact.getInstitution(), contact.getContactInfo());
  if(chromatogram.getOperator().isEmpty()) {

diff --git a/...se/chemclipse/msd/converter/supplier/mzdata/internal/io/ChromatogramReaderVersion105.java b/...se/chemclipse/msd/converter/supplier/mzdata/internal/io/ChromatogramReaderVersion105.java
@@ -73,7 +73,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
  chromatogram = new VendorChromatogram();
  //
  AdminType admin = mzData.getDescription().getAdmin();
- chromatogram.setDataName(admin.getSampleName());
+ chromatogram.setSampleName(admin.getSampleName());
  for(PersonType contact : admin.getContact()) {
  String contactDetails = String.join(", ", contact.getName(), contact.getInstitution(), contact.getContactInfo());
  if(chromatogram.getOperator().isEmpty()) {

diff --git a/...lipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion10.java b/...lipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion10.java
@@ -122,7 +122,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
  SampleListType sampleList = mzML.getSampleList();
  if(sampleList != null) {
  for(SampleType sample : sampleList.getSample()) {
- chromatogram.setDataName(sample.getName());
+ chromatogram.setSampleName(sample.getName());
  }
  }
  for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) {

diff --git a/...ipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion110.java b/...ipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion110.java
@@ -122,7 +122,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
  SampleListType sampleList = mzML.getSampleList();
  if(sampleList != null) {
  for(SampleType sample : sampleList.getSample()) {
- chromatogram.setDataName(sample.getName());
+ chromatogram.setSampleName(sample.getName());
  }
  }
  for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) {

diff --git a/...er.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion11.java b/...er.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion11.java
@@ -96,7 +96,7 @@ private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidP
  IdReferencesType sample = react.getSample();
  IWell well = new Well();
  well.setPosition(calculateCoordinate(w + 1, pcrFormatType));
- well.putHeaderData(IWell.SAMPLE_ID, sample.getId());
+ well.setSampleName(sample.getId());
  Channel channel = createChannel(rdml);
  for(DataType data : react.getData()) {
  for(DpAmpCurveType adp : data.getAdp()) {

diff --git a/...er.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion12.java b/...er.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion12.java
@@ -96,7 +96,7 @@ private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidP
  IdReferencesType sample = react.getSample();
  IWell well = new Well();
  well.setPosition(calculateCoordinate(w + 1, pcrFormatType));
- well.putHeaderData(IWell.SAMPLE_ID, sample.getId());
+ well.setSampleName(sample.getId());
  Channel channel = createChannel(rdml);
  for(DataType data : react.getData()) {
  for(DpAmpCurveType adp : data.getAdp()) {

diff --git a/...er.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion13.java b/...er.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion13.java
@@ -96,15 +96,15 @@ private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidP
  IdReferencesType sample = react.getSample();
  IWell well = new Well();
  well.setPosition(calculateCoordinate(w + 1, pcrFormatType));
- well.putHeaderData(IWell.SAMPLE_ID, sample.getId());
+ well.setSampleName(sample.getId());
  Channel channel = createChannel(rdml);
  for(DataType data : react.getData()) {
  for(DpAmpCurveType adp : data.getAdp()) {
  channel.getFluorescence().add((double)adp.getFluor());
  }
  }
  well.getChannels().put(0, channel);
- well.putHeaderData(IWell.SAMPLE_SUBSET, "Default");
+ well.putHeaderData(IWell.SAMPLE_SUBSET, "Default"); // TODO: should be optional
  vendorPlate.getWells().add(well);
  w++;
  }

diff --git a/...ins/org.eclipse.chemclipse.pcr.model/src/org/eclipse/chemclipse/pcr/model/core/IWell.java b/...ins/org.eclipse.chemclipse.pcr.model/src/org/eclipse/chemclipse/pcr/model/core/IWell.java
@@ -17,7 +17,6 @@
 
 public interface IWell extends Comparable<IWell>, IMeasurement {
 
- String SAMPLE_ID = "Sample ID";
  String TARGET_NAME = "Target Name";
  String TARGET_TYPE = "Target Type";
  String SAMPLE_SUBSET = "Sample Subset";
@@ -53,8 +52,6 @@ public interface IWell extends Comparable<IWell>, IMeasurement {
 
  Map<Integer, IChannel> getChannels();
 
- String getSampleId();
-
  String getSampleSubset();
 
  SampleType getSampleType();

diff --git a/...gins/org.eclipse.chemclipse.pcr.model/src/org/eclipse/chemclipse/pcr/model/core/Well.java b/...gins/org.eclipse.chemclipse.pcr.model/src/org/eclipse/chemclipse/pcr/model/core/Well.java
@@ -34,7 +34,6 @@ public class Well extends AbstractMeasurement implements IWell {
 
  public Well() {
 
- addProtectedKey(SAMPLE_ID);
  addProtectedKey(TARGET_NAME);
  addProtectedKey(SAMPLE_SUBSET);
  addProtectedKey(SAMPLE_TYPE);
@@ -46,7 +45,7 @@ public String getLabel() {
  if(isEmptyMeasurement()) {
  return getPosition().toString();
  } else {
- return getPosition().toString() + ": " + getSampleId();
+ return getPosition().toString() + ": " + getSampleName();
  }
  }
 
@@ -120,12 +119,6 @@ public int compareTo(IWell well) {
  }
  }
 
- @Override
- public String getSampleId() {
-
- return getHeaderDataOrDefault(SAMPLE_ID, "").trim();
- }
-
  @Override
  public String getSampleSubset() {
 
@@ -173,7 +166,7 @@ public void setTargetType(TargetType targetType) {
  @Override
  public boolean isEmptyMeasurement() {
 
- return ("".equals(getSampleId().trim()) || "_".equals(getSampleId().trim()));
+ return ("".equals(getSampleName().trim()) || "_".equals(getSampleName().trim()));
  }
 
  @Override
@@ -236,7 +229,6 @@ public IWell makeDeepCopy() {
  for(Entry<Integer, IChannel> set : channels.entrySet()) {
  well.getChannels().put(set.getKey(), set.getValue().makeDeepCopy());
  }
- well.putHeaderData(SAMPLE_ID, getSampleId());
  well.putHeaderData(TARGET_NAME, getTargetName());
  well.putHeaderData(SAMPLE_SUBSET, getSampleSubset());
  well.putHeaderData(SAMPLE_TYPE, getSampleType().toString());

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
@@ -143,7 +143,7 @@ void generateVirtualChannels(Set<IWell> wells, String targetSubset) {
  continue;
  }
  Pattern pattern = Pattern.compile(virtualChannel.getSample(), Pattern.CASE_INSENSITIVE);
- Matcher matcher = pattern.matcher(well.getSampleId());
+ Matcher matcher = pattern.matcher(well.getSampleName());
  if(!matcher.find()) {
  continue;
  }
@@ -176,7 +176,7 @@ void generateVirtualChannels(Set<IWell> wells, String targetSubset) {
  continue;
  }
  Pattern pattern = Pattern.compile(wellMapping.getSample(), Pattern.CASE_INSENSITIVE);
- Matcher matcher = pattern.matcher(well.getSampleId());
+ Matcher matcher = pattern.matcher(well.getSampleName());
  if(!matcher.find()) {
  continue;
  }
@@ -202,7 +202,7 @@ void generateVirtualChannels(Set<IWell> wells, String targetSubset) {
  targetChannel.setCrossingPoint(virtualCrossingPoint);
  }
  if(well.getChannels().containsKey(target - 1)) {
- logger.warn("Channel " + target + " for " + well.getSampleId() + " is already defined. Skipping.");
+ logger.warn("Channel " + target + " for " + well.getSampleName() + " is already defined. Skipping.");
  }
  well.getChannels().putIfAbsent(target - 1, targetChannel);
  }
@@ -224,7 +224,7 @@ void printResults(IPlate plate, String targetSubset, CSVPrinter csvPrinter) thro
  continue;
  }
  Pattern pattern = Pattern.compile(wellMapping.getSample(), Pattern.CASE_INSENSITIVE);
- Matcher matcher = pattern.matcher(well.getSampleId());
+ Matcher matcher = pattern.matcher(well.getSampleName());
  if(!matcher.find()) {
  continue;
  }

diff --git a/...src/org/eclipse/chemclipse/pcr/report/supplier/tabular/excel/core/PCRExportConverter.java b/...src/org/eclipse/chemclipse/pcr/report/supplier/tabular/excel/core/PCRExportConverter.java
@@ -173,11 +173,11 @@ private void printResultTable(IPlate plate, String targetSubset, XSSFSheet sheet
  String sampleSubset = dataMap.getOrDefault(IWell.SAMPLE_SUBSET, "");
  if(isSubsetMatch(sampleSubset, targetSubset)) {
  XSSFRow data = sheet.createRow(sheet.getLastRowNum() + 1);
- String sampleNumber = dataMap.getOrDefault(IWell.SAMPLE_ID, "");
+ String sampleName = well.getSampleName();
  String request = "";
  if(separator != null && !separator.isEmpty()) {
- String[] sampleSplit = sampleNumber.split(separator);
- sampleNumber = sampleSplit[0];
+ String[] sampleSplit = sampleName.split(separator);
+ sampleName = sampleSplit[0];
  if(sampleSplit.length > 1) {
  request = sampleSplit[1];
  }
@@ -186,7 +186,7 @@ private void printResultTable(IPlate plate, String targetSubset, XSSFSheet sheet
  positionCell.setCellValue(position.getRow() + position.getColumn());
  positionCell.setCellStyle(style);
  XSSFCell sampleNumberCell = data.createCell(1);
- sampleNumberCell.setCellValue(sampleNumber);
+ sampleNumberCell.setCellValue(sampleName);
  sampleNumberCell.setCellStyle(style);
  XSSFCell requestCell = data.createCell(2);
  requestCell.setCellValue(request);

diff --git a/....tabular/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/model/WellComparator.java b/....tabular/src/org/eclipse/chemclipse/pcr/report/supplier/tabular/model/WellComparator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021, 2022 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -20,9 +20,9 @@ public class WellComparator implements Comparator<IWell> {
  @Override
  public int compare(IWell firstWell, IWell secondWell) {
 
- if(firstWell.getSampleId().equals(secondWell.getSampleId())) {
+ if(firstWell.getSampleName().equals(secondWell.getSampleName())) {
  return firstWell.getPosition().compareTo(secondWell.getPosition());
  }
- return firstWell.getSampleId().compareTo(secondWell.getSampleId());
+ return firstWell.getSampleName().compareTo(secondWell.getSampleName());
  }
 }
diff --git a/...plier.txt/src/org/eclipse/chemclipse/pcr/report/supplier/txt/core/PCRExportConverter.java b/...plier.txt/src/org/eclipse/chemclipse/pcr/report/supplier/txt/core/PCRExportConverter.java
@@ -140,7 +140,7 @@ private void printResultTable(IPlate plate, String targetSubset, PrintWriter pri
  if(isSubsetMatch(sampleSubset, targetSubset)) {
  printWriter.print(position.getRow() + position.getColumn());
  printWriter.print(TAB);
- printWriter.print(well.getSampleId());
+ printWriter.print(well.getSampleName());
  printWriter.print(TAB);
  printWriter.print(well.getSampleSubset());
  printWriter.print(TAB);

diff --git a/...ipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/PCRPlate.java b/...ipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/PCRPlate.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2019, 2021 Lablicate GmbH.
+ * Copyright (c) 2019, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -197,7 +197,7 @@ private void showWellDetails(IWell well) {
  StringBuilder builder = new StringBuilder();
  String sampleSubset = well.getSampleSubset();
  String targetName = well.getTargetName();
- builder.append(well.getSampleId());
+ builder.append(well.getSampleName());
  if(!well.isEmptyMeasurement()) {
  builder.append(" | ");
  builder.append(sampleSubset.equals("") ? "--" : sampleSubset);
@@ -262,4 +262,4 @@ private void highlightComposite(PCRWell pcrWellHighlight) {
  }
  }
  }
-}
+}
diff --git a/...lipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/PCRWell.java b/...lipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/PCRWell.java
@@ -190,7 +190,7 @@ public String getWellInfo(IWell well) {
  } else {
  if(well.isActiveSubset()) {
  StringBuilder builder = new StringBuilder();
- builder.append(well.getSampleId());
+ builder.append(well.getSampleName());
  appendHeaderInfo(well, builder);
  appendCrossingPointInfo(well, builder);
  text = builder.toString();