Use sample name API.

OpenChrom · Dec 19, 2023 · ddcde6a · ddcde6a
1 parent c55b1d7
commit ddcde6a
Show file tree

Hide file tree

Showing 11 changed files with 31 additions and 27 deletions.
diff --git a/....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramReader.java b/....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramReader.java
@@ -199,7 +199,7 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t
 	private IVendorChromatogram readSample(AnIMLType animl, IVendorChromatogram chromatogram) {
 
 		SampleType sample = animl.getSampleSet().getSample().get(0);
-		chromatogram.setDataName(sample.getName());
+		chromatogram.setSampleName(sample.getName());
 		chromatogram.setBarcode(sample.getBarcode());
 		chromatogram.setDetailedInfo(sample.getSampleID());
 		chromatogram.setMiscInfo(sample.getComment());

diff --git a/....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramWriter.java b/....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramWriter.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
@@ -27,9 +27,6 @@
 import org.eclipse.chemclipse.support.history.IEditInformation;
 import org.eclipse.core.runtime.IProgressMonitor;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Marshaller;
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.BinaryReader;
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.Common;
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AnIMLType;
@@ -54,6 +51,10 @@
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.UnitType;
 import net.openchrom.xxd.converter.supplier.animl.preferences.PreferenceSupplier;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+
 public class ChromatogramWriter extends AbstractChromatogramCSDWriter {
 
 	private static final Logger logger = Logger.getLogger(ChromatogramWriter.class);
@@ -83,7 +84,7 @@ private SampleSetType createSampleSet(IChromatogramCSD chromatogram) {
 		SampleSetType sampleSet = new SampleSetType();
 		SampleType sample = new SampleType();
 		sample.setId("OPENCHROM_CSD_EXPORT");
-		sample.setName(chromatogram.getHeaderDataOrDefault("Sample Name", chromatogram.getDataName()));
+		sample.setName(chromatogram.getSampleName());
 		sample.setBarcode(chromatogram.getBarcode());
 		sample.setComment(chromatogram.getMiscInfo());
 		sample.setSampleID(FilenameUtils.removeExtension(chromatogram.getFile().getName()));

diff --git a/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/ChromatogramReader.java b/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/ChromatogramReader.java
@@ -41,7 +41,6 @@
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.xml.sax.SAXException;
 
-import jakarta.xml.bind.JAXBException;
 import net.openchrom.msd.converter.supplier.animl.model.IVendorChromatogram;
 import net.openchrom.msd.converter.supplier.animl.model.IVendorIon;
 import net.openchrom.msd.converter.supplier.animl.model.IVendorScan;
@@ -62,6 +61,8 @@
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SeriesType;
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.UnitType;
 
+import jakarta.xml.bind.JAXBException;
+
 public class ChromatogramReader extends AbstractChromatogramMSDReader {
 
 	private static final Logger logger = Logger.getLogger(ChromatogramReader.class);
@@ -273,7 +274,7 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t
 	private IVendorChromatogram readSample(AnIMLType animl, IVendorChromatogram chromatogram) {
 
 		SampleType sample = animl.getSampleSet().getSample().get(0);
-		chromatogram.setDataName(sample.getName());
+		chromatogram.setSampleName(sample.getName());
 		chromatogram.setBarcode(sample.getBarcode());
 		chromatogram.setDetailedInfo(sample.getSampleID());
 		chromatogram.setMiscInfo(sample.getComment());

diff --git a/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/ChromatogramWriter.java b/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/ChromatogramWriter.java
@@ -31,9 +31,6 @@
 import org.eclipse.chemclipse.support.history.IEditInformation;
 import org.eclipse.core.runtime.IProgressMonitor;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Marshaller;
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.BinaryReader;
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.Common;
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AnIMLType;
@@ -60,6 +57,10 @@
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.UnitType;
 import net.openchrom.xxd.converter.supplier.animl.preferences.PreferenceSupplier;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+
 public class ChromatogramWriter extends AbstractChromatogramMSDWriter {
 
 	private static final Logger logger = Logger.getLogger(ChromatogramWriter.class);
@@ -89,7 +90,7 @@ private SampleSetType createSampleSet(IChromatogramMSD chromatogram) {
 		SampleSetType sampleSet = new SampleSetType();
 		SampleType sample = new SampleType();
 		sample.setId("OPENCHROM_MSD_EXPORT");
-		sample.setName(chromatogram.getHeaderDataOrDefault("Sample Name", chromatogram.getDataName()));
+		sample.setName(chromatogram.getSampleName());
 		sample.setBarcode(chromatogram.getBarcode());
 		sample.setComment(chromatogram.getMiscInfo());
 		sample.setSampleID(FilenameUtils.removeExtension(chromatogram.getFile().getName()));

diff --git a/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumWriter.java b/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumWriter.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
@@ -26,9 +26,6 @@
 import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
 import org.eclipse.core.runtime.IProgressMonitor;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Marshaller;
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.BinaryReader;
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.Common;
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AnIMLType;
@@ -54,6 +51,10 @@
 import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.UnitType;
 import net.openchrom.xxd.converter.supplier.animl.preferences.PreferenceSupplier;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+
 public class MassSpectrumWriter implements IMassSpectraWriter {
 
 	private static final Logger logger = Logger.getLogger(MassSpectrumWriter.class);
@@ -114,7 +115,7 @@ private SampleSetType createSampleSet(IVendorStandaloneMassSpectrum massSpectrum
 		SampleSetType sampleSet = new SampleSetType();
 		SampleType sample = new SampleType();
 		sample.setId("OPENCHROM_MASS_SPECTRUM_EXPORT");
-		sample.setName(massSpectrum.getName());
+		sample.setName(massSpectrum.getSampleName());
 		sample.setComment(massSpectrum.getIdentifier());
 		sample.setSampleID(FilenameUtils.removeExtension(massSpectrum.getFile().getName()));
 		sample.setSourceDataLocation(massSpectrum.getFile().getAbsolutePath());
@@ -228,4 +229,4 @@ private AuditTrailEntrySetType createAuditTrail() {
 		auditTrail.setSoftware(Common.createSoftware());
 		return auditTrailEntrySet;
 	}
-}
+}
diff --git a/...er.supplier.mzdb/src/net/openchrom/msd/converter/supplier/mzdb/io/ChromatogramReader.java b/...er.supplier.mzdb/src/net/openchrom/msd/converter/supplier/mzdb/io/ChromatogramReader.java
@@ -79,7 +79,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
 				//
 				ResultSet nameResultSet = statement.executeQuery("SELECT name FROM sample;");
 				String sampleName = nameResultSet.getString(1);
-				chromatogram.setDataName(sampleName);
+				chromatogram.setSampleName(sampleName);
 				nameResultSet.close();
 				//
 				ResultSet dataProcessingSet = statement.executeQuery("SELECT name FROM data_processing ORDER BY id;");

diff --git a/...er.supplier.abif/src/net/openchrom/wsd/converter/supplier/abif/io/ChromatogramReader.java b/...er.supplier.abif/src/net/openchrom/wsd/converter/supplier/abif/io/ChromatogramReader.java
@@ -178,7 +178,7 @@ private IChromatogramWSD readChromatogram(File file, IProgressMonitor monitor) t
 					// Pascal style string (length is stored in first byte)
 					int length = in.read1BShortBE();
 					String sampleName = in.readBytesAsString(length);
-					chromatogram.setDataName(sampleName);
+					chromatogram.setSampleName(sampleName);
 					in.resetPosition();
 					in.seek(position);
 					break;

diff --git a/....supplier.animl/src/net/openchrom/wsd/converter/supplier/animl/io/ChromatogramReader.java b/....supplier.animl/src/net/openchrom/wsd/converter/supplier/animl/io/ChromatogramReader.java
@@ -153,7 +153,7 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t
 	private IVendorChromatogram readSample(AnIMLType animl, IVendorChromatogram chromatogram) {
 
 		SampleType sample = animl.getSampleSet().getSample().get(0);
-		chromatogram.setDataName(sample.getName());
+		chromatogram.setSampleName(sample.getName());
 		chromatogram.setBarcode(sample.getBarcode());
 		chromatogram.setDetailedInfo(sample.getSampleID());
 		chromatogram.setMiscInfo(sample.getComment());

diff --git a/....supplier.animl/src/net/openchrom/wsd/converter/supplier/animl/io/ChromatogramWriter.java b/....supplier.animl/src/net/openchrom/wsd/converter/supplier/animl/io/ChromatogramWriter.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
@@ -93,7 +93,7 @@ private SampleSetType createSampleSet(IChromatogramWSD chromatogram) {
 		SampleSetType sampleSet = new SampleSetType();
 		SampleType sample = new SampleType();
 		sample.setId("OPENCHROM_WSD_EXPORT");
-		sample.setName(chromatogram.getHeaderDataOrDefault("Sample Name", chromatogram.getDataName()));
+		sample.setName(chromatogram.getSampleName());
 		sample.setBarcode(chromatogram.getBarcode());
 		sample.setComment(chromatogram.getMiscInfo());
 		sample.setSampleID(FilenameUtils.removeExtension(chromatogram.getFile().getName()));

diff --git a/...hrom/wsd/identifier/supplier/geneident/ui/internal/runnables/NCBIqueuedBLASTRunnable.java b/...hrom/wsd/identifier/supplier/geneident/ui/internal/runnables/NCBIqueuedBLASTRunnable.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2023 Matthias Mailänder.
+ * Copyright (c) 2016, 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
@@ -79,7 +79,7 @@ public void run(IProgressMonitor monitor) throws InvocationTargetException, Inte
 				InputStream in = service.getAlignmentResults(requestID, outputProps);
 				reader = new BufferedReader(new InputStreamReader(in));
 				// Write BLAST output to specified file.
-				String sampleName = chromtogram.getDataName();
+				String sampleName = chromtogram.getSampleName();
 				File file = File.createTempFile(sampleName + "_" + requestID, ".txt");
 				StatusLineLogger.setInfo(InfoType.MESSAGE, "Saving query results in file " + file.getAbsolutePath());
 				writer = new FileWriter(file);

diff --git a/....abif.fragment.test/src/net/openchrom/wsd/converter/supplier/abif/io/EmptyFile_ITest.java b/....abif.fragment.test/src/net/openchrom/wsd/converter/supplier/abif/io/EmptyFile_ITest.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2018 Matthias Mailänder.
+ * Copyright (c) 2016, 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
@@ -42,6 +42,6 @@ public void testEmptySequence() {
 
 	public void testSampleName() {
 
-		assertEquals("226041_C-ME-19_pCAGseqF", chromatogram.getDataName());
+		assertEquals("226041_C-ME-19_pCAGseqF", chromatogram.getSampleName());
 	}
 }