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Improve AnIML HPLC-DAD standard conformity #454

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merged 4 commits into from
Feb 15, 2024
Merged

Improve AnIML HPLC-DAD standard conformity #454

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572a686
Code cleanup.
Mailaender Feb 15, 2024
62cc818
Start localising.
Mailaender Feb 15, 2024
982f452
More robust technique matching.
Mailaender Feb 15, 2024
ea4f5a9
Harmonize identifiers.
Mailaender Feb 15, 2024
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6 changes: 3 additions & 3 deletions ...src/net/openchrom/csd/converter/supplier/animl/converter/ChromatogramExportConverter.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2014, 2023 Lablicate GmbH.
* Copyright (c) 2014, 2024 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -24,7 +24,7 @@
import org.eclipse.core.runtime.IProgressMonitor;

import net.openchrom.csd.converter.supplier.animl.io.ChromatogramWriter;
import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.l10n.Messages;

public class ChromatogramExportConverter extends AbstractChromatogramExportConverter implements IChromatogramExportConverter {

Expand All @@ -39,7 +39,7 @@ public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> c
* Don't process if errors have occurred.
*/
if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramCSD chromatogramCSD) {
monitor.subTask(IConstants.EXPORT_CHROMATOGRAM);
monitor.subTask(Messages.exportChromatogram);
IChromatogramCSDWriter writer = new ChromatogramWriter();
try {
writer.writeChromatogram(file, chromatogramCSD, monitor);
Expand Down
15 changes: 8 additions & 7 deletions ...src/net/openchrom/csd/converter/supplier/animl/converter/ChromatogramImportConverter.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2008, 2021 Lablicate GmbH.
* Copyright (c) 2008, 2024 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -13,6 +13,7 @@
package net.openchrom.csd.converter.supplier.animl.converter;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.converter.chromatogram.AbstractChromatogramImportConverter;
import org.eclipse.chemclipse.csd.converter.io.IChromatogramCSDReader;
Expand All @@ -23,7 +24,7 @@
import org.eclipse.core.runtime.IProgressMonitor;

import net.openchrom.csd.converter.supplier.animl.io.ChromatogramReader;
import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.l10n.Messages;

public class ChromatogramImportConverter extends AbstractChromatogramImportConverter<IChromatogramCSD> {

Expand All @@ -39,13 +40,13 @@ public IProcessingInfo<IChromatogramCSD> convert(File file, IProgressMonitor mon
* Read the chromatogram.
*/
IChromatogramCSDReader reader = new ChromatogramReader();
monitor.subTask(IConstants.IMPORT_CHROMATOGRAM);
monitor.subTask(Messages.importChromatogram);
try {
IChromatogramCSD chromatogram = reader.read(file, monitor);
processingInfo.setProcessingResult(chromatogram);
} catch(Exception e) {
} catch(IOException e) {
logger.warn(e);
processingInfo.addErrorMessage(DESCRIPTION, "Something has definitely gone wrong with the file: " + file.getAbsolutePath());
processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file: " + file.getAbsolutePath());
}
}
return processingInfo;
Expand All @@ -60,9 +61,9 @@ public IProcessingInfo<IChromatogramOverview> convertOverview(File file, IProgre
try {
IChromatogramOverview chromatogramOverview = reader.readOverview(file, monitor);
processingInfo.setProcessingResult(chromatogramOverview);
} catch(Exception e) {
} catch(IOException e) {
logger.warn(e);
processingInfo.addErrorMessage(DESCRIPTION, "Something has definitely gone wrong with the file: " + file.getAbsolutePath());
processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file: " + file.getAbsolutePath());
}
}
return processingInfo;
Expand Down
9 changes: 5 additions & 4 deletions ...er.animl/src/net/openchrom/csd/converter/supplier/animl/converter/FileContentMatcher.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2021, 2023 Lablicate GmbH.
* Copyright (c) 2021, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -22,7 +22,8 @@
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;

import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AnIMLType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.TechniqueType;

public class FileContentMatcher extends AbstractFileContentMatcher implements IFileContentMatcher {

Expand All @@ -34,11 +35,11 @@ public boolean checkFileFormat(File file) {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList root = document.getElementsByTagName(IConstants.NODE_ANIML);
NodeList root = document.getElementsByTagName(AnIMLType.NODE_NAME);
if(root.getLength() != 1) {
return isValidFormat;
}
NodeList techniquesList = document.getElementsByTagName(IConstants.NODE_TECHNIQUE);
NodeList techniquesList = document.getElementsByTagName(TechniqueType.NODE_NAME);
int techniques = techniquesList.getLength();
for(int t = 0; t < techniques; t++) {
Element element = (Element)techniquesList.item(t);
Expand Down
30 changes: 15 additions & 15 deletions ....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramReader.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2021, 2023 Lablicate GmbH.
* Copyright (c) 2021, 2024 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -40,19 +40,19 @@
import net.openchrom.csd.converter.supplier.animl.model.IVendorChromatogram;
import net.openchrom.csd.converter.supplier.animl.model.VendorChromatogram;
import net.openchrom.csd.converter.supplier.animl.model.VendorScan;
import net.openchrom.xxd.converter.supplier.animl.internal.converter.BinaryReader;
import net.openchrom.xxd.converter.supplier.animl.internal.converter.XmlReader;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AnIMLType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AuthorType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.EncodedValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ExperimentStepType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SeriesSetType;
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 net.openchrom.xxd.converter.supplier.animl.converter.BinaryReader;
import net.openchrom.xxd.converter.supplier.animl.converter.XmlReader;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AnIMLType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AuthorType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.EncodedValueSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ExperimentStepType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SampleType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SeriesSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SeriesType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.UnitType;

import jakarta.xml.bind.JAXBException;

Expand Down Expand Up @@ -205,4 +205,4 @@ private IVendorChromatogram readSample(AnIMLType animl, IVendorChromatogram chro
chromatogram.setMiscInfo(sample.getComment());
return chromatogram;
}
}
}
46 changes: 23 additions & 23 deletions ....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramWriter.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2021, 2023 Lablicate GmbH.
* Copyright (c) 2021, 2024 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -27,28 +27,28 @@
import org.eclipse.chemclipse.support.history.IEditInformation;
import org.eclipse.core.runtime.IProgressMonitor;

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;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AuditTrailEntrySetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AuditTrailEntryType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AuthorType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.DependencyType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.EncodedValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ExperimentStepSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ExperimentStepType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ObjectFactory;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SeriesSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SeriesType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.TechniqueType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.UnitType;
import net.openchrom.xxd.converter.supplier.animl.converter.BinaryReader;
import net.openchrom.xxd.converter.supplier.animl.converter.Common;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AnIMLType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AuditTrailEntrySetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AuditTrailEntryType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AuthorType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.DependencyType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.EncodedValueSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ExperimentStepSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ExperimentStepType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ObjectFactory;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SampleSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SampleType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SeriesSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SeriesType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.TechniqueType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.UnitType;
import net.openchrom.xxd.converter.supplier.animl.preferences.PreferenceSupplier;

import jakarta.xml.bind.JAXBContext;
Expand Down
6 changes: 3 additions & 3 deletions ...src/net/openchrom/msd/converter/supplier/animl/converter/ChromatogramExportConverter.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2014, 2023 Lablicate GmbH.
* Copyright (c) 2014, 2024 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -26,7 +26,7 @@
import org.eclipse.core.runtime.IProgressMonitor;

import net.openchrom.msd.converter.supplier.animl.io.ChromatogramWriter;
import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.l10n.Messages;

public class ChromatogramExportConverter extends AbstractChromatogramExportConverter implements IChromatogramExportConverter {

Expand All @@ -41,7 +41,7 @@ public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> c
* Don't process if errors have occurred.
*/
if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramMSD chromatogramMSD) {
monitor.subTask(IConstants.EXPORT_CHROMATOGRAM);
monitor.subTask(Messages.exportChromatogram);
IChromatogramMSDWriter writer = new ChromatogramWriter();
try {
writer.writeChromatogram(file, chromatogramMSD, monitor);
Expand Down
9 changes: 5 additions & 4 deletions .../net/openchrom/msd/converter/supplier/animl/converter/ChromatogramFileContentMatcher.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2021, 2023 Lablicate GmbH.
* Copyright (c) 2021, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -22,7 +22,8 @@
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;

import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AnIMLType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.TechniqueType;

public class ChromatogramFileContentMatcher extends AbstractFileContentMatcher implements IFileContentMatcher {

Expand All @@ -34,11 +35,11 @@ public boolean checkFileFormat(File file) {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList root = document.getElementsByTagName(IConstants.NODE_ANIML);
NodeList root = document.getElementsByTagName(AnIMLType.NODE_NAME);
if(root.getLength() != 1) {
return isValidFormat;
}
NodeList techniquesList = document.getElementsByTagName(IConstants.NODE_TECHNIQUE);
NodeList techniquesList = document.getElementsByTagName(TechniqueType.NODE_NAME);
int techniques = techniquesList.getLength();
for(int t = 0; t < techniques; t++) {
Element element = (Element)techniquesList.item(t);
Expand Down
12 changes: 6 additions & 6 deletions ...src/net/openchrom/msd/converter/supplier/animl/converter/ChromatogramImportConverter.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2008, 2023 Lablicate GmbH.
* Copyright (c) 2008, 2024 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -24,7 +24,7 @@
import org.eclipse.core.runtime.IProgressMonitor;

import net.openchrom.msd.converter.supplier.animl.io.ChromatogramReader;
import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.l10n.Messages;

public class ChromatogramImportConverter extends AbstractChromatogramImportConverter<IChromatogramMSD> {

Expand All @@ -40,13 +40,13 @@ public IProcessingInfo<IChromatogramMSD> convert(File file, IProgressMonitor mon
* Read the chromatogram.
*/
IChromatogramMSDReader reader = new ChromatogramReader();
monitor.subTask(IConstants.IMPORT_CHROMATOGRAM);
monitor.subTask(Messages.importChromatogram);
try {
IChromatogramMSD chromatogram = reader.read(file, monitor);
processingInfo.setProcessingResult(chromatogram);
} catch(IOException e) {
logger.warn(e);
processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file: " + file.getAbsolutePath());
processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file: " + file.getAbsolutePath(), e);
} catch(InterruptedException e) {
logger.warn(e);
Thread.currentThread().interrupt();
Expand All @@ -64,9 +64,9 @@ public IProcessingInfo<IChromatogramOverview> convertOverview(File file, IProgre
try {
IChromatogramOverview chromatogramOverview = reader.readOverview(file, monitor);
processingInfo.setProcessingResult(chromatogramOverview);
} catch(Exception e) {
} catch(IOException e) {
logger.warn(e);
processingInfo.addErrorMessage(DESCRIPTION, "Something has definitely gone wrong with the file: " + file.getAbsolutePath());
processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file: " + file.getAbsolutePath());
}
}
return processingInfo;
Expand Down
9 changes: 5 additions & 4 deletions .../net/openchrom/msd/converter/supplier/animl/converter/MassSpectrumFileContentMatcher.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2016, 2023 Lablicate GmbH.
* Copyright (c) 2016, 2024 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -22,7 +22,8 @@
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;

import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.AnIMLType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.TechniqueType;

public class MassSpectrumFileContentMatcher extends AbstractFileContentMatcher implements IFileContentMatcher {

Expand All @@ -34,11 +35,11 @@ public boolean checkFileFormat(File file) {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList root = document.getElementsByTagName(IConstants.NODE_ANIML);
NodeList root = document.getElementsByTagName(AnIMLType.NODE_NAME);
if(root.getLength() != 1) {
return isValidFormat;
}
NodeList techniquesList = document.getElementsByTagName(IConstants.NODE_TECHNIQUE);
NodeList techniquesList = document.getElementsByTagName(TechniqueType.NODE_NAME);
int techniques = techniquesList.getLength();
for(int t = 0; t < techniques; t++) {
Element element = (Element)techniquesList.item(t);
Expand Down
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