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Avoid path resolver where it is not required.
1 parent c919060 commit d321b33

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272 files changed

+329
-851
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272 files changed

+329
-851
lines changed

‎chemclipse/plugins/org.eclipse.chemclipse.converter/src/org/eclipse/chemclipse/converter/PathResolver.java‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,10 +34,6 @@ public class PathResolver {
3434
*/
3535
public static File getFile(final Bundle bundle, final String path) throws IOException {
3636

37-
if(path == null || "".equals(path)) {
38-
throw new IOException();
39-
}
40-
4137
URL url = FileLocator.find(bundle, new Path(path), null);
4238
return new File(FileLocator.resolve(url).getPath());
4339
}

‎chemclipse/plugins/org.eclipse.chemclipse.msd.classifier.supplier.molpeak/src/org/eclipse/chemclipse/msd/classifier/supplier/molpeak/core/LibraryService.java‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,8 @@
1414
*******************************************************************************/
1515
package org.eclipse.chemclipse.msd.classifier.supplier.molpeak.core;
1616

17+
import java.io.IOException;
18+
1719
import org.eclipse.chemclipse.model.exceptions.ValueMustNotBeNullException;
1820
import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
1921
import org.eclipse.chemclipse.msd.classifier.supplier.molpeak.identifier.BasePeakIdentifier;
@@ -44,6 +46,8 @@ public IProcessingInfo<IMassSpectra> identify(IIdentificationTarget identificati
4446
processingInfo.setProcessingResult(massSpectra);
4547
} catch(ValueMustNotBeNullException e) {
4648
processingInfo.addErrorMessage("Base Peak Identifier", "The identification target is not available.");
49+
} catch(IOException e) {
50+
processingInfo.addErrorMessage("Base Peak Identifier", "Database not found.", e);
4751
}
4852

4953
return processingInfo;

‎chemclipse/plugins/org.eclipse.chemclipse.msd.classifier.supplier.molpeak/src/org/eclipse/chemclipse/msd/classifier/supplier/molpeak/identifier/BasePeakIdentifier.java‎

Lines changed: 8 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,6 @@ public class BasePeakIdentifier {
7878

7979
private final TargetBuilderMSD targetBuilder;
8080
// These one's are run when initializing the class
81-
private final IMassSpectra references = getStandardsMassSpectra();
8281
private static final IScanMSD syringyl = getSyringyl();
8382

8483
private String massSpectraFiles;
@@ -235,8 +234,9 @@ public void identifyMassSpectra(List<IScanMSD> massSpectrumList, IBasePeakSettin
235234
* @param identificationTarget
236235
* @param monitor
237236
* @return {@link IMassSpectra}
237+
* @throws IOException
238238
*/
239-
public IMassSpectra getMassSpectra(IIdentificationTarget identificationTarget) {
239+
public IMassSpectra getMassSpectra(IIdentificationTarget identificationTarget) throws IOException {
240240

241241
IMassSpectra massSpectra = new MassSpectra();
242242
if(identificationTarget != null) {
@@ -255,6 +255,7 @@ public IMassSpectra getMassSpectra(IIdentificationTarget identificationTarget) {
255255
* List mass spectra
256256
*/
257257
List<IScanMSD> identifiedMassSpectra = new ArrayList<>();
258+
IMassSpectra references = getStandardsMassSpectra();
258259
if(references != null) {
259260
for(IScanMSD reference : references.getList()) {
260261
/*
@@ -297,16 +298,12 @@ private static IScanMSD getSyringyl() {
297298
return massSpectrum;
298299
}
299300

300-
private IMassSpectra getStandardsMassSpectra() {
301+
private IMassSpectra getStandardsMassSpectra() throws IOException {
301302

302-
try {
303-
File file = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), REFERENCES);
304-
IProcessingInfo<IMassSpectra> processingInfo = DatabaseConverter.convert(file, new NullProgressMonitor());
305-
return processingInfo.getProcessingResult();
306-
} catch(IOException e) {
307-
logger.warn(e);
308-
}
309-
return new MassSpectra();
303+
Bundle bundle = FrameworkUtil.getBundle(getClass());
304+
File file = PathResolver.getFile(bundle, REFERENCES);
305+
IProcessingInfo<IMassSpectra> processingInfo = DatabaseConverter.convert(file, new NullProgressMonitor());
306+
return processingInfo.getProcessingResult();
310307
}
311308

312309
private void setLibraryInformationFields(ILibraryInformation libraryInformation, String name) {

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.classifier.supplier.wnc.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/classifier/supplier/wnc/internal/core/support/ChromatogramTestCase.java‎

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,6 @@
2222

2323
import org.eclipse.chemclipse.chromatogram.msd.classifier.supplier.wnc.TestPathHelper;
2424
import org.eclipse.chemclipse.chromatogram.msd.classifier.supplier.wnc.exceptions.ClassifierException;
25-
import org.eclipse.chemclipse.converter.PathResolver;
2625
import org.eclipse.chemclipse.model.settings.Delimiter;
2726
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
2827
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
@@ -36,8 +35,6 @@
3635
import org.junit.jupiter.api.Disabled;
3736
import org.junit.jupiter.api.TestInstance;
3837
import org.junit.jupiter.api.TestInstance.Lifecycle;
39-
import org.osgi.framework.Bundle;
40-
import org.osgi.framework.FrameworkUtil;
4138

4239
@Disabled
4340
@TestInstance(Lifecycle.PER_CLASS)
@@ -51,11 +48,10 @@ public class ChromatogramTestCase {
5148
public void setUp() throws IOException, ClassifierException {
5249

5350
PreferenceSupplier.setImportDelimiter(Delimiter.SEMICOLON);
54-
Bundle bundle = FrameworkUtil.getBundle(getClass());
55-
File file = PathResolver.getFile(bundle, TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1_ZIP);
51+
File file = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1_ZIP);
5652
try (ZipInputStream zipInputStream = new ZipInputStream(new FileInputStream(file))) {
5753
zipInputStream.getNextEntry();
58-
File folder = PathResolver.getFile(bundle, TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1_FOLDER);
54+
File folder = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1_FOLDER);
5955
chromatogramFile = new File(folder, File.separator + TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1_NAME);
6056
if(chromatogramFile.exists()) {
6157
chromatogramFile.delete();

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.filter.supplier.backfolding.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/filter/supplier/backfolding/core/ChromatogramImporterTestCase.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,6 @@
1717
import java.io.IOException;
1818

1919
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.backfolding.TestPathHelper;
20-
import org.eclipse.chemclipse.converter.PathResolver;
2120
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
2221
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
2322
import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
@@ -29,7 +28,6 @@
2928
import org.junit.jupiter.api.Disabled;
3029
import org.junit.jupiter.api.TestInstance;
3130
import org.junit.jupiter.api.TestInstance.Lifecycle;
32-
import org.osgi.framework.FrameworkUtil;
3331

3432
@Disabled
3533
@TestInstance(Lifecycle.PER_CLASS)
@@ -44,7 +42,7 @@ public void setUp() throws IOException {
4442
/*
4543
* Import
4644
*/
47-
File fileImport = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
45+
File fileImport = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
4846
IProcessingInfo<IChromatogramMSD> processingInfo = ChromatogramConverterMSD.getInstance().convert(fileImport, VersionConstants.CONVERTER_ID_CHROMATOGRAM, new NullProgressMonitor());
4947
chromatogram = processingInfo.getProcessingResult();
5048
chromatogramSelection = new ChromatogramSelectionMSD(chromatogram);

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/calculator/MassChromatographicQualityCalculator_1_ITest.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,6 @@
2222

2323
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.TestPathHelper;
2424
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.exceptions.CodaCalculatorException;
25-
import org.eclipse.chemclipse.converter.PathResolver;
2625
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
2726
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
2827
import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
@@ -34,7 +33,6 @@
3433
import org.junit.jupiter.api.Test;
3534
import org.junit.jupiter.api.TestInstance;
3635
import org.junit.jupiter.api.TestInstance.Lifecycle;
37-
import org.osgi.framework.FrameworkUtil;
3836

3937
@TestInstance(Lifecycle.PER_CLASS)
4038
public class MassChromatographicQualityCalculator_1_ITest {
@@ -47,7 +45,7 @@ public class MassChromatographicQualityCalculator_1_ITest {
4745
@BeforeAll
4846
public void setUp() throws IOException {
4947

50-
File importFile = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
48+
File importFile = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
5149
IProcessingInfo<IChromatogramMSD> processingInfo = ChromatogramConverterMSD.getInstance().convert(importFile, new NullProgressMonitor());
5250
IChromatogramMSD chromatogram = processingInfo.getProcessingResult();
5351
codaThreshold = 0.7f;

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/calculator/MassChromatographicQualityResult_1_ITest.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,6 @@
2121

2222
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.TestPathHelper;
2323
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.exceptions.CodaCalculatorException;
24-
import org.eclipse.chemclipse.converter.PathResolver;
2524
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
2625
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
2726
import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
@@ -33,7 +32,6 @@
3332
import org.junit.jupiter.api.Test;
3433
import org.junit.jupiter.api.TestInstance;
3534
import org.junit.jupiter.api.TestInstance.Lifecycle;
36-
import org.osgi.framework.FrameworkUtil;
3735

3836
@TestInstance(Lifecycle.PER_CLASS)
3937
public class MassChromatographicQualityResult_1_ITest {
@@ -44,7 +42,7 @@ public class MassChromatographicQualityResult_1_ITest {
4442
@BeforeAll
4543
public void setUp() throws IOException {
4644

47-
File importFile = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
45+
File importFile = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
4846
IProcessingInfo<IChromatogramMSD> processingInfo = ChromatogramConverterMSD.getInstance().convert(importFile, new NullProgressMonitor());
4947
IChromatogramMSD chromatogram = processingInfo.getProcessingResult();
5048
chromatogramSelection = new ChromatogramSelectionMSD(chromatogram);

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/core/ChromatogramImporterTestCase.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,6 @@
1717
import java.io.IOException;
1818

1919
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.TestPathHelper;
20-
import org.eclipse.chemclipse.converter.PathResolver;
2120
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
2221
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
2322
import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
@@ -27,7 +26,6 @@
2726
import org.eclipse.core.runtime.NullProgressMonitor;
2827
import org.junit.jupiter.api.BeforeAll;
2928
import org.junit.jupiter.api.Disabled;
30-
import org.osgi.framework.FrameworkUtil;
3129

3230
@Disabled
3331
public class ChromatogramImporterTestCase {
@@ -41,7 +39,7 @@ public void setUp() throws IOException {
4139
/*
4240
* Import
4341
*/
44-
File fileImport = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_2);
42+
File fileImport = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_2);
4543
IProcessingInfo<IChromatogramMSD> processingInfo = ChromatogramConverterMSD.getInstance().convert(fileImport, VersionConstants.CONVERTER_ID_CHROMATOGRAM, new NullProgressMonitor());
4644
chromatogram = processingInfo.getProcessingResult();
4745
chromatogramSelection = new ChromatogramSelectionMSD(chromatogram);

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.filter.supplier.denoising.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/filter/supplier/denoising/internal/core/support/ChromatogramImporterTestCase.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,6 @@
1717
import java.io.IOException;
1818

1919
import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.denoising.TestPathHelper;
20-
import org.eclipse.chemclipse.converter.PathResolver;
2120
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
2221
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
2322
import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
@@ -28,7 +27,6 @@
2827
import org.eclipse.core.runtime.NullProgressMonitor;
2928
import org.junit.jupiter.api.BeforeAll;
3029
import org.junit.jupiter.api.Disabled;
31-
import org.osgi.framework.FrameworkUtil;
3230

3331
@Disabled
3432
public class ChromatogramImporterTestCase {
@@ -42,7 +40,7 @@ public void setUp() throws IOException, FilterException {
4240
/*
4341
* Import
4442
*/
45-
File fileImport = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
43+
File fileImport = new File(TestPathHelper.TESTFILE_IMPORT_CHROMATOGRAM_1);
4644
IProcessingInfo<IChromatogramMSD> processingInfo = ChromatogramConverterMSD.getInstance().convert(fileImport, VersionConstants.CONVERTER_ID_CHROMATOGRAM, new NullProgressMonitor());
4745
chromatogram = processingInfo.getProcessingResult();
4846
chromatogramSelection = new ChromatogramSelectionMSD(chromatogram);

‎chemclipse/tests/org.eclipse.chemclipse.chromatogram.msd.process.supplier.peakidentification.fragment.test/src/org/eclipse/chemclipse/chromatogram/msd/process/supplier/peakidentification/io/PeakIdentificationBatchJobReader_1_ITest.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -22,13 +22,11 @@
2222
import org.eclipse.chemclipse.chromatogram.msd.process.supplier.peakidentification.model.IPeakIdentificationEntry;
2323
import org.eclipse.chemclipse.chromatogram.msd.process.supplier.peakidentification.model.IPeakInputEntry;
2424
import org.eclipse.chemclipse.chromatogram.msd.process.supplier.peakidentification.model.IPeakIntegrationEntry;
25-
import org.eclipse.chemclipse.converter.PathResolver;
2625
import org.eclipse.core.runtime.NullProgressMonitor;
2726
import org.junit.jupiter.api.BeforeAll;
2827
import org.junit.jupiter.api.Test;
2928
import org.junit.jupiter.api.TestInstance;
3029
import org.junit.jupiter.api.TestInstance.Lifecycle;
31-
import org.osgi.framework.FrameworkUtil;
3230

3331
@TestInstance(Lifecycle.PER_CLASS)
3432
public class PeakIdentificationBatchJobReader_1_ITest {
@@ -39,7 +37,7 @@ public class PeakIdentificationBatchJobReader_1_ITest {
3937
@BeforeAll
4038
public void setUp() throws IOException {
4139

42-
File file = PathResolver.getFile(FrameworkUtil.getBundle(getClass()), TestPathHelper.TESTFILE_IMPORT_BATCH_PROCESS_JOB);
40+
File file = new File(TestPathHelper.TESTFILE_IMPORT_BATCH_PROCESS_JOB);
4341
batchProcessJob = reader.read(file, new NullProgressMonitor());
4442
}
4543

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