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EVA-3308 - Set the output file to contain the input taxonomy accession #426

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merged 3 commits into from
Jan 15, 2024
Merged

EVA-3308 - Set the output file to contain the input taxonomy accession #426

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d7f6bc7
Set the output file to contain the input taxonomy accession
tcezard Jan 5, 2024
6d6502f
Fix test
tcezard Jan 5, 2024
59dc702
Fix test
tcezard Jan 5, 2024
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6 changes: 4 additions & 2 deletions ...ac/ebi/eva/remapping/source/configuration/batch/io/VariantContextWriterConfiguration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,14 +32,16 @@ public class VariantContextWriterConfiguration {
@Bean(BeanNames.EVA_SUBMITTED_VARIANT_WRITER)
public VariantContextWriter evaVariantContextWriter(InputParameters parameters) {
Path reportPath = ReportPathResolver.getEvaReportPath(parameters.getOutputFolder(),
parameters.getAssemblyAccession());
parameters.getAssemblyAccession(),
parameters.getTaxonomy());
return new VariantContextWriter(reportPath, parameters.getAssemblyAccession());
}

@Bean(BeanNames.DBSNP_SUBMITTED_VARIANT_WRITER)
public VariantContextWriter dbsnpVariantContextWriter(InputParameters parameters) {
Path reportPath = ReportPathResolver.getDbsnpReportPath(parameters.getOutputFolder(),
parameters.getAssemblyAccession());
parameters.getAssemblyAccession(),
parameters.getTaxonomy());
return new VariantContextWriter(reportPath, parameters.getAssemblyAccession());
}
}
8 changes: 4 additions & 4 deletions ...et-source/src/main/java/uk/ac/ebi/eva/remapping/source/parameters/ReportPathResolver.java
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Expand Up @@ -24,13 +24,13 @@
*/
public class ReportPathResolver {

public static Path getEvaReportPath(String outputFolder, String referenceAssembly) {
public static Path getEvaReportPath(String outputFolder, String referenceAssembly, int taxonomy) {
final String FILE_SUFFIX = "_eva.vcf";
return Paths.get(outputFolder).resolve(referenceAssembly + FILE_SUFFIX);
return Paths.get(outputFolder).resolve(referenceAssembly + '_' + taxonomy + FILE_SUFFIX);
}

public static Path getDbsnpReportPath(String outputFolder, String referenceAssembly) {
public static Path getDbsnpReportPath(String outputFolder, String referenceAssembly, int taxonomy) {
final String FILE_SUFFIX = "_dbsnp.vcf";
return Paths.get(outputFolder).resolve(referenceAssembly + FILE_SUFFIX);
return Paths.get(outputFolder).resolve(referenceAssembly + '_' + taxonomy + FILE_SUFFIX);
}
}
3 changes: 2 additions & 1 deletion ...ource/src/test/java/uk/ac/ebi/eva/remapping/source/batch/io/VariantContextWriterTest.java
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Expand Up @@ -74,7 +74,8 @@ public void basicWrite() throws Exception {
}

private File assertWriteVcf(File outputFolder, SubmittedVariantEntity... variants) throws Exception {
Path reportPath = ReportPathResolver.getEvaReportPath(outputFolder.getAbsolutePath(), REFERENCE_ASSEMBLY);
Path reportPath = ReportPathResolver.getEvaReportPath(outputFolder.getAbsolutePath(), REFERENCE_ASSEMBLY,
TAXONOMY_ACCESSION);
VariantContextWriter writer = new VariantContextWriter(reportPath, REFERENCE_ASSEMBLY);
writer.open(null);

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12 changes: 8 additions & 4 deletions ...emapping/source/configuration/batch/jobs/ExportSubmittedVariantsJobConfigurationTest.java
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Expand Up @@ -90,10 +90,12 @@ public void tearDown() throws Exception {

private void deleteOutputFiles() {
ReportPathResolver.getDbsnpReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile().delete();
ReportPathResolver.getEvaReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile().delete();
}

Expand Down Expand Up @@ -125,13 +127,15 @@ public void variantsWritten() throws Exception {

private FileInputStream getExportedEva() throws FileNotFoundException {
return new FileInputStream(ReportPathResolver.getEvaReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile());
}

private FileInputStream getExportedDbsnp() throws FileNotFoundException {
return new FileInputStream(ReportPathResolver.getDbsnpReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile());
}

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6 changes: 4 additions & 2 deletions ...c/ebi/eva/remapping/source/runner/AccessionRemappingJobLauncherCommandLineRunnerTest.java
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Expand Up @@ -74,10 +74,12 @@ public void tearDown() {

private void deleteOutputFiles() {
ReportPathResolver.getDbsnpReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile().delete();
ReportPathResolver.getEvaReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile().delete();
}

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6 changes: 4 additions & 2 deletions ...mapping/source/runner/AccessionRemappingJobLauncherCommandLineRunnerWithProjectsTest.java
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Expand Up @@ -74,10 +74,12 @@ public void tearDown() {

private void deleteOutputFiles() {
ReportPathResolver.getDbsnpReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile().delete();
ReportPathResolver.getEvaReportPath(inputParameters.getOutputFolder(),
inputParameters.getAssemblyAccession())
inputParameters.getAssemblyAccession(),
inputParameters.getTaxonomy())
.toFile().delete();
}

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