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EVA-2751 - move update of executionContext to fix resume in accessioning pipeline #331

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EVA-2751 - move update of executionContext to fix resume in accessioning pipeline #331

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045ab17
move update of executionContext to fix resume
apriltuesday Feb 10, 2022
851e84b
modify test
apriltuesday Feb 10, 2022
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3 changes: 1 addition & 2 deletions ...peline/src/main/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,6 @@ public void open(ExecutionContext executionContext) throws ItemStreamException {
boolean append = false;
this.contigsWriter = new BufferedWriter(new FileWriter(this.contigsOutput, append));
this.variantsWriter = new BufferedWriter(new FileWriter(this.variantsOutput, append));
executionContext.put(IS_HEADER_WRITTEN_KEY, IS_HEADER_WRITTEN_VALUE);
}
}
} catch (IOException e) {
Expand Down Expand Up @@ -176,7 +175,7 @@ private void loadContigMappingFromTemporaryFile(File contigMappingFile) throws I
}

public void update(ExecutionContext executionContext) throws ItemStreamException {

executionContext.put(IS_HEADER_WRITTEN_KEY, IS_HEADER_WRITTEN_VALUE);
}

public void close() throws ItemStreamException {
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1 change: 1 addition & 0 deletions ...ne/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriterTest.java
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Expand Up @@ -226,6 +226,7 @@ private void writeAndResumeAndWrite(String originalChromosome1, String contig1,
accessionReportWriter.write(Collections.singletonList(variant),
GetOrCreateAccessionWrapperCreator.convertToGetOrCreateAccessionWrapper(
Collections.singletonList(accessionWrapper)));
accessionReportWriter.update(executionContext);
accessionReportWriter.close();

// second writer
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