EVA-4059 duplicate SS accession QC job#493
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| public class DuplicateSSAccQCWriterConfiguration { | ||
| @Bean(DUPLICATE_SS_ACC_QC_WRITER) | ||
| @StepScope | ||
| DuplicateSSAccQCWriter duplicateSSAccQCWrite(InputParameters parameters) { |
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| DuplicateSSAccQCWriter duplicateSSAccQCWrite(InputParameters parameters) { | |
| DuplicateSSAccQCWriter duplicateSSAccQCWriter(InputParameters parameters) { |
| } | ||
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| @Override | ||
| public void open(org.springframework.batch.item.ExecutionContext executionContext) throws ItemStreamException { |
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should just import ExecutionContext
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Why does this one use the full path and the other do not ?
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It should not, it is because of copy-paste where sometimes IntelliJ automatically imports with full path.
Updated
| if (duplicateSSAccQCResultList != null && !duplicateSSAccQCResultList.isEmpty()) { | ||
| appendToFile(duplicateSSAccQCResultList); | ||
| } else { | ||
| logger.info("No duplicate SS IDs in the batch to append"); |
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Not sure we need to log in this case, as it's the normal case and might bloat the logs
| } | ||
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| @Test | ||
| public void contextLoads() { |
| } | ||
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| @Override | ||
| public void open(org.springframework.batch.item.ExecutionContext executionContext) throws ItemStreamException { |
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Why does this one use the full path and the other do not ?
| /** | ||
| * Read all SubmittedVariant Accessions from VCF file in batches | ||
| */ | ||
| public class DuplicateSSAccQCFileReader implements ItemStreamReader<List<Long>> { |
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Does this need to be called a DuplicateSSAccQCFileReader ? There is nothing that makes it specific to finding duplicates and it could be reused elsewhere is we want to read ids from a VCF.
| Query query = query(where(ACCESSION_FIELD).in(sveAccessions).and(REMAPPED_FROM_FIELD).exists(false)); | ||
| logger.info("Issuing find in EVA collection for SVEs containing the given accessions : {}", query); | ||
| List<SubmittedVariantEntity> evaResults = mongoTemplate.find(query, SubmittedVariantEntity.class); | ||
| List<DbsnpSubmittedVariantEntity> dbsnpResults = mongoTemplate.find(query, DbsnpSubmittedVariantEntity.class); |
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Do we need to query DbsnpSubmittedVariantEntity.class here since all new ssid will be added exclusively to SubmittedVariantEntity.class ?
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