EVA-3748 - Release from DB #468
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tcezard
approved these changes
Feb 13, 2025
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| /** | ||
| * The query performed in mongo can retrieve more variants than the actual ones because in some cases the same | ||
| * clustered variant is mapped against multiple locations. So we need to check that that clustered variant we are | ||
| * processing only appears in the VCF release file with the alleles from submitted variants matching the location. | ||
| */ |
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I'm wondering how much of this is still true. We should keep it for now but add a ticket to review this.
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will create a ticket.
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| private List<SubmittedVariantEntity> getSubmittedVariantEntities(Set<Long> cveAccs) { | ||
| Query query = query(where(SVE_RS_FIELD).in(cveAccs).and(SVE_ASSEMBLY_FIELD).is(assembly).and(SVE_TAX_FIELD).is(taxonomy)); | ||
| List<SubmittedVariantEntity> evaResults = mongoTemplate.find(query, SubmittedVariantEntity.class); | ||
| List<DbsnpSubmittedVariantEntity> dbsnpResults = mongoTemplate.find(query, DbsnpSubmittedVariantEntity.class); | ||
| return Stream.concat(evaResults.stream(), dbsnpResults.stream()).collect(Collectors.toList()); |
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It might never be a problem but this function can in theory return a very large number of variant creating a memory issue. It will be especially true in the merged and deprecated use case, less so in the case of active variants.
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can refactor as part of the next ticket when we write the queries for the operations
apriltuesday
approved these changes
Feb 14, 2025
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