In the ClinVar new XML, ClassifiedRecord.Classifications omits classification types as children when there were no submissions of that type. IncludedRecord.Classifications includes all three classification types as children and says there were no submissions for them. Since a ClassifiedRecord which does not have (for exaple) a SomaticClinicalImpact submission will not generate a VariationArchiveClassification with type SomaticClinicalImpact, an IncludedRecord with no submissions should not generate any VariationArchiveClassifications at all.
The code as-is generates 3 VariationArchiveClassifications for every IncludedRecord, and sets num_submissions=0, review_status="no ...", etc on each of them.
This XML should yield no VariationArchiveClassification objects:
<Classifications>
<GermlineClassification NumberOfSubmissions="0" NumberOfSubmitters="0">
<ReviewStatus>no classification for the single variant</ReviewStatus>
<Description>no classification for the single variant</Description>
</GermlineClassification>
<SomaticClinicalImpact NumberOfSubmissions="0" NumberOfSubmitters="0">
<ReviewStatus>no classification for the single variant</ReviewStatus>
<Description>no classification for the single variant</Description>
</SomaticClinicalImpact>
<OncogenicityClassification NumberOfSubmissions="0" NumberOfSubmitters="0">
<ReviewStatus>no classification for the single variant</ReviewStatus>
<Description>no classification for the single variant</Description>
</OncogenicityClassification>
</Classifications>
In the ClinVar new XML,
ClassifiedRecord.Classifications
omits classification types as children when there were no submissions of that type.IncludedRecord.Classifications
includes all three classification types as children and says there were no submissions for them. Since aClassifiedRecord
which does not have (for exaple) aSomaticClinicalImpact
submission will not generate aVariationArchiveClassification
with typeSomaticClinicalImpact
, anIncludedRecord
with no submissions should not generate anyVariationArchiveClassification
s at all.The code as-is generates 3
VariationArchiveClassification
s for every IncludedRecord, and setsnum_submissions=0
,review_status="no ..."
, etc on each of them.This XML should yield no
VariationArchiveClassification
objects: