Saved variant timeout #3510
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Saved variant timeout #3510
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ShifaSZ
suggested changes
Jul 25, 2023
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| for family_guid in var['familyGuids']: | ||
| family_genes[family_guid].update(var.get('transcripts', {}).keys()) |
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Do we need to include the families who have no transcripts?
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yes overall, as this is used for the the list of families for filtering which projects to return etc. However, I can add an extra filter before we get the family list for rna data, as theres no reason to include rna data for families with no genes
seqr/views/utils/variant_utils.py
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| return { | ||
| agg['sample__individual__family__guid']: {'tpmGenes': [ | ||
| gene for gene in agg['genes'] if gene in family_genes[agg['sample__individual__family__guid']] | ||
| ]} for agg in tpm_family_genes |
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Should we filter out the families with no genes in the family_genes?
ShifaSZ
approved these changes
Jul 25, 2023
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The issue appears to be that the increase in the number of TPM models now that we loaded TPM==0 has increased the size of the response and we are actually losing most of the time serializing and deserializing the response. This updates the behavior so we only return TPM genes for a family if the family has a variant in that gene, instead of if any family has a variant in that gene. For RGP this redoes the response size by over 100Mb