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snpdb/annotation: fix N+1 queries on the variant details page #1730 #1732

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Merged
davmlaw merged 1 commit into from
Aug 14, 2026
Merged

snpdb/annotation: fix N+1 queries on the variant details page #1730 #1732

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3 changes: 2 additions & 1 deletion annotation/transcripts_annotation_selections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -275,7 +275,8 @@ def _add_other_annotation_consortium_transcripts(self, variant: Variant):
# Convert once to explicit, then pass this around
variant_coordinate = variant.coordinate.as_external_explicit(self.genome_build)
has_other_annotation_consortium_transcripts = False
for transcript_version in TranscriptVersion.objects.filter(**kwargs).order_by("-version"):
transcript_version_qs = TranscriptVersion.objects.filter(**kwargs).select_related("gene_version")
for transcript_version in transcript_version_qs.order_by("-version"):
# Don't duplicate ones already available via RefSeq/Ensembl equivalence
# and only take the highest version we have
if transcript_version.transcript_id not in existing_other_transcripts:
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7 changes: 5 additions & 2 deletions snpdb/variant_sample_information.py
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Expand Up @@ -391,7 +391,7 @@ def _get_classifications_by_sample_id(self, sample_ids: set[int]) -> dict[int, l
classifications_by_sample_id = defaultdict(list)
qs = ClassificationModification.latest_for_user(self.user, allele=allele, published=True,
classification__sample__in=sample_ids)
for cm in qs:
for cm in qs.select_related("classification__lab"):
classification = cm.classification
pills = clinical_significance_pills(classification.summary_typed, classification.allele_origin_bucket)
classification_json = {
Expand Down Expand Up @@ -441,7 +441,10 @@ def _row_to_json(row: dict) -> dict:
def _get_locus_counts(self) -> list[dict]:
""" Zygosity counts for every variant at this locus, this variant first """
counts_by_variant_id = self._get_locus_zygosity_counts()
variant_by_id = {v.pk: v for v in Variant.objects.filter(pk__in=counts_by_variant_id)}
# str(v) and v.alt.seq below reach through to the locus/sequence rows
variant_qs = Variant.objects.filter(pk__in=counts_by_variant_id) \
.select_related("locus__contig", "locus__ref", "alt")
variant_by_id = {v.pk: v for v in variant_qs}

sorted_rows = []
for variant_id, zygosity_counts in counts_by_variant_id.items():
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