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fix: import fails with error 'intron_variant' (#2203)
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@stolpeo
stolpeo committed Feb 20, 2025
1 parent 515343a commit e1fb197
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Showing 16 changed files with 289 additions and 12 deletions.
8 changes: 4 additions & 4 deletions backend/importer/management/commands/rebuild_variant_summary.py
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Expand Up @@ -16,15 +16,15 @@ class Command(BaseCommand):

def add_arguments(self, parser):
"""Add the command's argument to the ``parser``."""
parser.add_argument("--async", help="Run the rebuild asynchronously.", action="store_false")
parser.add_argument("--async", help="Run the rebuild asynchronously.", action="store_true")

@transaction.atomic
def handle(self, *args, **options):
"""Perform rebuilding the statistics."""
if options["async"]:
models.refresh_variants_smallvariantsummary()
msg = "Done rebuilding variant summary."
else:
refresh_variants_smallvariantsummary.delay()
msg = "Pushed rebuilding variant summary to background."
else:
models.refresh_variants_smallvariantsummary()
msg = "Done rebuilding variant summary."
self.stdout.write(self.style.SUCCESS(msg))
10 changes: 10 additions & 0 deletions backend/variants/forms.py
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Expand Up @@ -38,6 +38,16 @@
"effect_3_prime_UTR_intron_variant": "3_prime_UTR_intron_variant",
"effect_transcript_ablation": "transcript_ablation",
"effect_upstream_gene_variant": "upstream_gene_variant",
# new mehari effects
"effect_coding_sequence_variant": "coding_sequence_variant",
"effect_conservative_inframe_deletion": "conservative_inframe_deletion",
"effect_conservative_inframe_insertion": "conservative_inframe_insertion",
"effect_intron_variant": "intron_variant",
"effect_splice_donor_5th_base_variant": "splice_donor_5th_base_variant",
"effect_splice_donor_region_variant": "splice_donor_region_variant",
"effect_splice_polypyrimidine_tract_variant": "splice_polypyrimidine_tract_variant",
"effect_start_retained_variant": "start_retained_variant",
"effect_transcript_amplification": "transcript_amplification",
}

FILTER_FORM_TRANSLATE_INHERITANCE = {
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39 changes: 39 additions & 0 deletions backend/variants/query_presets.py
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Expand Up @@ -571,6 +571,8 @@ class _ImpactPresets:
"stop_lost",
"structural_variant",
"transcript_ablation",
# new mehari effects
"transcript_amplification",
],
}
#: Presets for "amino acid change and splicing" impact
Expand Down Expand Up @@ -604,6 +606,13 @@ class _ImpactPresets:
"stop_lost",
"structural_variant",
"transcript_ablation",
# new mehari effects
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"transcript_amplification",
],
}
#: Presets for "all coding and deep intronic" impact
Expand Down Expand Up @@ -639,6 +648,16 @@ class _ImpactPresets:
"structural_variant",
"synonymous_variant",
"transcript_ablation",
# new mehari effects
"coding_sequence_variant",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
}
#: Presets for "whole transcript" impact
Expand Down Expand Up @@ -683,6 +702,16 @@ class _ImpactPresets:
"synonymous_variant",
"transcript_ablation",
"upstream_gene_variant",
# new mehari effects
"coding_sequence_variant",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
}
#: Presets for "any" impact
Expand Down Expand Up @@ -728,6 +757,16 @@ class _ImpactPresets:
"synonymous_variant",
"transcript_ablation",
"upstream_gene_variant",
# new mehari effects
"coding_sequence_variant",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
}

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10 changes: 10 additions & 0 deletions backend/variants/query_schemas.py
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Expand Up @@ -92,6 +92,16 @@ class Effects(Enum):
SYNONYMOUS_VARIANT = "synonymous_variant"
TRANSCRIPT_ABLATION = "transcript_ablation"
UPSTREAM_GENE_VARIANT = "upstream_gene_variant"
# new mehari effects
CODING_SEQUENCE_VARIANT = "coding_sequence_variant"
CONSERVATIVE_INFRAME_DELETION = "conservative_inframe_deletion"
CONSERVATIVE_INFRAME_INSERTION = "conservative_inframe_insertion"
INTRON_VARIANT = "intron_variant"
SPLICE_DONOR_5TH_BASE_VARIANT = "splice_donor_5th_base_variant"
SPLICE_DONOR_REGION_VARIANT = "splice_donor_region_variant"
SPLICE_POLYPYRIMIDINE_TRACT_VARIANT = "splice_polypyrimidine_tract_variant"
START_RETAINED_VARIANT = "start_retained_variant"
TRANSCRIPT_AMPLIFICATION = "transcript_amplification"


@unique
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11 changes: 10 additions & 1 deletion backend/variants/schemas/case-query-v1.json
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Expand Up @@ -73,7 +73,16 @@
"structural_variant",
"synonymous_variant",
"transcript_ablation",
"upstream_gene_variant"
"upstream_gene_variant",
"coding_sequence_variant",
"conservative_inframe_deletion",
"conservative_inframe_insertion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification"
]
}
},
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4 changes: 2 additions & 2 deletions backend/variants/tests/data/query_settings.py
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9 changes: 9 additions & 0 deletions backend/variants/tests/factories.py
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Expand Up @@ -187,6 +187,15 @@ class FormDataFactory(FormDataFactoryBase):
effect_3_prime_UTR_intron_variant: bool = True
effect_transcript_ablation: bool = True
effect_upstream_gene_variant: bool = True
effect_coding_sequence_variant: bool = True
effect_conservative_inframe_deletion: bool = True
effect_conservative_inframe_insertion: bool = True
effect_intron_variant: bool = True
effect_splice_donor_5th_base_variant: bool = True
effect_splice_donor_region_variant: bool = True
effect_splice_polypyrimidine_tract_variant: bool = True
effect_start_retained_variant: bool = True
effect_transcript_amplification: bool = True
gene_blocklist: str = ""
genomic_region: str = ""
gene_allowlist: str = ""
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1 change: 1 addition & 0 deletions backend/variants/tests/test_models_presets.py
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Expand Up @@ -180,6 +180,7 @@ def test_create_as_copy_of_factory_preset(self):
"stop_lost",
"structural_variant",
"transcript_ablation",
"transcript_amplification",
],
}
self.assertDictEqual(result, expected)
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9 changes: 9 additions & 0 deletions backend/variants/tests/test_queries.py
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Expand Up @@ -1988,6 +1988,15 @@ def test_effects_include_missing_annotation(self):
"synonymous_variant",
"transcript_ablation",
"upstream_gene_variant",
"coding_sequence_variant",
"conservative_inframe_deletion",
"conservative_inframe_insertion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
},
4,
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44 changes: 44 additions & 0 deletions backend/variants/tests/test_query_presets.py
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Expand Up @@ -1033,6 +1033,10 @@ def testToSettingsAny(self):


class TestEnumImpact(TestCase):
def setUp(self):
super().setUp()
self.maxDiff = None

def testValues(self):
self.assertEqual(query_presets.Impact.NULL_VARIANT.value, "null_variant")
self.assertEqual(query_presets.Impact.AA_CHANGE_SPLICING.value, "aa_change_splicing")
Expand Down Expand Up @@ -1066,6 +1070,7 @@ def testToSettingsNullVariant(self):
"stop_lost",
"structural_variant",
"transcript_ablation",
"transcript_amplification",
],
},
)
Expand Down Expand Up @@ -1103,6 +1108,12 @@ def testToSettingsAaChangeSplicing(self):
"stop_lost",
"structural_variant",
"transcript_ablation",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"transcript_amplification",
],
},
)
Expand Down Expand Up @@ -1142,6 +1153,15 @@ def testToSettingsAllCodingDeepIntronic(self):
"structural_variant",
"synonymous_variant",
"transcript_ablation",
"coding_sequence_variant",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
},
)
Expand Down Expand Up @@ -1190,6 +1210,15 @@ def testToSettingsWholeTranscript(self):
"synonymous_variant",
"transcript_ablation",
"upstream_gene_variant",
"coding_sequence_variant",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
},
)
Expand Down Expand Up @@ -1239,6 +1268,15 @@ def testToSettingsAny(self):
"synonymous_variant",
"transcript_ablation",
"upstream_gene_variant",
"coding_sequence_variant",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"intron_variant",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"start_retained_variant",
"transcript_amplification",
],
},
)
Expand Down Expand Up @@ -1737,6 +1775,12 @@ def testToSettingsDefaults(self):
"stop_lost",
"structural_variant",
"transcript_ablation",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"transcript_amplification",
],
"exac_enabled": True,
"exac_frequency": 0.002,
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10 changes: 10 additions & 0 deletions backend/variants/tests/test_ui.py
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Expand Up @@ -225,4 +225,14 @@ def assert_element_exists(self, kwargs, element_id, exists):
"id_effect_structural_variant": False,
"id_effect_transcript_ablation": False,
"id_effect_complex_substitution": False,
# new mehari effects
"id_effect_coding_sequence_variant": False,
"id_effect_conservative_inframe_deletion": False,
"id_effect_conservative_inframe_insertion": False,
"id_effect_intron_variant": False,
"id_effect_splice_donor_5th_base_variant": False,
"id_effect_splice_donor_region_variant": False,
"id_effect_splice_polypyrimidine_tract_variant": False,
"id_effect_start_retained_variant": False,
"id_effect_transcript_amplification": False,
}
6 changes: 6 additions & 0 deletions backend/variants/tests/test_views_api.py
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Expand Up @@ -720,6 +720,12 @@ def test_get_success(self):
"stop_lost",
"structural_variant",
"transcript_ablation",
"conservative_inframe_insertion",
"conservative_inframe_deletion",
"splice_donor_5th_base_variant",
"splice_donor_region_variant",
"splice_polypyrimidine_tract_variant",
"transcript_amplification",
],
"quality": {
f"{self.case.index}": {
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5 changes: 4 additions & 1 deletion frontend/src/seqvars/components/PresetsEditor/lib/consequence.ts
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Expand Up @@ -118,10 +118,10 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [
'stop_lost',
'disruptive_inframe_deletion',
'disruptive_inframe_insertion',
'coding_sequence_variant',
'conservative_inframe_insertion',
'conservative_inframe_deletion',
'missense_variant',
'coding_sequence_variant',
],
},
{
Expand All @@ -145,10 +145,13 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [
'exon_loss_variant',
'frameshift_variant',
'start_lost',
'start_retained_variant',
'stop_gained',
'stop_lost',
'stop_retained_variant',
'disruptive_inframe_deletion',
'disruptive_inframe_insertion',
'coding_sequence_variant',
'conservative_inframe_insertion',
'conservative_inframe_deletion',
'missense_variant',
Expand Down
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