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feat: display seqvars query execution results in UI (#1952) #1957

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Oct 10, 2024
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feat: display seqvars query execution results in UI (#1952) #1957

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feat: display seqvars query execution results in UI (#1952)
holtgrewe Sep 4, 2024
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holtgrewe Oct 10, 2024
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holtgrewe Oct 10, 2024
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holtgrewe Oct 10, 2024
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holtgrewe Oct 10, 2024
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Update frontend/src/seqvars/components/QueryResults/CellGeneFlags.vue
holtgrewe Oct 10, 2024
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128 changes: 128 additions & 0 deletions backend/cases_import/tests/snapshots/snap_test_models_executor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,3 +32,131 @@
"sex": 2,
},
]

snapshots["ImportCreateWithSeqvarsVcfTest::test_run external files"] = [
{
"available": None,
"designation": "variant_calls",
"file_attributes": {
"checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82",
"designation": "variant_calls",
"genomebuild": "grch37",
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"variant_type": "seqvars",
},
"identifier_map": {"index": "NA12878-PCRF450-1"},
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"path": "file://cases_import/tests/data/sample-brca1.vcf.gz",
},
{
"available": None,
"designation": "variant_calls",
"file_attributes": {
"checksum": "sha256:6b137335b7803623c3389424e7b64d704fb1c9f3f55792db2916d312e2da27ef",
"designation": "variant_calls",
"genomebuild": "grch37",
"mimetype": "application/octet-stream+x-tabix-tbi-index",
"variant_type": "seqvars",
},
"identifier_map": {"index": "NA12878-PCRF450-1"},
"mimetype": "application/octet-stream+x-tabix-tbi-index",
"path": "file://cases_import/tests/data/sample-brca1.vcf.gz.tbi",
},
]

snapshots["ImportCreateWithSeqvarsVcfTest::test_run internal files"] = [
{
"checksum": None,
"designation": "variant_calls/seqvars/orig-copy",
"file_attributes": {
"checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82",
"designation": "variant_calls",
"genomebuild": "grch37",
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"variant_type": "seqvars",
},
"identifier_map": {"index": "NA12878-PCRF450-1"},
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/seqvars/external-copy-0.vcf.gz",
},
{
"checksum": None,
"designation": "variant_calls/seqvars/ingested-vcf",
"file_attributes": {},
"identifier_map": {},
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/seqvars/ingested.vcf.gz",
},
{
"checksum": None,
"designation": "variant_calls/seqvars/ingested-tbi",
"file_attributes": {},
"identifier_map": {},
"mimetype": "application/octet-stream+x-tabix-tbi-index",
"path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/seqvars/ingested.vcf.gz.tbi",
},
]
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💡 Codebase verification

Checksum assignments not found in the codebase.

The snapshots show that the checksum field is None for all entries in ImportCreateWithSeqvarsVcfTest::test_run internal files. Additionally, the codebase does not assign values to file_attributes["checksum"], which may result in missing checksum validations.

Please ensure that checksum values are correctly calculated and assigned to maintain data integrity.

🔗 Analysis chain

Well-structured snapshot for internal files, with a few points to verify.

The snapshot for ImportCreateWithSeqvarsVcfTest::test_run internal files is well-organized and includes the expected files (original copy, ingested VCF, and index). The use of UUIDs in paths is a good practice for ensuring unique storage per case.

However, please verify the following:

  1. The checksum field is None for all entries. Is this intentional?
  2. The file_attributes and identifier_map are empty for ingested files. Is this expected behavior?

Re-running verification to check checksum implementations.

Further verification needed for checksum assignments.

To ensure that checksum values are being correctly calculated and assigned, please run the following script:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Verify if the checksum calculation is implemented for internal files
rg --type python 'def calculate_checksum|checksum =' backend/cases_import/

Length of output: 107

Script:

#!/bin/bash
# Verify if the checksum calculation is implemented for internal files by searching for 'def calculate_checksum' or 'checksum =' in Python files
rg --glob '*.py' 'def calculate_checksum|checksum =' backend/cases_import/

Length of output: 167

Script:

#!/bin/bash
# Search for assignments to file_attributes["checksum"] in Python files
rg --glob '*.py' 'file_attributes\["checksum"\]\s*=' backend/cases_import/

Length of output: 76


snapshots["ImportCreateWithStrucvarsVcfTest::test_run external files"] = [
{
"available": None,
"designation": "variant_calls",
"file_attributes": {
"checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82",
"designation": "variant_calls",
"genomebuild": "grch37",
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"variant_type": "strucvars",
},
"identifier_map": {"index": "NA12878-PCRF450-1"},
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"path": "file://cases_import/tests/data/sample-brca1.vcf.gz",
},
{
"available": None,
"designation": "variant_calls",
"file_attributes": {
"checksum": "sha256:6b137335b7803623c3389424e7b64d704fb1c9f3f55792db2916d312e2da27ef",
"designation": "variant_calls",
"genomebuild": "grch37",
"mimetype": "application/octet-stream+x-tabix-tbi-index",
"variant_type": "strucvars",
},
"identifier_map": {"index": "NA12878-PCRF450-1"},
"mimetype": "application/octet-stream+x-tabix-tbi-index",
"path": "file://cases_import/tests/data/sample-brca1.vcf.gz.tbi",
},
]

snapshots["ImportCreateWithStrucvarsVcfTest::test_run internal files"] = [
{
"checksum": None,
"designation": "variant_calls/strucvars/orig-copy",
"file_attributes": {
"checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82",
"designation": "variant_calls",
"genomebuild": "grch37",
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"variant_type": "strucvars",
},
"identifier_map": {"index": "NA12878-PCRF450-1"},
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/strucvars/external-copy-0.vcf.gz",
},
{
"checksum": None,
"designation": "variant_calls/strucvars/ingested-vcf",
"file_attributes": {},
"identifier_map": {},
"mimetype": "text/plain+x-bgzip+x-variant-call-format",
"path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/strucvars/ingested.vcf.gz",
},
{
"checksum": None,
"designation": "variant_calls/strucvars/ingested-tbi",
"file_attributes": {},
"identifier_map": {},
"mimetype": "application/octet-stream+x-tabix-tbi-index",
"path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/strucvars/ingested.vcf.gz.tbi",
},
]
27 changes: 27 additions & 0 deletions backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py
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@@ -0,0 +1,27 @@
# Generated by Django 3.2.25 on 2024-10-09 06:39

from django.db import migrations, models


class Migration(migrations.Migration):

dependencies = [
("ext_gestaltmatcher", "0002_smallvariantquerypediascores"),
]

operations = [
migrations.AlterField(
model_name="smallvariantquerygestaltmatcherscores",
name="id",
field=models.BigAutoField(
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
),
),
migrations.AlterField(
model_name="smallvariantquerypediascores",
name="id",
field=models.BigAutoField(
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
),
),
]
20 changes: 20 additions & 0 deletions backend/protos/seqvars/protos/output.proto
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Expand Up @@ -166,12 +166,32 @@ message GeneRelatedConsequences {
repeated seqvars.pbs.query.Consequence consequences = 3;
}

// Enumerations with modes of inheritance from HPO.
enum ModeOfInheritance {
// Unspecified mode of inheritance.
MODE_OF_INHERITANCE_UNSPECIFIED = 0;
// Autosomal dominant inheritance (HP:0000006).
MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT = 1;
// Autosomal recessive inheritance (HP:0000007).
MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE = 2;
// X-linked dominant inheritance (HP:0001419).
MODE_OF_INHERITANCE_X_LINKED_DOMINANT = 3;
// X-linked recessive inheritance (HP:0001423).
MODE_OF_INHERITANCE_X_LINKED_RECESSIVE = 4;
// Y-linked inheritance (HP:0001450).
MODE_OF_INHERITANCE_Y_LINKED = 5;
// Mitochondrial inheritance (HP:0001427).
MODE_OF_INHERITANCE_MITOCHONDRIAL = 6;
}

// Phenotype-related information, if any.
message GeneRelatedPhenotypes {
// ACMG supplementary finding list.
bool is_acmg_sf = 1;
// Whether is a known disease gene.
bool is_disease_gene = 2;
// Linked modes of inheritance.
repeated ModeOfInheritance mode_of_inheritances = 3;
}

// Gene-wise constraints.
Expand Down
32 changes: 32 additions & 0 deletions backend/seqvars/migrations/0010_auto_20240905_1017.py
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@@ -0,0 +1,32 @@
# Generated by Django 3.2.25 on 2024-09-05 10:17

from django.db import migrations, models


class Migration(migrations.Migration):

dependencies = [
("seqvars", "0009_alter_seqvarsresultrow_genome_release"),
]

operations = [
migrations.AlterModelOptions(
name="seqvarsqueryexecutionbackgroundjob",
options={"ordering": ["-pk"]},
),
migrations.AlterModelOptions(
name="seqvarsresultrow",
options={"ordering": ["chrom_no", "pos", "ref_allele", "alt_allele"]},
),
migrations.AlterModelOptions(
name="seqvarsresultset",
options={"ordering": ["-date_created"]},
),
migrations.AlterField(
model_name="seqvarsresultrow",
name="genome_release",
field=models.CharField(
choices=[("grch37", "GRCh37"), ("grch38", "GRCh38")], max_length=32
),
),
]
30 changes: 26 additions & 4 deletions backend/seqvars/models/base.py
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Expand Up @@ -2055,13 +2055,26 @@ class GeneRelatedConsequencesPydantic(pydantic.BaseModel):
consequences: list[SeqvarsVariantConsequenceChoice]


class SeqvarsModeOfInheritance(str, Enum):
"""Mode of inheritance gene annotation."""

AUTOSOMAL_DOMINANT = "autosomal_dominant"
AUTOSOMAL_RECESSIVE = "autosomal_recessive"
X_LINKED_DOMINANT = "x_linked_dominant"
X_LINKED_RECESSIVE = "x_linked_recessive"
Y_LINKED = "y_linked"
MITOCHONDRIAL = "mitochondrial"


class GeneRelatedPhenotypesPydantic(pydantic.BaseModel):
"""Phenotype-related information, if any."""

#: ACMG supplementary finding list.
is_acmg_sf: bool = False
#: Whether is a known disease gene.
is_disease_gene: bool = False
#: Modes of inheritance.
mode_of_inheritances: list[SeqvarsModeOfInheritance] = []


class GnomadConstraintsPydantic(pydantic.BaseModel):
Expand Down Expand Up @@ -2161,13 +2174,13 @@ class GeneRelatedAnnotationPydantic(pydantic.BaseModel):
"""Store gene-related annotation (always for a single gene)."""

#: Gene ID information.
identity: GeneIdentityPydantic
identity: typing.Optional[GeneIdentityPydantic]
#: Gene-related consequences, if any (none if intergenic).
consequences: GeneRelatedConsequencesPydantic
consequences: typing.Optional[GeneRelatedConsequencesPydantic]
#: Gene-related phenotype information, if any.
phenotypes: GeneRelatedPhenotypesPydantic
phenotypes: typing.Optional[GeneRelatedPhenotypesPydantic]
#: Gene-wise constraints on the gene, if any.
constraints: GeneRelatedConstraintsPydantic
constraints: typing.Optional[GeneRelatedConstraintsPydantic]


class SeqvarsNuclearFrequencyPydantic(pydantic.BaseModel):
Expand Down Expand Up @@ -2373,6 +2386,9 @@ def get_absolute_url(self) -> str:
def __str__(self):
return f"SeqvarsResultSet '{self.sodar_uuid}'"

class Meta:
ordering = ["-date_created"]


class SeqvarsResultRow(models.Model):
"""One entry in the result set."""
Expand Down Expand Up @@ -2414,6 +2430,9 @@ def __str__(self):
f"{self.pos}-{self.ref_allele}-{self.alt_allele}'"
)

class Meta:
ordering = ["chrom_no", "pos", "ref_allele", "alt_allele"]


class SeqvarsQueryExecutionBackgroundJobManager(models.Manager):
"""Custom manager class that allows to create a ``SeqvarsQueryExeuctionBackgroundJob``
Expand Down Expand Up @@ -2478,3 +2497,6 @@ class SeqvarsQueryExecutionBackgroundJob(JobModelMessageMixin, models.Model):

def get_human_readable_type(self):
return self.task_desc

class Meta:
ordering = ["-pk"]
23 changes: 23 additions & 0 deletions backend/seqvars/models/protobufs.py
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Expand Up @@ -32,6 +32,7 @@
SeqvarsGnomadMitochondrialFrequencySettingsPydantic,
SeqvarsHelixMtDbFrequencyPydantic,
SeqvarsHelixMtDbFrequencySettingsPydantic,
SeqvarsModeOfInheritance,
SeqvarsNuclearFrequencyPydantic,
SeqvarsNuclearFrequencySettingsPydantic,
SeqvarsOutputHeaderPydantic,
Expand Down Expand Up @@ -84,6 +85,7 @@
GnomadConstraints,
GnomadMitochondrialFrequency,
HelixMtDbFrequency,
ModeOfInheritance,
NuclearFrequency,
OutputHeader,
OutputRecord,
Expand Down Expand Up @@ -772,10 +774,31 @@ def _consequences_from_protobuf(
)


MODE_OF_INHERITANCE_MAPPING: dict[
ModeOfInheritance.ValueType : SeqvarsVariantScoreColumnTypeChoice
] = {
ModeOfInheritance.MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT: SeqvarsModeOfInheritance.AUTOSOMAL_DOMINANT,
ModeOfInheritance.MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE: SeqvarsModeOfInheritance.AUTOSOMAL_RECESSIVE,
ModeOfInheritance.MODE_OF_INHERITANCE_X_LINKED_DOMINANT: SeqvarsModeOfInheritance.X_LINKED_DOMINANT,
ModeOfInheritance.MODE_OF_INHERITANCE_X_LINKED_RECESSIVE: SeqvarsModeOfInheritance.X_LINKED_RECESSIVE,
ModeOfInheritance.MODE_OF_INHERITANCE_Y_LINKED: SeqvarsModeOfInheritance.Y_LINKED,
ModeOfInheritance.MODE_OF_INHERITANCE_MITOCHONDRIAL: SeqvarsModeOfInheritance.MITOCHONDRIAL,
}


def _mode_of_inheritance_from_protobuf(
mode_of_inheritance: ModeOfInheritance.ValueType,
) -> SeqvarsModeOfInheritance:
return MODE_OF_INHERITANCE_MAPPING[mode_of_inheritance]


def _phenotypes_from_protobuf(phenotypes: GeneRelatedPhenotypes) -> GeneRelatedPhenotypesPydantic:
return GeneRelatedPhenotypesPydantic(
is_acmg_sf=phenotypes.is_acmg_sf,
is_disease_gene=phenotypes.is_disease_gene,
mode_of_inheritances=list(
map(_mode_of_inheritance_from_protobuf, phenotypes.mode_of_inheritances)
),
)


Expand Down
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