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

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

backend/cases_import/tests/snapshots/snap_test_models_executor.py

@@ -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",
+    },
+]
+
+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",
+    },
+]

backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py

@@ -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"
+            ),
+        ),
+    ]

backend/protos/seqvars/protos/output.proto

@@ -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.

backend/seqvars/migrations/0010_auto_20240905_1017.py

@@ -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
+            ),
+        ),
+    ]

backend/seqvars/models/base.py

@@ -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):
@@ -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):
@@ -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."""
@@ -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``
@@ -2478,3 +2497,6 @@ class SeqvarsQueryExecutionBackgroundJob(JobModelMessageMixin, models.Model):
 
     def get_human_readable_type(self):
         return self.task_desc
+
+    class Meta:
+        ordering = ["-pk"]

backend/seqvars/models/protobufs.py

@@ -32,6 +32,7 @@
     SeqvarsGnomadMitochondrialFrequencySettingsPydantic,
     SeqvarsHelixMtDbFrequencyPydantic,
     SeqvarsHelixMtDbFrequencySettingsPydantic,
+    SeqvarsModeOfInheritance,
     SeqvarsNuclearFrequencyPydantic,
     SeqvarsNuclearFrequencySettingsPydantic,
     SeqvarsOutputHeaderPydantic,
@@ -84,6 +85,7 @@
     GnomadConstraints,
     GnomadMitochondrialFrequency,
     HelixMtDbFrequency,
+    ModeOfInheritance,
     NuclearFrequency,
     OutputHeader,
     OutputRecord,
@@ -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)
+        ),
     )