Extending models with release field for GRCh37/GRCh38

HISTORY.rst

@@ -10,6 +10,9 @@ End-User Summary
 ================
 
 - Fixing Kiosk mode of VarFish.
+- VarFish now allows for the import of GRCh38 annotated variants.
+  For this, GRCh38 background data must be imported.
+  Kiosk mode does not support GRCh38 yet.
 
 Full Change List
 ================
@@ -19,6 +22,8 @@ Full Change List
     - Using custom middleware for kiosk user (#215).
 - Kiosk annotation now uses ``set -x`` flag if ``settings.DEBUG`` is true.
 - Mapping kiosk jobs to import queue.
+- Adjusting models and UI for supporting GRCh38 annotated cases.
+  It is currently not possible to migrate a GRCh37 case to GRCh38.
 
 -------
 v0.23.9

clinvar/migrations/0007_alter_clinvar_details.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations
+import varfish.utils
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("clinvar", "0006_clinvarpathogenicgenes"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="clinvar", name="details", field=varfish.utils.JSONField(),
+        ),
+    ]

clinvar_export/migrations/0003_auto_20211008_1015.py

@@ -0,0 +1,31 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations
+import varfish.utils
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("clinvar_export", "0002_bootstrap_records"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="family",
+            name="pedigree",
+            field=varfish.utils.JSONField(
+                blank=True, default=list, help_text="Pedigree information.", null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="submission",
+            name="diseases",
+            field=varfish.utils.JSONField(blank=True, default=list, null=True),
+        ),
+        migrations.AlterField(
+            model_name="submissionindividual",
+            name="phenotypes",
+            field=varfish.utils.JSONField(blank=True, default=list, null=True),
+        ),
+    ]

extra_annos/migrations/0004_alter_extraanno_anno_data.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations
+import varfish.utils
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("extra_annos", "0003_alter_extraanno_anno_data"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="extraanno", name="anno_data", field=varfish.utils.JSONField(default=dict),
+        ),
+    ]

importer/migrations/0009_auto_20211008_1015.py

@@ -0,0 +1,22 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations, models
+import varfish.utils
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("importer", "0008_variantsetimportinfo_state"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="caseimportinfo",
+            name="release",
+            field=models.CharField(default="GRCh37", max_length=32, null=True),
+        ),
+        migrations.AlterField(
+            model_name="caseimportinfo", name="pedigree", field=varfish.utils.JSONField(),
+        ),
+    ]

importer/models.py

@@ -141,7 +141,7 @@ class VariantSetImportInfo(models.Model):
 
     genomebuild = models.CharField(
         max_length=32,
-        choices=(("GRCh37", "GRCh37"),),
+        choices=(("GRCh37", "GRCh37"), ("GRCh38", "GRCh38")),
         default="GRCh37",
         help_text="Genome build used in the variant set.",
     )

importer/serializers.py

@@ -207,6 +207,7 @@ class Meta:
             "date_modified",
             "owner",
             "case",
+            "release",
             "project",
             "name",
             "index",

regmaps/migrations/0002_auto_20211008_1015.py

@@ -0,0 +1,22 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations
+import varfish.utils
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("regmaps", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="regelement", name="extra_data", field=varfish.utils.JSONField(null=True),
+        ),
+        migrations.AlterField(
+            model_name="reginteraction",
+            name="extra_data",
+            field=varfish.utils.JSONField(null=True),
+        ),
+    ]

svs/migrations/0016_structuralvariantset_release.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("svs", "0015_set_logged_table"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="structuralvariantset",
+            name="release",
+            field=models.CharField(default="GRCh37", max_length=32, null=True),
+        ),
+    ]

svs/models.py

@@ -121,6 +121,8 @@ class StructuralVariantSet(models.Model):
     case = models.ForeignKey(
         Case, on_delete=models.CASCADE, null=False, help_text="The case that this set is for"
     )
+    #: Genome build
+    release = models.CharField(max_length=32, null=True, default="GRCh37")
     #: The state of the variant set.
     state = models.CharField(
         max_length=16,

variants/migrations/0083_auto_20211008_1015.py

@@ -0,0 +1,93 @@
+# Generated by Django 3.2.7 on 2021-10-08 10:15
+
+from django.db import migrations, models
+import varfish.utils
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("variants", "0082_auto_20210617_1409"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="case",
+            name="release",
+            field=models.CharField(default="GRCh37", max_length=32, null=True),
+        ),
+        migrations.AddField(
+            model_name="smallvariantset",
+            name="release",
+            field=models.CharField(default="GRCh37", max_length=32, null=True),
+        ),
+        migrations.AlterField(
+            model_name="caddpathogenicityscorecache", name="info", field=varfish.utils.JSONField(),
+        ),
+        migrations.AlterField(
+            model_name="caddsubmissionbgjob",
+            name="query_args",
+            field=varfish.utils.JSONField(help_text="(Validated) query parameters"),
+        ),
+        migrations.AlterField(model_name="case", name="pedigree", field=varfish.utils.JSONField(),),
+        migrations.AlterField(
+            model_name="casealignmentstats",
+            name="bam_stats",
+            field=varfish.utils.JSONField(default=dict),
+        ),
+        migrations.AlterField(
+            model_name="distillersubmissionbgjob",
+            name="query_args",
+            field=varfish.utils.JSONField(help_text="(Validated) query parameters"),
+        ),
+        migrations.AlterField(
+            model_name="exportfilebgjob",
+            name="query_args",
+            field=varfish.utils.JSONField(help_text="(Validated) query parameters"),
+        ),
+        migrations.AlterField(
+            model_name="exportprojectcasesfilebgjob",
+            name="query_args",
+            field=varfish.utils.JSONField(help_text="(Validated) query parameters"),
+        ),
+        migrations.AlterField(
+            model_name="projectcasessmallvariantquery",
+            name="query_settings",
+            field=varfish.utils.JSONField(help_text="The query settings"),
+        ),
+        migrations.AlterField(
+            model_name="projectcasessmallvariantqueryvariantscores",
+            name="info",
+            field=varfish.utils.JSONField(default=dict),
+        ),
+        migrations.AlterField(
+            model_name="samplevariantstatistics",
+            name="ontarget_dps",
+            field=varfish.utils.JSONField(),
+        ),
+        migrations.AlterField(
+            model_name="samplevariantstatistics",
+            name="ontarget_effect_counts",
+            field=varfish.utils.JSONField(),
+        ),
+        migrations.AlterField(
+            model_name="samplevariantstatistics",
+            name="ontarget_indel_sizes",
+            field=varfish.utils.JSONField(),
+        ),
+        migrations.AlterField(
+            model_name="smallvariantquery",
+            name="query_settings",
+            field=varfish.utils.JSONField(help_text="The query settings"),
+        ),
+        migrations.AlterField(
+            model_name="smallvariantqueryvariantscores",
+            name="info",
+            field=varfish.utils.JSONField(default=dict),
+        ),
+        migrations.AlterField(
+            model_name="spanrsubmissionbgjob",
+            name="query_args",
+            field=varfish.utils.JSONField(help_text="(Validated) query parameters"),
+        ),
+    ]

variants/models.py

@@ -470,6 +470,8 @@ def find(self, search_terms, _keywords=None):
 class CoreCase(models.Model):
     """Abstract base class for Case core fields."""
 
+    #: Genome build
+    release = models.CharField(max_length=32, null=True, default="GRCh37")
     #: Name of the case.
     name = models.CharField(max_length=512)
     #: Identifier of the index in ``pedigree``.
@@ -949,6 +951,8 @@ class SmallVariantSet(models.Model):
     case = models.ForeignKey(
         Case, on_delete=models.CASCADE, null=False, help_text="The case that this set is for"
     )
+    #: Genome build
+    release = models.CharField(max_length=32, null=True, default="GRCh37")
     #: The state of the variant set.
     state = models.CharField(
         max_length=16,

variants/tests/factories.py

@@ -337,6 +337,7 @@ class Params:
         #: affected.
         inheritance = "denovo"
 
+    release = factory.Sequence(lambda n: "GRCh%d" % (37 + n % 2))
     name = factory.LazyAttributeSequence(lambda o, n: "case %03d: %s" % (n, o.structure))
     index = factory.Sequence(lambda n: "index_%03d-N1-DNA1-WES1" % n)
     pedigree = []