Merge 69dab18 into 8680015

HISTORY.rst

@@ -30,6 +30,7 @@ Full Change List
 - Improving Clinvar record aggregation (#640).
 - Fixing Docker builds (#660).
 - Fixing ClinVar submission XML generation (#677).
+- Adding regular task to sync ClinVar submission ``Individual`` sex from the one from the ``Case``.
 
 -----------------
 v1.2.2 (anthenea)

clinvar_export/management/commands/refresh_individuals.py

@@ -0,0 +1,16 @@
+"""Django management command for triggering clinvar_export individual update."""
+
+from django.core.management.base import BaseCommand
+
+from clinvar_export.models import refresh_individual_sex_affected
+
+
+class Command(BaseCommand):
+    #: Help message displayed on the command line.
+    help = "Refresh ClinVar export individual sex/affected attributes."
+
+    def handle(self, *args, **options):
+        """The actual implementation is in ``_handle()``, splitting to get commit times."""
+        self.stderr.write(self.style.NOTICE("Refreshing all clinvar_xml individuals"))
+        refresh_individual_sex_affected()
+        self.stderr.write(self.style.NOTICE("All done. Have a nice day!"))

clinvar_export/models.py

@@ -17,6 +17,20 @@
 #: Django user model.
 AUTH_USER_MODEL = getattr(settings, "AUTH_USER_MODEL", "auth.User")
 
+#: Map pedigree value for "sex" to value for models.
+SEX_MAP = {
+    0: "unknown",
+    1: "male",
+    2: "female",
+}
+
+#: Map pedigree value for "affected" to value for models.
+AFFECTED_MAP = {
+    0: "unknown",
+    1: "no",
+    2: "yes",
+}
+
 
 class FamilyManager(models.Manager):
     """Custom ``Manager`` that allows to easily get or create a ``Family`` from a project with a given name."""
@@ -123,16 +137,6 @@ class Meta:
 
 def create_families_and_individuals(project: Project) -> None:
     """Create missing families and individuals for the given ``project``."""
-    sex_map = {
-        0: "unknown",
-        1: "male",
-        2: "female",
-    }
-    affected_map = {
-        0: "unknown",
-        1: "no",
-        2: "yes",
-    }
     with transaction.atomic():
         for case in Case.objects.filter(project=project):
             family = Family.objects.get_or_create_in_project(project, case=case)
@@ -141,8 +145,8 @@ def create_families_and_individuals(project: Project) -> None:
                     project,
                     entry["patient"],
                     family=family,
-                    sex=sex_map.get(entry.get("sex", 0), "unknown"),
-                    affected=affected_map.get(entry.get("affected", 0), "unknown"),
+                    sex=SEX_MAP.get(entry.get("sex", 0), "unknown"),
+                    affected=AFFECTED_MAP.get(entry.get("affected", 0), "unknown"),
                 )
 
 
@@ -388,3 +392,17 @@ def get_project(self):
 
     class Meta:
         ordering = ("sort_order",)
+
+
+def refresh_individual_sex_affected():
+    """Update the ``Individual.sex`` field from the upstream case.
+
+    This is done regularly in a related task.
+    """
+    for family in Family.objects.select_related("case").prefetch_related("individual_set").all():
+        ped_entries = {entry["patient"]: entry for entry in family.case.pedigree}
+        for individual in family.individual_set.all():
+            related_ped_entry = ped_entries[individual.name]
+            individual.sex = SEX_MAP.get(related_ped_entry["sex"], "unknown")
+            individual.affected = AFFECTED_MAP.get(related_ped_entry["affected"], "unknown")
+            individual.save()

clinvar_export/tasks.py

@@ -0,0 +1,15 @@
+from celery.schedules import crontab
+from config.celery import app
+
+from clinvar_export import models
+
+
+@app.task(bind=True)
+def refresh_individual_sex_affected(_self):
+    models.refresh_individual_sex_affected()
+
+
+@app.on_after_finalize.connect
+def setup_periodic_tasks(sender, **_kwargs):
+    """Register periodic tasks"""
+    sender.add_periodic_task(schedule=crontab(minute=11), sig=refresh_individual_sex_affected.s())

clinvar_export/tests/test_models.py

@@ -2,28 +2,30 @@
 
 from test_plus.test import TestCase
 
-from ..models import (
+from variants.models import Case
+from variants.tests.factories import CaseFactory
+
+from clinvar_export.models import (
+    AssertionMethod,
     Family,
     Individual,
-    AssertionMethod,
-    Submitter,
     Organisation,
+    Submission,
     SubmissionSet,
+    Submitter,
     SubmittingOrg,
-    Submission,
+    refresh_individual_sex_affected,
 )
-from .factories import (
+from clinvar_export.tests.factories import (
+    AssertionMethodFactory,
     FamilyFactory,
     IndividualFactory,
-    AssertionMethodFactory,
-    SubmitterFactory,
     OrganisationFactory,
+    SubmissionFactory,
     SubmissionSetFactory,
+    SubmitterFactory,
     SubmittingOrgFactory,
-    SubmissionFactory,
 )
-from variants.models import Case
-from variants.tests.factories import CaseFactory
 
 
 class TestFamily(TestCase):
@@ -168,3 +170,19 @@ def testCreate(self):
         self.assertEquals(Submission.objects.count(), 0)
         SubmissionFactory()
         self.assertEquals(Submission.objects.count(), 1)
+
+
+class TestUpdateIndividualSexAffectedTask(TestCase):
+    """Test the task that updates the sex/affected of ``Individual`` records from upstream case."""
+
+    def testRun(self):
+        individual = IndividualFactory(sex="male", affected="yes")
+        individual.sex = "unknown"
+        individual.affected = "unknown"
+        individual.save()
+        self.assertEquals(individual.sex, "unknown")
+        self.assertEquals(individual.sex, "unknown")
+        refresh_individual_sex_affected()
+        individual.refresh_from_db()
+        self.assertEquals(individual.sex, "male")
+        self.assertEquals(individual.affected, "yes")