Complete adding death_table boolean to SR table and update rules + migration

app/api/api/views.py

@@ -1101,7 +1101,7 @@ def post(self, request, *args, **kwargs):
                 status=status.HTTP_400_BAD_REQUEST,
             )
         # validate the destination_table
-        destination_table = _find_destination_table(concept)
+        destination_table = _find_destination_table(concept, table)
         if destination_table is None:
             return Response(
                 {

app/api/mapping/migrations/0015_scanreporttable_death_table.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.8 on 2026-02-23 10:45
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("mapping", "0014_alter_scanreportfield_name_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="scanreporttable",
+            name="death_table",
+            field=models.BooleanField(default=False, null=True),
+        ),
+    ]

app/api/mapping/models.py

@@ -269,6 +269,7 @@ class ScanReportTable(BaseModel):
 
     scan_report = models.ForeignKey(ScanReport, on_delete=models.CASCADE)
     name = models.CharField(max_length=256, db_index=True)
+    death_table = models.BooleanField(default=False, null=True)
 
     # Quick notes:
     # - "ScanReportField", instead of ScanReportField,

app/api/services/rules.py

@@ -23,6 +23,7 @@
     "procedure_occurrence",
     "device_exposure",
     "specimen",
+    "death",
 ]
 
 # look up of date-events in all the allowed (destination) tables
@@ -38,6 +39,7 @@
         "device_exposure_end_datetime",
     ],
     "specimen": ["specimen_datetime"],
+    "death": ["death_datetime"],
 }
 
 
@@ -279,7 +281,9 @@ def _get_date_rules(
     return date_rules
 
 
-def _find_destination_table(concept: Concept) -> Optional[OmopTable]:
+def _find_destination_table(
+    concept: Concept, table: ScanReportTable
+) -> Optional[OmopTable]:
     """
     Get the destination table for a given Concept
 
@@ -291,10 +295,13 @@ def _find_destination_table(concept: Concept) -> Optional[OmopTable]:
     """
     domain = concept.domain_id.lower()
     # get the omop field for the source_concept_id for this domain
-    # if the domain is "meas value" then point directly to its field and table
-    if domain == "meas value":
+
+    # For death tables (not gender, race, ethnicity) use cause_source_concept_id
+    if table.death_table and domain not in ["gender", "race", "ethnicity"]:
+        omop_field = _get_omop_field("cause_source_concept_id", "death")
+    elif domain == "meas value":
         omop_field = _get_omop_field("value_as_concept_id", "measurement")
-    #  if the domain is "specimen" or "spec anatomic site" then point directly to one field in the table "specimen"
+    # if the domain is "specimen" or "spec anatomic site" then point directly to one field in the table "specimen"
     elif domain == "specimen" or domain == "spec anatomic site":
         omop_field = _get_omop_field("specimen_concept_id", "specimen")
     else:
@@ -337,13 +344,14 @@ def save_mapping_rules(
     # Convert "spec anatomic site" to "anatomic_site" to match the name in OMOP CDM
     if domain == "spec anatomic site":
         domain = "anatomic_site"
+
+    source_table = source_field.scan_report_table
+
     # start looking up what table we're looking at
-    destination_table = _find_destination_table(concept)
+    destination_table = _find_destination_table(concept, source_table)
     if destination_table is None:
         return []
 
-    source_table = source_field.scan_report_table
-
     # check whether the person_id and date events for this table are valid
     # if not, we dont want to create any rules for this concept
     if not _validate_person_id_and_date(source_table):
@@ -360,6 +368,10 @@ def save_mapping_rules(
     )
     rules += date_rules
 
+    # Convert domain of concepts added to Death table to "CAUSE", in order to facilitate the get OMOP field process
+    if source_table.death_table and domain not in ["gender", "race", "ethnicity"]:
+        domain = "cause"
+
     # In case of domain = "meas value", this rule will not be generated.
     # And because of the conversion of domain in the line after "rules.append(rule_domain_value_as_concept_id)", this block needs to be upfront
     if domain == "measurement":