feat: add is_deleted soft-delete to ClickHouse IDENTITIES table

api/clickhouse/migrations/0002_identities_add_is_deleted.py

@@ -0,0 +1,17 @@
+from django.db import migrations
+
+_ADD_COLUMN_DDL = (
+    "ALTER TABLE IDENTITIES ADD COLUMN IF NOT EXISTS is_deleted Bool DEFAULT false"
+)
+
+
+class Migration(migrations.Migration):
+    # ClickHouse has no transactional DDL.
+    atomic = False
+    dependencies = [("clickhouse", "0001_create_identities")]
+    operations = [
+        migrations.RunSQL(
+            _ADD_COLUMN_DDL,
+            reverse_sql=("ALTER TABLE IDENTITIES DROP COLUMN IF EXISTS is_deleted"),
+        )
+    ]

api/edge_api/identities/models.py

@@ -2,6 +2,7 @@
 import typing
 from contextlib import suppress
 
+from django.conf import settings
 from django.db.models import Prefetch, Q
 
 from api_keys.user import APIKeyUser
@@ -194,6 +195,18 @@ def delete(self, user: FFAdminUser | APIKeyUser = None) -> None:  # type: ignore
             user=user,
         )
         self._reset_initial_state()  # type: ignore[no-untyped-call]
+        if settings.CLICKHOUSE_ENABLED:
+            from segment_membership.tasks import (
+                write_identity_deletion_tombstone_to_clickhouse,
+            )
+
+            write_identity_deletion_tombstone_to_clickhouse.delay(
+                args=(
+                    self.engine_identity_model.environment_api_key,
+                    self.engine_identity_model.identifier,
+                    self.engine_identity_model.composite_key,
+                )
+            )
 
     def synchronise_features(self, valid_feature_names: typing.Collection[str]) -> None:
         identity_feature_names = {

api/segment_membership/mappers.py

@@ -2,16 +2,18 @@
 
 from flagsmith_schemas import dynamodb
 
-# (environment_id, identifier, identity_key, traits)
-ClickHouseIdentityRow = tuple[str, str, str, dict[str, object] | None]
+# (environment_id, identifier, identity_key, traits, is_deleted)
+ClickHouseIdentityRow = tuple[str, str, str, dict[str, object] | None, bool]
 
 
 def map_identity_document_to_clickhouse_row(
     env_key: str,
     identity_doc: dynamodb.Identity,
+    *,
+    is_deleted: bool = False,
 ) -> ClickHouseIdentityRow:
     """Project a Dynamo identity document onto an IDENTITIES row tuple
-    `(environment_id, identifier, identity_key, traits)`."""
+    `(environment_id, identifier, identity_key, traits, is_deleted)`."""
     identifier = identity_doc["identifier"]
     composite_key = identity_doc["composite_key"]
     raw_traits = identity_doc.get("identity_traits")
@@ -21,6 +23,7 @@ def map_identity_document_to_clickhouse_row(
         identifier,
         composite_key,
         traits,
+        is_deleted,
     )
 
 

api/segment_membership/services.py

@@ -104,7 +104,9 @@ def compute_segment_counts_for_project(
             f"SELECT {seg.id} AS segment_id, "
             f"i.environment_id AS env_key, count() AS c "
             f"FROM IDENTITIES AS i FINAL "
-            f"WHERE i.environment_id IN %(env_keys)s AND ({predicate}) "
+            f"WHERE i.environment_id IN %(env_keys)s "
+            f"AND i.is_deleted = false "
+            f"AND ({predicate}) "
             f"GROUP BY i.environment_id"
         )
 

api/segment_membership/tasks.py

@@ -18,6 +18,7 @@
 )
 
 from environments.dynamodb.wrappers.identity_wrapper import DynamoIdentityWrapper
+from environments.models import Environment
 from projects.models import Project
 from segment_membership.mappers import map_identity_document_to_clickhouse_row
 from segment_membership.metrics import (
@@ -45,6 +46,7 @@
     "identifier",
     "identity_key",
     "traits",
+    "is_deleted",
 )
 
 _INSERT_IDENTITIES_SQL = (
@@ -188,3 +190,62 @@ def refresh_project_segment_counts(project_id: int) -> None:
             membership_counts__count=len(membership_counts),
             stale_counts__count=stale_deleted,
         )
+
+
+@register_task_handler()
+def write_identity_deletion_tombstone_to_clickhouse(
+    env_key: str,
+    identifier: str,
+    identity_key: str,
+) -> None:
+    """Insert a tombstone row for a deleted identity so it is excluded from
+    segment membership counts at the next refresh.
+
+    ReplacingMergeTree(inserted_at) keeps the row with the highest
+    inserted_at per (environment_id, identifier). Because this row is
+    written after the identity is removed from Dynamo its inserted_at
+    will be newer than any prior live row, so FINAL deduplication will
+    always surface the tombstone.
+    """
+    if not settings.CLICKHOUSE_ENABLED:
+        logger.info(
+            "tombstone.skipped",
+            reason="clickhouse_not_configured",
+            env_key=env_key,
+            identifier=identifier,
+        )
+        return
+
+    try:
+        environment = Environment.objects.select_related("project__organisation").get(
+            api_key=env_key
+        )
+    except Environment.DoesNotExist:
+        logger.info(
+            "tombstone.skipped",
+            reason="environment_not_found",
+            env_key=env_key,
+            identifier=identifier,
+        )
+        return
+
+    if not is_membership_enabled(environment.project.organisation):
+        logger.info(
+            "tombstone.skipped",
+            reason="segment_membership_disabled",
+            env_key=env_key,
+            identifier=identifier,
+        )
+        return
+
+    log_comment = f"flagsmith:segment_membership:tombstone:env_{env_key}"
+    with open_clickhouse_cursor(log_comment=log_comment) as cursor:
+        cursor.executemany(
+            _INSERT_IDENTITIES_SQL,
+            [(env_key, identifier, identity_key, None, True)],
+        )
+    logger.info(
+        "tombstone.written",
+        env_key=env_key,
+        identifier=identifier,
+    )

api/tests/unit/edge_api/identities/test_edge_identity_models.py

@@ -6,6 +6,7 @@
 from django.utils import timezone
 from freezegun import freeze_time
 from pytest_django import DjangoAssertNumQueries
+from pytest_django.fixtures import SettingsWrapper
 from pytest_lazyfixture import lazy_fixture  # type: ignore[import-untyped]
 from pytest_mock import MockerFixture
 
@@ -509,6 +510,56 @@ def test_save__feature_override_updated__generates_audit_records(
     )
 
 
+def test_edge_identity_delete__clickhouse_enabled__dispatches_tombstone_task(
+    mocker: MockerFixture,
+    edge_identity_model: EdgeIdentity,
+    edge_identity_dynamo_wrapper_mock: MagicMock,
+    settings: SettingsWrapper,
+) -> None:
+    # Given
+    settings.CLICKHOUSE_ENABLED = True
+    mock_tombstone_task = mocker.MagicMock()
+    mocker.patch(
+        "segment_membership.tasks.write_identity_deletion_tombstone_to_clickhouse",
+        mock_tombstone_task,
+    )
+
+    # When
+    edge_identity_model.delete()
+
+    # Then
+    edge_identity_dynamo_wrapper_mock.delete_item.assert_called_once()
+    mock_tombstone_task.delay.assert_called_once_with(
+        args=(
+            edge_identity_model.environment_api_key,
+            edge_identity_model.identifier,
+            edge_identity_model.engine_identity_model.composite_key,
+        )
+    )
+
+
+def test_edge_identity_delete__clickhouse_disabled__no_tombstone_dispatched(
+    mocker: MockerFixture,
+    edge_identity_model: EdgeIdentity,
+    edge_identity_dynamo_wrapper_mock: MagicMock,
+    settings: SettingsWrapper,
+) -> None:
+    # Given
+    settings.CLICKHOUSE_ENABLED = False
+    mock_tombstone_task = mocker.MagicMock()
+    mocker.patch(
+        "segment_membership.tasks.write_identity_deletion_tombstone_to_clickhouse",
+        mock_tombstone_task,
+    )
+
+    # When
+    edge_identity_model.delete()
+
+    # Then
+    edge_identity_dynamo_wrapper_mock.delete_item.assert_called_once()
+    mock_tombstone_task.delay.assert_not_called()
+
+
 def test_get_all_feature_states__post_v2_versioning_migration__returns_latest_overrides(
     environment: Environment,
     feature: Feature,

api/tests/unit/segment_membership/test_unit_segment_membership_mappers.py

@@ -22,7 +22,7 @@
                     {"trait_key": "plan", "trait_value": "growth"},
                 ],
             },
-            ("env-key", "alice", "env_x_alice", {"plan": "growth"}),
+            ("env-key", "alice", "env_x_alice", {"plan": "growth"}, False),
             id="single string trait",
         ),
         pytest.param(
@@ -34,7 +34,7 @@
                 "created_date": "2026-05-08T00:00:00Z",
                 "identity_traits": [],
             },
-            ("env-key", "alice", "env_x_alice", None),
+            ("env-key", "alice", "env_x_alice", None, False),
             id="empty traits collapse to NULL",
         ),
         pytest.param(
@@ -48,7 +48,7 @@
                     {"trait_key": "age", "trait_value": Decimal("18")},
                 ],
             },
-            ("env-key", "alice", "env_x_alice", {"age": 18}),
+            ("env-key", "alice", "env_x_alice", {"age": 18}, False),
             id="whole-number Decimal narrows to int",
         ),
         pytest.param(
@@ -62,7 +62,7 @@
                     {"trait_key": "score", "trait_value": Decimal("1.5")},
                 ],
             },
-            ("env-key", "alice", "env_x_alice", {"score": 1.5}),
+            ("env-key", "alice", "env_x_alice", {"score": 1.5}, False),
             id="fractional Decimal narrows to float",
         ),
         pytest.param(
@@ -82,16 +82,35 @@
                 "alice",
                 "env_x_alice",
                 {"plan": "growth", "team": "alpha"},
+                False,
             ),
             id="multiple traits flatten to a single dict",
         ),
     ],
 )
 def test_map_identity_document_to_clickhouse_row__cases__return_expected(
     doc: DynamoIdentity,
-    expected: tuple[str, str, str, dict[str, object] | None],
+    expected: tuple[str, str, str, dict[str, object] | None, bool],
 ) -> None:
     # Given a Dynamo identity document
     # When mapped onto an IDENTITIES row
     # Then it lines up positionally with the IDENTITIES schema
     assert map_identity_document_to_clickhouse_row("env-key", doc) == expected
+
+
+def test_map_identity_document_to_clickhouse_row__is_deleted_true__sets_flag() -> None:
+    # Given a Dynamo identity document and is_deleted=True
+    doc: DynamoIdentity = {
+        "identity_uuid": UUID_A,
+        "identifier": "alice",
+        "environment_api_key": "env-key",
+        "composite_key": "env_x_alice",
+        "created_date": "2026-05-08T00:00:00Z",
+        "identity_traits": [],
+    }
+
+    # When mapped with is_deleted=True
+    result = map_identity_document_to_clickhouse_row("env-key", doc, is_deleted=True)
+
+    # Then the flag is set in the returned tuple
+    assert result == ("env-key", "alice", "env_x_alice", None, True)