From 219029b45e36e71fa27559f9822f2b93d22640d1 Mon Sep 17 00:00:00 2001
From: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com>
Date: Mon, 11 Nov 2024 11:43:02 +0100
Subject: [PATCH] 3714 Validate sample sex in cg add relationship Command
 (#3863)

Added
A check to check sex for father and mother for the CLI command add relationship
Added a test to test if sex is incorrect, mother having sex = male, etc.

Changed
Command add relationship will now be sex sensitive, and mother needs to have sex female, father needs to have sex male.

Fixed
This will fix situations when prod needs to add a relationship manually.
---
 cg/cli/add.py                              |  8 +++
 tests/cli/add/test_cli_add_relationship.py | 73 ++++++++++++++++++++++
 2 files changed, 81 insertions(+)

diff --git a/cg/cli/add.py b/cg/cli/add.py
index ce0c8cf505..86a097a0bf 100644
--- a/cg/cli/add.py
+++ b/cg/cli/add.py
@@ -337,12 +337,20 @@ def link_sample_to_case(
             LOG.error(f"{mother_id}: mother not found")
             raise click.Abort
 
+        if mother.sex != Sex.FEMALE:
+            LOG.error(f"{mother_id}: mother is not {Sex.FEMALE}")
+            raise click.Abort
+
     if father_id:
         father: Sample = status_db.get_sample_by_internal_id(internal_id=father_id)
         if father is None:
             LOG.error(f"{father_id}: father not found")
             raise click.Abort
 
+        if father.sex != Sex.MALE:
+            LOG.error(f"{father_id}: father is not {Sex.MALE}")
+            raise click.Abort
+
     new_record: CaseSample = status_db.relate_sample(
         case=case_obj, sample=sample, status=status, mother=mother, father=father
     )
diff --git a/tests/cli/add/test_cli_add_relationship.py b/tests/cli/add/test_cli_add_relationship.py
index c11a33c3bb..bc0b960964 100644
--- a/tests/cli/add/test_cli_add_relationship.py
+++ b/tests/cli/add/test_cli_add_relationship.py
@@ -3,6 +3,7 @@
 from click.testing import CliRunner
 
 from cg.cli.add import add
+from cg.constants import EXIT_FAIL
 from cg.constants.subject import Sex
 from cg.models.cg_config import CGConfig
 from cg.store.models import CaseSample
@@ -257,3 +258,75 @@ def test_add_relationship_bad_father(
     # THEN it should not be added
     assert result.exit_code == 1
     assert disk_store._get_query(table=CaseSample).count() == 0
+
+
+def test_add_relationship_mother_not_female(
+    cli_runner: CliRunner, base_context: CGConfig, helpers: StoreHelpers
+):
+    """Test to add a relationship where the mother is not female"""
+    # GIVEN a database with a sample, a case, and a male sample labeled as mother
+    disk_store: Store = base_context.status_db
+    sample: Sample = helpers.add_sample(disk_store)
+    sample_id: str = sample.internal_id
+
+    male_mother: Sample = helpers.add_sample(disk_store, sex=Sex.MALE, name="mother")
+    male_mother_id: str = male_mother.internal_id
+
+    case: Case = helpers.add_case(disk_store)
+    case_id: str = case.internal_id
+    status = "affected"
+
+    # WHEN adding a relationship with a male mother
+    result = cli_runner.invoke(
+        add,
+        [
+            "relationship",
+            case_id,
+            sample_id,
+            "-s",
+            status,
+            "-m",
+            male_mother_id,
+        ],
+        obj=base_context,
+    )
+
+    # THEN it should fail because the mother is not female
+    assert result.exit_code == EXIT_FAIL
+    assert disk_store._get_query(table=CaseSample).count() == 0
+
+
+def test_add_relationship_father_not_male(
+    cli_runner: CliRunner, base_context: CGConfig, helpers: StoreHelpers
+):
+    """Test to add a relationship where the father is not male"""
+    # GIVEN a database with a sample, a case, and a female sample labeled as father
+    disk_store: Store = base_context.status_db
+    sample: Sample = helpers.add_sample(disk_store)
+    sample_id: str = sample.internal_id
+
+    female_father: Sample = helpers.add_sample(disk_store, sex=Sex.FEMALE, name="father")
+    female_father_id: str = female_father.internal_id
+
+    case: Case = helpers.add_case(disk_store)
+    case_id: str = case.internal_id
+    status = "affected"
+
+    # WHEN adding a relationship with a female father
+    result = cli_runner.invoke(
+        add,
+        [
+            "relationship",
+            case_id,
+            sample_id,
+            "-s",
+            status,
+            "-f",
+            female_father_id,
+        ],
+        obj=base_context,
+    )
+
+    # THEN it should fail because the father is not male
+    assert result.exit_code == EXIT_FAIL
+    assert disk_store._get_query(table=CaseSample).count() == 0