Add basic tests for scripts/create_custom_cohort.py

Fix the script's template_id type, reflecting CohortBody's corresponding
member's change from str to int in d705285.

scripts/create_custom_cohort.py

@@ -44,11 +44,11 @@ def main(
 
 
 def get_cohort_spec(
-    cohort_name: str, cohort_description: str, cohort_template_id: int
+    cohort_name: str, cohort_description: str, cohort_template_id: str
 ) -> CohortBody:
     """Get the cohort spec"""
 
-    cohort_body_spec: dict[str, int | str] = {}
+    cohort_body_spec: dict[str, str] = {}
 
     if cohort_name:
         cohort_body_spec['name'] = cohort_name
@@ -69,7 +69,7 @@ def get_cohort_spec(
     parser.add_argument('--name', type=str, help='The name of the cohort')
     parser.add_argument('--description', type=str, help='The description of the cohort')
     parser.add_argument(
-        '--template_id', required=False, type=int, help='The template id of the cohort'
+        '--template_id', required=False, type=str, help='The template id of the cohort'
     )
     parser.add_argument(
         '--projects',

test/test_cohort_builder.py

@@ -0,0 +1,82 @@
+from test.testbase import DbIsolatedTest, run_as_sync
+from unittest.mock import patch
+
+import metamist.model.cohort_body
+import metamist.model.cohort_criteria
+from metamist.models import CohortBody
+from models.utils.cohort_template_id_format import cohort_template_id_format
+from scripts.create_custom_cohort import get_cohort_spec, main
+
+
+class TestCohortBuilder(DbIsolatedTest):
+    """Test custom cohort builder script"""
+
+    @run_as_sync
+    async def setUp(self):
+        super().setUp()
+
+    @run_as_sync
+    async def test_get_cohort_spec(self):
+        """Test get_cohort_spec(), invoked by the creator script"""
+        ctemplate_id = cohort_template_id_format(28)
+        result = get_cohort_spec('My cohort', 'Describing the cohort', ctemplate_id)
+        self.assertIsInstance(result, metamist.model.cohort_body.CohortBody)
+        self.assertEqual(result.name, 'My cohort')
+        self.assertEqual(result.description, 'Describing the cohort')
+        self.assertEqual(result.template_id, ctemplate_id)
+
+    @run_as_sync
+    @patch('metamist.apis.CohortApi.create_cohort_from_criteria')
+    async def test_empty_main(self, mock):
+        """Test main with no criteria"""
+        mock.return_value = {'cohort_id': 'COH1', 'sequencing_group_ids': ['SG1', 'SG2']}
+        main(
+            project='greek-myth',
+            cohort_body_spec=CohortBody(name='Empty cohort', description='No criteria'),
+            projects=None,
+            sg_ids_internal=[],
+            excluded_sg_ids=[],
+            sg_technologies=[],
+            sg_platforms=[],
+            sg_types=[],
+            sample_types=[],
+            dry_run=False,
+        )
+        mock.assert_called_once()
+
+    @run_as_sync
+    @patch('metamist.apis.CohortApi.create_cohort_from_criteria')
+    async def test_epic_main(self, mock):
+        """Test"""
+        mock.return_value = {'cohort_id': 'COH2', 'sequencing_group_ids': ['SG3']}
+        main(
+            project='greek-myth',
+            cohort_body_spec=CohortBody(name='Epic cohort', description='Every criterion'),
+            projects=['alpha', 'beta'],
+            sg_ids_internal=['SG3'],
+            excluded_sg_ids=['SG1', 'SG2'],
+            sg_technologies=['short-read'],
+            sg_platforms=['illumina'],
+            sg_types=['genome'],
+            sample_types=['blood'],
+            dry_run=False,
+        )
+        mock.assert_called_once()
+        self.assertEqual(mock.call_args.kwargs['project'], 'greek-myth')
+
+        body = mock.call_args.kwargs['body_create_cohort_from_criteria']
+        spec = body['cohort_spec']
+        self.assertEqual(spec.name, 'Epic cohort')
+        self.assertEqual(spec.description, 'Every criterion')
+
+        criteria = body['cohort_criteria']
+        self.assertIsInstance(criteria, metamist.model.cohort_criteria.CohortCriteria)
+        self.assertListEqual(criteria.projects, ['alpha', 'beta'])
+        self.assertListEqual(criteria.sg_ids_internal, ['SG3'])
+        self.assertListEqual(criteria.excluded_sgs_internal, ['SG1', 'SG2'])
+        self.assertListEqual(criteria.sg_technology, ['short-read'])
+        self.assertListEqual(criteria.sg_platform, ['illumina'])
+        self.assertListEqual(criteria.sg_type, ['genome'])
+        self.assertListEqual(criteria.sample_types, ['blood'])
+
+        self.assertFalse(body['dry_run'])