rename U19Etl

pyproject.toml

@@ -18,7 +18,8 @@ dynamic = ["version"]
 
 dependencies = [
     "aind-data-schema-models>=0.3.2",
-    "pydantic-settings>=2.0"
+    "pydantic-settings>=2.0",
+    "aind-data-schema==1.0.0"
 ]
 
 [project.optional-dependencies]

src/aind_metadata_mapper/u19/procedures.py

@@ -34,7 +34,7 @@ def strings_to_dates(strings):
     return [date1, date2]
 
 
-class U19Etl(GenericEtl[JobSettings]):
+class SmartSPIMSpecimenIngester(GenericEtl[JobSettings]):
     """U19 ETL class."""
 
     # TODO: Deprecate this constructor. Use GenericEtl constructor instead
@@ -423,5 +423,5 @@ def extract_spec_procedures(self, subj_id, row):  # noqa: C901
 if __name__ == "__main__":
     sys_args = sys.argv[1:]
     main_job_settings = JobSettings.from_args(sys_args)
-    etl = U19Etl(job_settings=main_job_settings)
+    etl = SmartSPIMSpecimenIngester(job_settings=main_job_settings)
     etl.run_job()

tests/test_U19/test_procedures.py

@@ -18,7 +18,7 @@
 
 from aind_metadata_mapper.u19.models import JobSettings
 from aind_metadata_mapper.u19.procedures import (
-    U19Etl,
+    SmartSPIMSpecimenIngester,
     get_dates,
     strings_to_dates,
 )
@@ -62,31 +62,35 @@ def setUpClass(self):
         )
 
     @patch(
-        "aind_metadata_mapper.u19.procedures.U19Etl.download_procedure_file"
+        "aind_metadata_mapper.u19."
+        "procedures.SmartSPIMSpecimenIngester."
+        "download_procedure_file"
     )
     def test_run_job(self, mock_download_procedure):
         """Test run_job method."""
 
         with open(EXAMPLE_DOWNLOAD_PROCEDURE, "r") as f:
             mock_download_procedure.return_value = json.load(f)
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         job_response = etl.run_job()
 
         actual_output = json.loads(job_response.data)
 
         self.assertEqual(self.example_output, actual_output)
 
     @patch(
-        "aind_metadata_mapper.u19.procedures.U19Etl.download_procedure_file"
+        "aind_metadata_mapper.u19."
+        "procedures.SmartSPIMSpecimenIngester."
+        "download_procedure_file"
     )
     def test_extract(self, mock_download_procedure):
         """Test extract method."""
 
         with open(EXAMPLE_DOWNLOAD_PROCEDURE, "r") as f:
             mock_download_procedure.return_value = json.load(f)
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         extracted = etl._extract(self.example_job_settings.subject_to_ingest)
 
         self.assertEqual(
@@ -97,7 +101,7 @@ def test_extract(self, mock_download_procedure):
     def test_transform(self):
         """Test transform method."""
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         etl.load_specimen_procedure_file()
 
         with open(EXAMPLE_DOWNLOAD_PROCEDURE, "r") as f:
@@ -116,15 +120,18 @@ def test_transform(self):
             ),
         )
 
-    @patch("aind_metadata_mapper.u19.procedures.U19Etl._transform")
+    @patch(
+        "aind_metadata_mapper.u19.procedures."
+        "SmartSPIMSpecimenIngester._transform"
+    )
     def test_load(self, mock_transform):
         """Test load method."""
 
         mock_transform.return_value = construct_new_model(
             self.example_output, Procedures, True
         )
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         transformed = etl._transform(
             self.example_job_settings.subject_to_ingest
         )
@@ -140,7 +147,7 @@ def test_load(self, mock_transform):
     def test_find_sheet_row(self):
         """Test find_sheet_row method."""
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         etl.load_specimen_procedure_file()
         row = etl.find_sheet_row(self.example_job_settings.subject_to_ingest)
 
@@ -157,7 +164,7 @@ def test_download_procedure_file(self, mock_requests):
             )
             mock_requests.return_value.status_code = 200
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         response = etl.download_procedure_file(
             self.example_job_settings.subject_to_ingest
         )
@@ -170,7 +177,7 @@ def test_download_procedure_file(self, mock_requests):
     def test_load_specimen_procedure_file(self):
         """Test load_specimen_procedure_file method."""
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         etl.load_specimen_procedure_file()
 
         self.assertTrue(len(etl.tissue_sheets) == 2)
@@ -192,7 +199,7 @@ def test_strings_to_dates(self):
     def test_extract_spec_procedures(self):
         """Test extract_spec_procedures method."""
 
-        etl = U19Etl(self.example_job_settings)
+        etl = SmartSPIMSpecimenIngester(self.example_job_settings)
         etl.load_specimen_procedure_file()
 
         row = etl.find_sheet_row(self.example_job_settings.subject_to_ingest)

tests/test_open_ephys/test_utils/test_behavior_utils.py

@@ -475,7 +475,7 @@ def test_get_visual_stimuli_df(
         expected_df = pd.DataFrame(expected_data, columns=expected_columns)
 
         # Perform assertions
-        self.assertEquals(result_df["time"].all(), expected_df["time"].all())
+        self.assertEqual(result_df["time"].all(), expected_df["time"].all())
 
     def test_get_image_names(self):
         """
@@ -870,7 +870,7 @@ def test_fingerprint_from_stimulus_file(self):
         expected_df = pd.DataFrame(expected_data, columns=expected_columns)
 
         # Assert that the result matches the expected DataFrame
-        self.assertEquals(
+        self.assertEqual(
             expected_df["movie_frame_index"].values.tolist(),
             result["movie_frame_index"].values.tolist(),
         )
@@ -1036,7 +1036,7 @@ def test_from_stimulus_file(
         expected_df = pd.DataFrame(expected_data, columns=expected_columns)
 
         # Assert that the result matches the expected DataFrame
-        self.assertEquals(
+        self.assertEqual(
             expected_df["start_time"].all(), result["start_time"].all()
         )
 
@@ -1086,23 +1086,23 @@ def test_postprocess(self):
 
         processed_presentations = pd.DataFrame(processed_presentations)
         # Assert that the result matches the expected DataFrame
-        self.assertEquals(
+        self.assertEqual(
             expected_df["duration"].all(),
             processed_presentations["duration"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             expected_df["start_time"].all(),
             processed_presentations["start_time"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             expected_df["image_name"].all(),
             processed_presentations["image_name"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             expected_df["omitted"].all(),
             processed_presentations["omitted"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             expected_df["boolean_col"].all(),
             processed_presentations["boolean_col"].all(),
         )
@@ -1130,7 +1130,7 @@ def test_check_for_errant_omitted_stimulus(self):
         }
         expected_df = pd.DataFrame(expected_data)
         # Assert that the result matches the expected DataFrame
-        self.assertEquals(
+        self.assertEqual(
             processed_df["omitted"].all(), expected_df["omitted"].all()
         )
 
@@ -1200,7 +1200,7 @@ def test_get_spontaneous_stimulus(self):
         expected_df = pd.DataFrame(expected_data)
 
         # Assert that the result matches the expected DataFrame
-        self.assertEquals(
+        self.assertEqual(
             processed_df["start_frame"].all(), expected_df["start_frame"].all()
         )
 
@@ -1261,7 +1261,7 @@ def test_add_fingerprint_stimulus(self):
         expected_df = pd.DataFrame(expected_data)
 
         # Assert that the result matches the expected DataFrame
-        self.assertEquals(
+        self.assertEqual(
             processed_df["start_frame"].all(), expected_df["start_frame"].all()
         )
 

tests/test_open_ephys/test_utils/test_stim_utils.py

@@ -304,19 +304,19 @@ def mock_spontaneous_activity_tabler(stimulus_tables):
             mock_stimulus_tabler,
             mock_spontaneous_activity_tabler,
         )
-        self.assertEquals(
+        self.assertEqual(
             result_stim_table_full["start_time"].all(),
             expected_stim_table_full["start_time"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             result_stim_table_full["end_time"].all(),
             expected_stim_table_full["end_time"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             result_stim_table_full["stim_param"].all(),
             expected_stim_table_full["stim_param"].all(),
         )
-        self.assertEquals(
+        self.assertEqual(
             result_stim_table_full["stim_block"].all(),
             expected_stim_table_full["stim_block"].all(),
         )