rename u19 etl (#192)

* rename u19 etl

* linters

docs/source/conf.py

@@ -2,9 +2,10 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-from pathlib import Path
 from datetime import date
 from os.path import abspath, dirname
+from pathlib import Path
+
 from aind_metadata_mapper import __version__ as package_version
 
 INSTITUTE_NAME = "Allen Institute for Neural Dynamics"

src/aind_metadata_mapper/bruker/models.py

@@ -1,4 +1,5 @@
 """Module defining JobSettings for Bruker ETL"""
+
 from pathlib import Path
 from typing import List, Literal, Optional, Union
 

src/aind_metadata_mapper/bruker/session.py

@@ -1,4 +1,5 @@
 """Sets up the MRI ingest ETL"""
+
 import argparse
 import json
 import logging

src/aind_metadata_mapper/mesoscope/session.py

@@ -1,4 +1,5 @@
 """Mesoscope ETL"""
+
 import argparse
 import json
 import logging

src/aind_metadata_mapper/models.py

@@ -1,4 +1,5 @@
 """Module to define models for Gather Metadata Job"""
+
 from pathlib import Path
 from typing import List, Literal, Optional, Union
 

src/aind_metadata_mapper/open_ephys/camstim_ephys_session.py

@@ -107,8 +107,8 @@ def __init__(
             logger.debug("building stim table")
             self.build_stimulus_table()
         if self.opto_pkl_path.exists() and (
-            not self.opto_table_path.exists() or
-            self.job_settings.overwrite_tables
+            not self.opto_table_path.exists()
+            or self.job_settings.overwrite_tables
         ):
             logger.debug("building opto table")
             self.build_optogenetics_table()

src/aind_metadata_mapper/open_ephys/models.py

@@ -1,7 +1,8 @@
 """Module defining JobSettings for Mesoscope ETL"""
 
-from typing import Literal, Union
 from pathlib import Path
+from typing import Literal, Union
+
 from aind_metadata_mapper.core_models import BaseJobSettings
 
 DEFAULT_OPTO_CONDITIONS = {

src/aind_metadata_mapper/smartspim/models.py

@@ -1,4 +1,5 @@
 """Module defining JobSettings for SmartSPIM ETL"""
+
 from pathlib import Path
 from typing import Literal, Optional, Union
 

src/aind_metadata_mapper/stimulus/camstim.py

@@ -49,7 +49,7 @@ def __init__(
         else:
             self.opto_conditions_map = self.job_settings["opto_conditions_map"]
 
-        sessions_root = Path(self.job_settings.get('sessions_root'))
+        sessions_root = Path(self.job_settings.get("sessions_root"))
         self.session_path = self.get_session_path(session_id, sessions_root)
         self.folder = self.get_folder(session_id, sessions_root)
 
@@ -79,14 +79,14 @@ def __init__(
 
         if (
             not self.stim_table_path.exists()
-            or self.job_settings['overwrite_tables']
+            or self.job_settings["overwrite_tables"]
         ):
             print("building stim table")
             self.build_stimulus_table()
         if (
             self.opto_pkl_path.exists()
             and not self.opto_table_path.exists()
-            or self.job_settings['overwrite_tables']
+            or self.job_settings["overwrite_tables"]
         ):
             print("building opto table")
             self.build_optogenetics_table()

src/aind_metadata_mapper/u19/models.py

@@ -1,4 +1,5 @@
 """Defines Job Settings for U19 ETL"""
+
 from pathlib import Path
 from typing import List, Literal, Optional, Union
 

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
@@ -92,9 +92,9 @@ def _transform(self, existing_procedure, subj_id):
             if row is None:
                 logging.warning(f"Could not find row for {subj_id}")
                 return
-            existing_procedure[
-                "specimen_procedures"
-            ] = self.extract_spec_procedures(subj_id, row)
+            existing_procedure["specimen_procedures"] = (
+                self.extract_spec_procedures(subj_id, row)
+            )
 
             return construct_new_model(
                 existing_procedure,
@@ -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/integration/bergamo/session.py

@@ -8,6 +8,7 @@
 from pathlib import Path
 
 from aind_data_schema.core.session import Session
+
 from aind_metadata_mapper.bergamo.models import JobSettings
 from aind_metadata_mapper.bergamo.session import BergamoEtl
 

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 +62,33 @@ 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 +99,7 @@ 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 +118,18 @@ 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 +145,7 @@ 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 +162,7 @@ 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 +175,7 @@ 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 +197,7 @@ 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_bergamo/test_session.py

@@ -9,6 +9,7 @@
 from unittest.mock import MagicMock, patch
 
 from aind_data_schema.core.session import Session
+
 from aind_metadata_mapper.bergamo.session import BergamoEtl, JobSettings
 
 RESOURCES_DIR = (

tests/test_bruker/test_session.py

@@ -17,6 +17,7 @@
     ScannerLocation,
 )
 from aind_data_schema.core.session import Session
+
 from aind_metadata_mapper.bruker.session import JobSettings, MRIEtl
 
 RESOURCES_DIR = (

tests/test_dynamic_routing/test_mvr_rig.py

@@ -1,12 +1,13 @@
 """Tests for the MVR rig ETL."""
 
-import os
 import json
+import os
 import unittest
 from pathlib import Path
 from unittest.mock import MagicMock, patch
 
 from aind_data_schema.core.rig import Rig
+
 from aind_metadata_mapper.dynamic_routing.mvr_rig import (  # type: ignore
     MvrRigEtl,
 )

tests/test_dynamic_routing/test_sync_rig.py

@@ -1,15 +1,16 @@
 """Tests for Sync rig ETL."""
 
-import os
 import json
+import os
 import unittest
 from pathlib import Path
 from unittest.mock import MagicMock, patch
 
+from aind_data_schema.core.rig import Rig
+
 from aind_metadata_mapper.dynamic_routing.sync_rig import (  # type: ignore
     SyncRigEtl,
 )
-from aind_data_schema.core.rig import Rig
 
 RESOURCES_DIR = (
     Path(os.path.dirname(os.path.realpath(__file__)))

tests/test_open_ephys/test_rig.py

@@ -1,7 +1,7 @@
 """Tests for the dynamic_routing open open_ephys rig ETL."""
 
-import os
 import json
+import os
 import unittest
 from pathlib import Path
 from unittest.mock import MagicMock, patch

tests/test_open_ephys/test_utils/test_stim_utils.py

@@ -142,8 +142,8 @@ def test_get_stimulus_image_name(self):
             "image_path_list": [
                 "somepath\\passive\\image1.jpg",
                 "somepath\\passive\\image2.jpg",
-                "somepath\\passive\\image3.jpg"
-            ]
+                "somepath\\passive\\image3.jpg",
+            ],
         }
 
         # Expected image names