Merge pull request #2187 from AllenInstitute/rc/2.13.0

rc/2.13.0

CHANGELOG.md

@@ -1,6 +1,9 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.13.0] = 2021-09-22
+- Major internal refactor to BehaviorSession, BehaviorOphysExperiment classes. Implements DataObject pattern for fetching and serialization of data.
+
 ## [2.12.4] = 2021-09-21
 - Documentation changes ahead of SWDB 2021
 - Bugfix to CloudCache; it is now possible for multiple users to share a cache.

allensdk/__init__.py

@@ -35,7 +35,7 @@
 #
 import logging
 
-__version__ = '2.12.4'
+__version__ = '2.13.0'
 
 
 try:

allensdk/brain_observatory/behavior/behavior_project_cache/project_apis/data_io/behavior_project_cloud_api.py

@@ -271,7 +271,8 @@ def get_behavior_ophys_experiment(self, ophys_experiment_id: int
                                f" there are {row.shape[0]} entries.")
         file_id = str(int(row[self.cache.file_id_column]))
         data_path = self._get_data_path(file_id=file_id)
-        return BehaviorOphysExperiment.from_nwb_path(str(data_path))
+        return BehaviorOphysExperiment.from_nwb_path(
+            str(data_path))
 
     def _get_ophys_session_table(self):
         session_table_path = self._get_metadata_path(

allensdk/brain_observatory/behavior/behavior_project_cache/project_apis/data_io/behavior_project_lims_api.py

@@ -7,8 +7,6 @@
     BehaviorSession)
 from allensdk.brain_observatory.behavior.behavior_ophys_experiment import (
     BehaviorOphysExperiment)
-from allensdk.brain_observatory.behavior.session_apis.data_io import (
-    BehaviorLimsApi, BehaviorOphysLimsApi)
 from allensdk.internal.api import db_connection_creator
 from allensdk.brain_observatory.ecephys.ecephys_project_api.http_engine \
     import (HttpEngine)
@@ -327,8 +325,8 @@ def get_behavior_ophys_experiment(self, ophys_experiment_id: int
         :type ophys_experiment_id: int
         :rtype: BehaviorOphysExperiment
         """
-        return BehaviorOphysExperiment(
-                BehaviorOphysLimsApi(ophys_experiment_id))
+        return BehaviorOphysExperiment.from_lims(
+            ophys_experiment_id=ophys_experiment_id)
 
     def _get_ophys_experiment_table(self) -> pd.DataFrame:
         """
@@ -484,7 +482,8 @@ def get_behavior_session(
         :type behavior_session_id: int
         :rtype: BehaviorSession
         """
-        return BehaviorSession(BehaviorLimsApi(behavior_session_id))
+        return BehaviorSession.from_lims(
+            behavior_session_id=behavior_session_id)
 
     def get_ophys_experiment_table(
             self,

allensdk/brain_observatory/behavior/behavior_project_cache/tables/sessions_table.py

@@ -13,10 +13,16 @@
 from allensdk.brain_observatory.behavior.behavior_project_cache.tables \
     .project_table import \
     ProjectTable
-from allensdk.brain_observatory.behavior.metadata.behavior_metadata import \
-    BehaviorMetadata
 from allensdk.brain_observatory.behavior.behavior_project_cache.project_apis.data_io import BehaviorProjectLimsApi  # noqa: E501
 
+from allensdk.brain_observatory.behavior.data_objects.metadata\
+    .subject_metadata.full_genotype import \
+    FullGenotype
+
+from allensdk.brain_observatory.behavior.data_objects.metadata\
+    .subject_metadata.reporter_line import \
+    ReporterLine
+
 
 class SessionsTable(ProjectTable):
     """Class for storing and manipulating project-level data
@@ -45,11 +51,11 @@ def __init__(
 
     def postprocess_additional(self):
         self._df['reporter_line'] = self._df['reporter_line'].apply(
-            BehaviorMetadata.parse_reporter_line)
+            ReporterLine.parse)
         self._df['cre_line'] = self._df['full_genotype'].apply(
-            BehaviorMetadata.parse_cre_line)
+            lambda x: FullGenotype(x).parse_cre_line())
         self._df['indicator'] = self._df['reporter_line'].apply(
-            BehaviorMetadata.parse_indicator)
+            lambda x: ReporterLine(x).parse_indicator())
 
         self.__add_session_number()