Merge pull request #1789 from AllenInstitute/1769-modify-behavior-ophys-inheritence

1769 modify behavior ophys inheritence

Author: njmei

allensdk/brain_observatory/behavior/behavior_ophys_api/__init__.py

@@ -6,9 +6,8 @@
 
 
 from allensdk.brain_observatory.session_api_utils import ParamsMixin
-from allensdk.internal.api.behavior_ophys_api import BehaviorOphysLimsApi
-from allensdk.brain_observatory.behavior.behavior_ophys_api\
-    .behavior_ophys_nwb_api import BehaviorOphysNwbApi
+from allensdk.brain_observatory.behavior.session_apis.data_io import (
+    BehaviorOphysNwbApi, BehaviorOphysLimsApi)
 from allensdk.deprecated import legacy
 from allensdk.brain_observatory.behavior.trials_processing import (
     calculate_reward_rate)

allensdk/brain_observatory/behavior/behavior_ophys_session.py

@@ -6,10 +6,10 @@
 
 from allensdk.api.cache import Cache
 
-from allensdk.brain_observatory.behavior.behavior_project_lims_api import (
+from allensdk.brain_observatory.behavior.project_apis.data_io import (
     BehaviorProjectLimsApi)
-from allensdk.brain_observatory.behavior.internal.behavior_project_base\
-    import BehaviorProjectBase
+from allensdk.brain_observatory.behavior.project_apis.abcs import (
+    BehaviorProjectBase)
 from allensdk.api.caching_utilities import one_file_call_caching, call_caching
 from allensdk.core.authentication import DbCredentials
 

allensdk/brain_observatory/behavior/behavior_project_cache.py

@@ -4,14 +4,15 @@
 import numpy as np
 import inspect
 
-from allensdk.internal.api.behavior_data_lims_api import BehaviorDataLimsApi
-from allensdk.brain_observatory.behavior.internal import BehaviorBase
+from allensdk.brain_observatory.behavior.session_apis.data_io import (
+    BehaviorLimsApi)
+from allensdk.brain_observatory.behavior.session_apis.abcs import BehaviorBase
 from allensdk.brain_observatory.running_speed import RunningSpeed
 
 BehaviorDataApi = Type[BehaviorBase]
 
 
-class BehaviorDataSession(object):
+class BehaviorSession(object):
     def __init__(self, api: Optional[BehaviorDataApi] = None):
         self.api = api
         # Initialize attributes to be lazily evaluated
@@ -29,12 +30,12 @@ def __init__(self, api: Optional[BehaviorDataApi] = None):
         self._metadata = None
 
     @classmethod
-    def from_lims(cls, behavior_session_id: int) -> "BehaviorDataSession":
-        return cls(api=BehaviorDataLimsApi(behavior_session_id))
+    def from_lims(cls, behavior_session_id: int) -> "BehaviorSession":
+        return cls(api=BehaviorLimsApi(behavior_session_id))
 
     @classmethod
     def from_nwb_path(
-            cls, nwb_path: str, **api_kwargs: Any) -> "BehaviorDataSession":
+            cls, nwb_path: str, **api_kwargs: Any) -> "BehaviorSession":
         return NotImplementedError
 
     @property
@@ -301,7 +302,7 @@ def cache_clear(self) -> None:
     def list_api_methods(self) -> List[Tuple[str, str]]:
         """Convenience method to expose list of API `get` methods. These methods
         can be accessed by referencing the API used to initialize this
-        BehaviorDataSession via its `api` instance attribute.
+        BehaviorSession via its `api` instance attribute.
         :rtype: list of tuples, where the first value in the tuple is the
         method name, and the second value is the method docstring.
         """

…vatory/behavior/behavior_data_session.py …observatory/behavior/behavior_session.pyallensdk/brain_observatory/behavior/behavior_data_session.py renamed to allensdk/brain_observatory/behavior/behavior_session.py allensdk/brain_observatory/behavior/behavior_data_session.py renamed to allensdk/brain_observatory/behavior/behavior_session.py

@@ -0,0 +1 @@
+from allensdk.brain_observatory.behavior.project_apis.abcs.behavior_project_base import BehaviorProjectBase  # noqa: F401, E501

allensdk/brain_observatory/behavior/internal/__init__.py

@@ -3,8 +3,8 @@
 
 from allensdk.brain_observatory.behavior.behavior_ophys_session import (
     BehaviorOphysSession)
-from allensdk.brain_observatory.behavior.behavior_data_session import (
-    BehaviorDataSession)
+from allensdk.brain_observatory.behavior.behavior_session import (
+    BehaviorSession)
 import pandas as pd
 
 
@@ -27,12 +27,12 @@ def get_session_table(self) -> pd.DataFrame:
 
     @abstractmethod
     def get_behavior_only_session_data(
-            self, behavior_session_id: int) -> BehaviorDataSession:
-        """Returns a BehaviorDataSession object that contains methods to
+            self, behavior_session_id: int) -> BehaviorSession:
+        """Returns a BehaviorSession object that contains methods to
         analyze a single behavior session.
         :param behavior_session_id: id that corresponds to a behavior session
         :type behavior_session_id: int
-        :rtype: BehaviorDataSession
+        :rtype: BehaviorSession
         """
         pass
 

allensdk/brain_observatory/behavior/project_apis/abcs/__init__.py

@@ -0,0 +1 @@
+from allensdk.brain_observatory.behavior.project_apis.data_io.behavior_project_lims_api import BehaviorProjectLimsApi  # noqa: F401, E501

…havior/internal/behavior_project_base.py …oject_apis/abcs/behavior_project_base.pyallensdk/brain_observatory/behavior/internal/behavior_project_base.py renamed to allensdk/brain_observatory/behavior/project_apis/abcs/behavior_project_base.py allensdk/brain_observatory/behavior/internal/behavior_project_base.py renamed to allensdk/brain_observatory/behavior/project_apis/abcs/behavior_project_base.py

@@ -2,19 +2,19 @@
 from typing import Optional, List, Dict, Any, Iterable
 import logging
 
-from allensdk.brain_observatory.behavior.internal.behavior_project_base\
-    import BehaviorProjectBase
-from allensdk.brain_observatory.behavior.behavior_data_session import (
-    BehaviorDataSession)
+from allensdk.brain_observatory.behavior.project_apis.abcs import (
+    BehaviorProjectBase)
+from allensdk.brain_observatory.behavior.behavior_session import (
+    BehaviorSession)
 from allensdk.brain_observatory.behavior.behavior_ophys_session import (
     BehaviorOphysSession)
-from allensdk.internal.api.behavior_data_lims_api import BehaviorDataLimsApi
-from allensdk.internal.api.behavior_ophys_api import BehaviorOphysLimsApi
-from allensdk.internal.api import PostgresQueryMixin
+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)
 from allensdk.core.typing import SupportsStr
-from allensdk.core.authentication import DbCredentials, credential_injector
+from allensdk.core.authentication import DbCredentials
 from allensdk.core.auth_config import (
     MTRAIN_DB_CREDENTIAL_MAP, LIMS_DB_CREDENTIAL_MAP)
 
@@ -96,26 +96,13 @@ def default(
         _app_kwargs = {"scheme": "http", "host": "lims2"}
         if app_kwargs:
             _app_kwargs.update(app_kwargs)
-        if lims_credentials:
-            lims_engine = PostgresQueryMixin(
-                dbname=lims_credentials.dbname, user=lims_credentials.user,
-                host=lims_credentials.host, password=lims_credentials.password,
-                port=lims_credentials.port)
-        else:
-            # Currying is equivalent to decorator syntactic sugar
-            lims_engine = (credential_injector(LIMS_DB_CREDENTIAL_MAP)
-                           (PostgresQueryMixin)())
-
-        if mtrain_credentials:
-            mtrain_engine = PostgresQueryMixin(
-                dbname=mtrain_credentials.dbname, user=mtrain_credentials.user,
-                host=mtrain_credentials.host, password=mtrain_credentials.password,
-                port=mtrain_credentials.port)
-        else:
-            # Currying is equivalent to decorator syntactic sugar
-            mtrain_engine = (
-                credential_injector(MTRAIN_DB_CREDENTIAL_MAP)
-                (PostgresQueryMixin)())
+
+        lims_engine = db_connection_creator(
+            credentials=lims_credentials,
+            fallback_credentials=LIMS_DB_CREDENTIAL_MAP)
+        mtrain_engine = db_connection_creator(
+            credentials=mtrain_credentials,
+            fallback_credentials=MTRAIN_DB_CREDENTIAL_MAP)
 
         app_engine = HttpEngine(**_app_kwargs)
         return cls(lims_engine, mtrain_engine, app_engine)
@@ -430,14 +417,14 @@ def get_session_table(
         return table
 
     def get_behavior_only_session_data(
-            self, behavior_session_id: int) -> BehaviorDataSession:
-        """Returns a BehaviorDataSession object that contains methods to
+            self, behavior_session_id: int) -> BehaviorSession:
+        """Returns a BehaviorSession object that contains methods to
         analyze a single behavior session.
         :param behavior_session_id: id that corresponds to a behavior session
         :type behavior_session_id: int
-        :rtype: BehaviorDataSession
+        :rtype: BehaviorSession
         """
-        return BehaviorDataSession(BehaviorDataLimsApi(behavior_session_id))
+        return BehaviorSession(BehaviorLimsApi(behavior_session_id))
 
     def get_experiment_table(
             self,

allensdk/brain_observatory/behavior/project_apis/data_io/__init__.py

@@ -0,0 +1,2 @@
+from allensdk.brain_observatory.behavior.session_apis.abcs.behavior_base import BehaviorBase  # noqa: F401, E501
+from allensdk.brain_observatory.behavior.session_apis.abcs.behavior_ophys_base import BehaviorOphysBase  # noqa: F401, E501