Merge pull request #2179 from AllenInstitute/rc/2.11.3

rc/2.11.3

CHANGELOG.md

@@ -1,6 +1,8 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.11.3] = 2021-08-04
+- Bugfixes related to NWB creation for BehaviorSessions
 
 ## [2.11.2] = 2021-05-21
 - Fixed mkdir error for non-existing ecephys upload directory

allensdk/__init__.py

@@ -35,7 +35,7 @@
 #
 import logging
 
-__version__ = '2.11.2'
+__version__ = '2.11.3'
 
 
 try:

allensdk/brain_observatory/behavior/metadata/behavior_metadata.py

@@ -238,12 +238,6 @@ def reporter_line(self) -> Optional[str]:
         reporter_line = self._extractor.get_reporter_line()
         return self.parse_reporter_line(reporter_line=reporter_line, warn=True)
 
-    @property
-    def indicator(self) -> Optional[str]:
-        """Parses indicator from reporter"""
-        reporter_line = self.reporter_line
-        return self.parse_indicator(reporter_line=reporter_line, warn=True)
-
     @property
     def cre_line(self) -> Optional[str]:
         """Parses cre_line from full_genotype"""

allensdk/brain_observatory/behavior/metadata/behavior_ophys_metadata.py

@@ -25,6 +25,12 @@ def __init__(self, extractor: BehaviorOphysDataExtractorBase,
         # since it's only exposed internally
         self._exclude_from_equals = {'project_code'}
 
+    @property
+    def indicator(self) -> Optional[str]:
+        """Parses indicator from reporter"""
+        reporter_line = self.reporter_line
+        return self.parse_indicator(reporter_line=reporter_line, warn=True)
+
     @property
     def emission_lambda(self) -> float:
         return 520.0

allensdk/brain_observatory/behavior/session_apis/abcs/data_extractor_base/behavior_data_extractor_base.py

@@ -1,7 +1,10 @@
 import abc
+import pandas as pd
 from datetime import datetime
 from typing import List
 
+from allensdk.api.warehouse_cache.cache import memoize
+
 
 class BehaviorDataExtractorBase(abc.ABC):
     """Abstract base class implementing required methods for extracting
@@ -34,11 +37,25 @@ def get_age(self) -> str:
         """Get the age code of the subject (ie P123)"""
         raise NotImplementedError()
 
-    @abc.abstractmethod
+    @memoize
     def get_stimulus_name(self) -> str:
-        """Get the name of the stimulus presented for a behavior or
-        behavior + ophys experiment"""
-        raise NotImplementedError()
+        """Get the stimulus set used from the behavior session pkl file
+        :rtype: str
+        """
+        behavior_stimulus_path = self.get_behavior_stimulus_file()
+        pkl = pd.read_pickle(behavior_stimulus_path)
+
+        try:
+            stimulus_name = pkl["items"]["behavior"]["cl_params"]["stage"]
+        except KeyError:
+            raise RuntimeError(
+                f"Could not obtain stimulus_name/stage information from "
+                f"the *.pkl file ({behavior_stimulus_path}) "
+                f"for the behavior session to save as NWB! The "
+                f"following series of nested keys did not work: "
+                f"['items']['behavior']['cl_params']['stage']"
+            )
+        return stimulus_name
 
     @abc.abstractmethod
     def get_reporter_line(self) -> List[str]:

allensdk/brain_observatory/behavior/session_apis/data_io/behavior_json_api.py

@@ -51,10 +51,6 @@ def get_age(self) -> str:
         """Get the age code of the subject (ie P123)"""
         return self.data['age']
 
-    def get_stimulus_name(self) -> str:
-        """Get the name of the stimulus presented for the experiment"""
-        return self.data['stimulus_name']
-
     def get_reporter_line(self) -> str:
         """Get the (gene) reporter line for the subject associated with an
         experiment"""

allensdk/brain_observatory/behavior/session_apis/data_io/behavior_lims_api.py

@@ -4,8 +4,6 @@
 from typing import Dict, List, Optional, Union
 import pytz
 
-import pandas as pd
-
 from allensdk.api.warehouse_cache.cache import memoize
 from allensdk.brain_observatory.behavior.session_apis.abcs.\
     data_extractor_base.behavior_data_extractor_base import \
@@ -254,26 +252,6 @@ def get_equipment_name(self) -> str:
         """
         return self.lims_db.fetchone(query, strict=True)
 
-    @memoize
-    def get_stimulus_name(self) -> str:
-        """Get the stimulus set used from the behavior session pkl file
-        :rtype: str
-        """
-        behavior_stimulus_path = self.get_behavior_stimulus_file()
-        pkl = pd.read_pickle(behavior_stimulus_path)
-
-        try:
-            stimulus_name = pkl["items"]["behavior"]["cl_params"]["stage"]
-        except KeyError:
-            raise RuntimeError(
-                f"Could not obtain stimulus_name/stage information from "
-                f"the *.pkl file ({behavior_stimulus_path}) "
-                f"for the behavior session to save as NWB! The "
-                f"following series of nested keys did not work: "
-                f"['items']['behavior']['cl_params']['stage']"
-            )
-        return stimulus_name
-
     @memoize
     def get_reporter_line(self) -> List[str]:
         """Returns the genotype name(s) of the reporter line(s).

allensdk/brain_observatory/session_api_utils.py

@@ -17,6 +17,7 @@
 from allensdk.core.lazy_property import LazyProperty
 
 logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 def is_equal(a: Any, b: Any) -> bool:

allensdk/test/brain_observatory/behavior/test_behavior_metadata.py

@@ -246,7 +246,7 @@ def test_get_task_parameters_task_id_exception():
     }
 
     with pytest.raises(RuntimeError) as error:
-        _ = get_task_parameters(input_data)
+        get_task_parameters(input_data)
     assert "does not know how to parse 'task_id'" in error.value.args[0]
 
 
@@ -285,7 +285,7 @@ def test_get_task_parameters_flash_duration_exception():
     }
 
     with pytest.raises(RuntimeError) as error:
-        _ = get_task_parameters(input_data)
+        get_task_parameters(input_data)
     shld_be = "'images' and/or 'grating' not a valid key"
     assert shld_be in error.value.args[0]
 
@@ -585,57 +585,3 @@ def dummy_init(self, extractor, behavior_stimulus_file):
             obt_date = metadata.date_of_acquisition
 
         assert obt_date == extractor_expt_date
-
-
-def test_indicator(monkeypatch):
-    """Test that indicator is parsed from full_genotype"""
-
-    class MockExtractor:
-        def get_reporter_line(self):
-            return 'Ai148(TIT2L-GC6f-ICL-tTA2)'
-
-    extractor = MockExtractor()
-
-    with monkeypatch.context() as ctx:
-        def dummy_init(self):
-            self._extractor = extractor
-
-        ctx.setattr(BehaviorMetadata,
-                    '__init__',
-                    dummy_init)
-
-        metadata = BehaviorMetadata()
-
-        assert metadata.indicator == 'GCaMP6f'
-
-
-@pytest.mark.parametrize("input_reporter_line, warning_msg, expected", (
-        (None, 'Error parsing reporter line. It is null.', None),
-        ('foo', 'Could not parse indicator from reporter because none'
-                'of the expected substrings were found in the reporter', None)
-)
-                         )
-def test_indicator_edge_cases(monkeypatch, input_reporter_line, warning_msg,
-                              expected):
-    """Test indicator parsing edge cases"""
-
-    class MockExtractor:
-        def get_reporter_line(self):
-            return input_reporter_line
-
-    extractor = MockExtractor()
-
-    with monkeypatch.context() as ctx:
-        def dummy_init(self):
-            self._extractor = extractor
-
-        ctx.setattr(BehaviorMetadata,
-                    '__init__',
-                    dummy_init)
-
-        metadata = BehaviorMetadata()
-
-        with pytest.warns(UserWarning) as record:
-            indicator = metadata.indicator
-        assert indicator is expected
-        assert str(record[0].message) == warning_msg

allensdk/test/brain_observatory/behavior/test_behavior_ophys_metadata.py

@@ -0,0 +1,58 @@
+import pytest
+
+from allensdk.brain_observatory.behavior.metadata.behavior_ophys_metadata \
+        import BehaviorOphysMetadata
+
+
+def test_indicator(monkeypatch):
+    """Test that indicator is parsed from full_genotype"""
+
+    class MockExtractor:
+        def get_reporter_line(self):
+            return 'Ai148(TIT2L-GC6f-ICL-tTA2)'
+
+    extractor = MockExtractor()
+
+    with monkeypatch.context() as ctx:
+        def dummy_init(self):
+            self._extractor = extractor
+
+        ctx.setattr(BehaviorOphysMetadata,
+                    '__init__',
+                    dummy_init)
+
+        metadata = BehaviorOphysMetadata()
+
+        assert metadata.indicator == 'GCaMP6f'
+
+
+@pytest.mark.parametrize("input_reporter_line, warning_msg, expected", (
+        (None, 'Error parsing reporter line. It is null.', None),
+        ('foo', 'Could not parse indicator from reporter because none'
+                'of the expected substrings were found in the reporter', None)
+)
+                         )
+def test_indicator_edge_cases(monkeypatch, input_reporter_line, warning_msg,
+                              expected):
+    """Test indicator parsing edge cases"""
+
+    class MockExtractor:
+        def get_reporter_line(self):
+            return input_reporter_line
+
+    extractor = MockExtractor()
+
+    with monkeypatch.context() as ctx:
+        def dummy_init(self):
+            self._extractor = extractor
+
+        ctx.setattr(BehaviorOphysMetadata,
+                    '__init__',
+                    dummy_init)
+
+        metadata = BehaviorOphysMetadata()
+
+        with pytest.warns(UserWarning) as record:
+            indicator = metadata.indicator
+        assert indicator is expected
+        assert str(record[0].message) == warning_msg

doc_template/index.rst

@@ -119,6 +119,11 @@ The Allen SDK provides Python code for accessing experimental metadata along wit
 See the `mouse connectivity section <connectivity.html>`_ for more details.
 
 
+What's New - 2.11.3
+-----------------------------------------------------------------------
+- Bugfixes related to NWB creation for BehaviorSessions
+
+
 What's New - 2.11.2
 -----------------------------------------------------------------------
 - Fixed mkdir error for non-existing ecephys upload directory