Merge pull request #2626 from AllenInstitute/ticket/2441/dev

Remove to_json from data objects and their associated tests

allensdk/brain_observatory/behavior/data_files/demix_file.py

@@ -1,5 +1,5 @@
 import json
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 import h5py
@@ -34,9 +34,6 @@ def from_json(cls, dict_repr: dict) -> "DemixFile":
         filepath = dict_repr["demix_file"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"demix_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/dff_file.py

@@ -1,6 +1,6 @@
 import json
 import numpy as np
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 import h5py
@@ -35,9 +35,6 @@ def from_json(cls, dict_repr: dict) -> "DFFFile":
         filepath = dict_repr["dff_file"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"dff_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/event_detection_file.py

@@ -1,6 +1,6 @@
 import json
 import numpy as np
-from typing import Dict, Union, Tuple
+from typing import Union, Tuple
 from pathlib import Path
 
 import h5py
@@ -36,9 +36,6 @@ def from_json(cls, dict_repr: dict) -> "EventDetectionFile":
         filepath = dict_repr["events_file"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"events_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/eye_tracking_file.py

@@ -1,4 +1,4 @@
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 import pandas as pd
@@ -23,9 +23,6 @@ def from_json(cls, dict_repr: dict) -> "EyeTrackingFile":
         filepath = dict_repr["eye_tracking_filepath"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"eye_tracking_filepath": str(self.filepath)}
-
     @classmethod
     def from_lims(
         cls, db: PostgresQueryMixin,

allensdk/brain_observatory/behavior/data_files/eye_tracking_metadata_file.py

@@ -27,11 +27,6 @@ def from_lims(cls):
         raise NotImplementedError(
                 "from_lims not yet supported for EyeTrackingMetadataFile")
 
-    @classmethod
-    def to_json(cls):
-        raise NotImplementedError(
-                "from_json not yet supported for EyeTrackingMetadataFile")
-
     @classmethod
     def from_json(
             cls,

allensdk/brain_observatory/behavior/data_files/eye_tracking_video.py

@@ -8,8 +8,6 @@
 
 class EyeTrackingVideo(DataFile):
     """Eye tracking video"""
-    def to_json(self) -> dict:
-        raise NotImplementedError
 
     @classmethod
     def from_lims(

allensdk/brain_observatory/behavior/data_files/neuropil_corrected_file.py

@@ -1,5 +1,5 @@
 import json
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 import h5py
@@ -34,9 +34,6 @@ def from_json(cls, dict_repr: dict) -> "NeuropilCorrectedFile":
         filepath = dict_repr["neuropil_corrected_file"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"neuropil_corrected_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/neuropil_file.py

@@ -1,5 +1,5 @@
 import json
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 import h5py
@@ -34,9 +34,6 @@ def from_json(cls, dict_repr: dict) -> "NeuropilFile":
         filepath = dict_repr["neuropil_file"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"neuropil_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/rigid_motion_transform_file.py

@@ -1,5 +1,5 @@
 import json
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 from cachetools import cached, LRUCache
@@ -34,9 +34,6 @@ def from_json(cls, dict_repr: dict) -> "RigidMotionTransformFile":
         filepath = dict_repr["rigid_motion_transform_file"]
         return cls(filepath=filepath)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"rigid_motion_transform_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/stimulus_file.py

@@ -69,9 +69,6 @@ def from_json(cls, dict_repr: dict) -> "_StimulusFile":
     def _from_json(cls, stimulus_file_path: str) -> "_StimulusFile":
         return cls(filepath=stimulus_file_path)
 
-    def to_json(self) -> Dict[str, str]:
-        return {self.file_path_key(): str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_files/sync_file.py

@@ -1,6 +1,6 @@
 import abc
 import json
-from typing import Dict, Union
+from typing import Union
 from pathlib import Path
 
 from cachetools import cached, LRUCache
@@ -71,9 +71,6 @@ def from_json(cls,
         filepath = dict_repr["sync_file"]
         return cls(filepath=filepath, permissive=permissive)
 
-    def to_json(self) -> Dict[str, str]:
-        return {"sync_file": str(self.filepath)}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/behavior_metadata.py

@@ -16,7 +16,7 @@
     JsonReadableInterface, NwbReadableInterface, \
     LimsReadableInterface
 from allensdk.core import \
-    JsonWritableInterface, NwbWritableInterface
+    NwbWritableInterface
 from allensdk.brain_observatory.behavior.data_objects.metadata\
     .behavior_metadata.behavior_session_uuid import \
     BehaviorSessionUUID
@@ -181,7 +181,6 @@ def get_task_parameters(data: Dict) -> Dict:
 class BehaviorMetadata(DataObject, LimsReadableInterface,
                        JsonReadableInterface,
                        NwbReadableInterface,
-                       JsonWritableInterface,
                        NwbWritableInterface):
     """Container class for behavior metadata"""
     def __init__(self,
@@ -334,9 +333,6 @@ def is_pretest(self):
     def is_training(self):
         return self.session_type.lower().startswith('training_0')
 
-    def to_json(self) -> dict:
-        pass
-
     def to_nwb(self, nwbfile: NWBFile) -> NWBFile:
         self._subject_metadata.to_nwb(nwbfile=nwbfile)
         self._equipment.to_nwb(nwbfile=nwbfile)

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/behavior_session_id.py

@@ -5,8 +5,6 @@
 
 from allensdk.core import \
     JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
-from allensdk.core import \
-    JsonWritableInterface
 from allensdk.internal.api import PostgresQueryMixin
 from allensdk.core import DataObject
 
@@ -18,17 +16,14 @@ def from_lims_cache_key(cls, db, ophys_experiment_id: int):
 class BehaviorSessionId(DataObject, LimsReadableInterface,
                         JsonReadableInterface,
                         NwbReadableInterface,
-                        JsonWritableInterface):
+                        ):
     def __init__(self, behavior_session_id: int):
         super().__init__(name="behavior_session_id", value=behavior_session_id)
 
     @classmethod
     def from_json(cls, dict_repr: dict) -> "BehaviorSessionId":
         return cls(behavior_session_id=dict_repr["behavior_session_id"])
 
-    def to_json(self) -> dict:
-        return {"behavior_session_id": self.value}
-
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     # TODO should be from_ophys_experiment_id

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/equipment.py

@@ -5,8 +5,7 @@
 from allensdk.core import DataObject
 from allensdk.core import \
     JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
-from allensdk.core import \
-    JsonWritableInterface, NwbWritableInterface
+from allensdk.core import NwbWritableInterface
 from allensdk.internal.api import PostgresQueryMixin
 
 
@@ -16,8 +15,7 @@ class EquipmentType(Enum):
 
 
 class Equipment(DataObject, JsonReadableInterface, LimsReadableInterface,
-                NwbReadableInterface, JsonWritableInterface,
-                NwbWritableInterface):
+                NwbReadableInterface, NwbWritableInterface):
     """the name of the experimental rig."""
     def __init__(self, equipment_name: str):
         super().__init__(name="equipment_name", value=equipment_name)
@@ -26,9 +24,6 @@ def __init__(self, equipment_name: str):
     def from_json(cls, dict_repr: dict) -> "Equipment":
         return cls(equipment_name=dict_repr["rig_name"])
 
-    def to_json(self) -> dict:
-        return {"eqipment_name": self.value}
-
     @classmethod
     def from_lims(cls, behavior_session_id: int,
                   lims_db: PostgresQueryMixin) -> "Equipment":

allensdk/brain_observatory/behavior/data_objects/metadata/subject_metadata/sex.py

@@ -3,13 +3,11 @@
 from allensdk.core import DataObject
 from allensdk.core import \
     JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
-from allensdk.core import \
-    JsonWritableInterface
 from allensdk.internal.api import PostgresQueryMixin
 
 
 class Sex(DataObject, LimsReadableInterface, JsonReadableInterface,
-          NwbReadableInterface, JsonWritableInterface):
+          NwbReadableInterface):
     """sex of the animal (M/F)"""
     def __init__(self, sex: str):
         super().__init__(name="sex", value=sex)
@@ -18,9 +16,6 @@ def __init__(self, sex: str):
     def from_json(cls, dict_repr: dict) -> "Sex":
         return cls(sex=dict_repr["sex"])
 
-    def to_json(self) -> dict:
-        return {"sex": self.value}
-
     @classmethod
     def from_lims(cls, behavior_session_id: int,
                   lims_db: PostgresQueryMixin) -> "Sex":

allensdk/brain_observatory/behavior/data_objects/metadata/subject_metadata/subject_metadata.py

@@ -8,8 +8,7 @@
 from allensdk.brain_observatory.behavior.data_objects import BehaviorSessionId
 from allensdk.core import \
     JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
-from allensdk.core import \
-    JsonWritableInterface, NwbWritableInterface
+from allensdk.core import NwbWritableInterface
 from allensdk.brain_observatory.behavior.data_objects.metadata \
     .subject_metadata.age import \
     Age
@@ -36,7 +35,7 @@
 
 class SubjectMetadata(DataObject, LimsReadableInterface, NwbReadableInterface,
                       NwbWritableInterface, JsonReadableInterface,
-                      JsonWritableInterface):
+                      ):
     """Subject metadata"""
 
     def __init__(self,
@@ -115,9 +114,6 @@ def from_json(cls, dict_repr: dict) -> "SubjectMetadata":
             death_on=death_on
         )
 
-    def to_json(self) -> dict:
-        pass
-
     @classmethod
     def from_nwb(cls, nwbfile: NWBFile) -> "SubjectMetadata":
         mouse_id = MouseId.from_nwb(nwbfile=nwbfile)

allensdk/core/__init__.py

@@ -40,5 +40,5 @@
     DataFileReadableInterface
 )
 from ._data_object_base.writable_interfaces import (    # noqa F401
-    JsonWritableInterface, NwbWritableInterface
+    NwbWritableInterface
 )

allensdk/core/_data_object_base/writable_interfaces.py

@@ -3,22 +3,6 @@
 from pynwb import NWBFile
 
 
-class JsonWritableInterface(abc.ABC):
-    """Marks a data object as writable to NWB"""
-    @abc.abstractmethod
-    def to_json(self) -> dict:  # pragma: no cover
-        """Given an already populated DataObject, return the dict that
-        when used with the `from_json()` classmethod would produce the same
-        DataObject
-
-        Returns
-        -------
-        dict:
-            The JSON (in dict form) that would produce the DataObject.
-        """
-        raise NotImplementedError()
-
-
 class NwbWritableInterface(abc.ABC):
     """Marks a data object as writable to NWB"""
     @abc.abstractmethod

allensdk/internal/core/_data_file.py

@@ -52,19 +52,6 @@ def from_json(cls,
         # return cls.instantiate(filepath=filepath)
         raise NotImplementedError()
 
-    @abc.abstractmethod
-    def to_json(self) -> dict:  # pragma: no cover
-        """Given an already populated DataFile, return the dict that
-        when used with the `from_json()` classmethod would produce the same
-        DataFile
-
-        Returns
-        -------
-        dict:
-            The JSON (in dict form) that would produce the DataFile.
-        """
-        raise NotImplementedError()
-
     @classmethod
     @abc.abstractmethod
     def from_lims(cls) -> "DataFile":  # pragma: no cover