Merge pull request #1269 from AllenNeuralDynamics/release-v1.4.0

dbirman · web-flow · commit 8f86f18ac3ba · 2025-02-28T10:55:18.000-08:00
Release v1.4.0
diff --git a/examples/bergamo_ophys_session.json b/examples/bergamo_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.1",
+   "schema_version": "1.1.2",
    "protocol_id": [],
    "experimenter_full_name": [
       "John Doe"
@@ -153,6 +153,7 @@
          "stimulus_device_names": [],
          "speaker_config": null,
          "light_source_config": [],
+         "objects_in_arena": null,
          "output_parameters": {},
          "reward_consumed_during_epoch": null,
          "reward_consumed_unit": "microliter",
diff --git a/examples/ephys_rig.json b/examples/ephys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "1.0.4",
+   "schema_version": "1.1.1",
    "rig_id": "323_EPHYS1_20231003",
    "modification_date": "2023-10-03",
    "mouse_platform": {
diff --git a/examples/ephys_session.json b/examples/ephys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.1",
+   "schema_version": "1.1.2",
    "protocol_id": [],
    "experimenter_full_name": [
       "Max Quibble",
@@ -326,6 +326,7 @@
          "stimulus_device_names": [],
          "speaker_config": null,
          "light_source_config": [],
+         "objects_in_arena": null,
          "output_parameters": {},
          "reward_consumed_during_epoch": null,
          "reward_consumed_unit": "microliter",
@@ -368,6 +369,7 @@
          "stimulus_device_names": [],
          "speaker_config": null,
          "light_source_config": [],
+         "objects_in_arena": null,
          "output_parameters": {},
          "reward_consumed_during_epoch": null,
          "reward_consumed_unit": "microliter",
diff --git a/examples/fip_behavior_rig.json b/examples/fip_behavior_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "1.0.4",
+   "schema_version": "1.1.1",
    "rig_id": "447_FIP-Behavior_20000101",
    "modification_date": "2000-01-01",
    "mouse_platform": {
diff --git a/examples/fip_ophys_rig.json b/examples/fip_ophys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "1.0.4",
+   "schema_version": "1.1.1",
    "rig_id": "428_FIP1_20231003",
    "modification_date": "2023-10-03",
    "mouse_platform": {
diff --git a/examples/mri_session.json b/examples/mri_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.1",
+   "schema_version": "1.1.2",
    "protocol_id": [
       "dx.doi.org/10.57824/protocols.io.bh7kl4n6"
    ],
diff --git a/examples/multiplane_ophys_session.json b/examples/multiplane_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.1",
+   "schema_version": "1.1.2",
    "protocol_id": [],
    "experimenter_full_name": [
       "John Doe"
diff --git a/examples/ophys_session.json b/examples/ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.1",
+   "schema_version": "1.1.2",
    "protocol_id": [],
    "experimenter_full_name": [
       "John Doe"
diff --git a/pyproject.toml b/pyproject.toml
@@ -15,17 +15,15 @@ dynamic = ["version"]
 
 dependencies = [
     'aind-data-schema-models>=0.5.4, <1.0.0',
-    'dictdiffer',
     'pydantic>=2.7',
-    'inflection',
-    'jsonschema',
     'semver'
 ]
 
 [project.optional-dependencies]
 dev = [
     'aind_data_schema[linters]',
-    'pydantic>=2.7, !=2.9.0, !=2.9.1'
+    'pydantic>=2.7, !=2.9.0, !=2.9.1',
+    'dictdiffer',
 ]
 
 linters = [
@@ -35,7 +33,7 @@ linters = [
     'flake8',
     'interrogate',
     'isort',
-    'aind-flake8-extensions==0.5.2'
+    'aind-flake8-extensions>=0.6,<0.7'
 ]
 
 docs = [
diff --git a/schemas/metadata_schema.json b/schemas/metadata_schema.json
@@ -57247,8 +57247,8 @@
                "type": "string"
             },
             "schema_version": {
-               "const": "1.0.4",
-               "default": "1.0.4",
+               "const": "1.1.1",
+               "default": "1.1.1",
                "title": "Schema Version",
                "type": "string"
             },
@@ -62306,8 +62306,8 @@
                "type": "string"
             },
             "schema_version": {
-               "const": "1.1.1",
-               "default": "1.1.1",
+               "const": "1.1.2",
+               "default": "1.1.2",
                "title": "Schema Version",
                "type": "string"
             },
@@ -70874,6 +70874,21 @@
                "description": "Light sources for stimulation",
                "title": "Light source config"
             },
+            "objects_in_arena": {
+               "anyOf": [
+                  {
+                     "items": {
+                        "type": "string"
+                     },
+                     "type": "array"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Objects in arena"
+            },
             "output_parameters": {
                "$ref": "#/$defs/AindGeneric",
                "default": {},
@@ -70961,6 +70976,7 @@
          "description": "Types of stimulus modalities",
          "enum": [
             "Auditory",
+            "Free moving",
             "Olfactory",
             "Optogenetics",
             "None",
@@ -72341,6 +72357,30 @@
                "$ref": "#/$defs/SizeUnit",
                "default": "centimeter",
                "title": "Width unit"
+            },
+            "encoder": {
+               "anyOf": [
+                  {
+                     "$ref": "#/$defs/Device"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Encoder"
+            },
+            "pulse_per_revolution": {
+               "anyOf": [
+                  {
+                     "type": "integer"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Pulse per revolution"
             }
          },
          "required": [
@@ -107144,8 +107184,8 @@
          "type": "string"
       },
       "schema_version": {
-         "const": "1.1.2",
-         "default": "1.1.2",
+         "const": "1.2.1",
+         "default": "1.2.1",
          "title": "Schema Version",
          "type": "string"
       },
diff --git a/schemas/rig_schema.json b/schemas/rig_schema.json
@@ -12505,6 +12505,30 @@
                "$ref": "#/$defs/SizeUnit",
                "default": "centimeter",
                "title": "Width unit"
+            },
+            "encoder": {
+               "anyOf": [
+                  {
+                     "$ref": "#/$defs/Device"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Encoder"
+            },
+            "pulse_per_revolution": {
+               "anyOf": [
+                  {
+                     "type": "integer"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Pulse per revolution"
             }
          },
          "required": [
@@ -18777,8 +18801,8 @@
          "type": "string"
       },
       "schema_version": {
-         "const": "1.0.4",
-         "default": "1.0.4",
+         "const": "1.1.1",
+         "default": "1.1.1",
          "title": "Schema Version",
          "type": "string"
       },
diff --git a/schemas/session_schema.json b/schemas/session_schema.json
@@ -27601,6 +27601,21 @@
                "description": "Light sources for stimulation",
                "title": "Light source config"
             },
+            "objects_in_arena": {
+               "anyOf": [
+                  {
+                     "items": {
+                        "type": "string"
+                     },
+                     "type": "array"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Objects in arena"
+            },
             "output_parameters": {
                "$ref": "#/$defs/AindGeneric",
                "default": {},
@@ -27688,6 +27703,7 @@
          "description": "Types of stimulus modalities",
          "enum": [
             "Auditory",
+            "Free moving",
             "Olfactory",
             "Optogenetics",
             "None",
@@ -58914,8 +58930,8 @@
          "type": "string"
       },
       "schema_version": {
-         "const": "1.1.1",
-         "default": "1.1.1",
+         "const": "1.1.2",
+         "default": "1.1.2",
          "title": "Schema Version",
          "type": "string"
       },
diff --git a/src/aind_data_schema/__init__.py b/src/aind_data_schema/__init__.py
@@ -1,4 +1,4 @@
 """ imports for AindModel subclasses
 """
 
-__version__ = "1.3.0"
+__version__ = "1.4.0"
diff --git a/src/aind_data_schema/base.py b/src/aind_data_schema/base.py
@@ -3,6 +3,7 @@
 import json
 import re
 import logging
+import warnings
 from pathlib import Path
 from typing import Any, Generic, Optional, TypeVar, get_args
 
@@ -85,10 +86,13 @@ class AindGeneric(BaseModel, extra="allow"):
 
     @model_validator(mode="after")
     def validate_fieldnames(self):
-        """Ensure that field names do not contain forbidden characters"""
+        """Warn users when field names contain forbidden characters
+
+        These characters will cause issues with MongoDB queries
+        """
         model_dict = json.loads(self.model_dump_json(by_alias=True))
         if is_dict_corrupt(model_dict):
-            raise ValueError("Field names cannot contain '.' or '$'")
+            warnings.warn("MongoDB queries may not work as expected for fields that contain '.' or '$'")
         return self
 
 
diff --git a/src/aind_data_schema/components/devices.py b/src/aind_data_schema/components/devices.py
@@ -777,6 +777,8 @@ class Treadmill(MousePlatform):
     device_type: Literal["Treadmill"] = "Treadmill"
     treadmill_width: Decimal = Field(..., title="Width of treadmill (mm)")
     width_unit: SizeUnit = Field(default=SizeUnit.CM, title="Width unit")
+    encoder: Optional[Device] = Field(default=None, title="Encoder")
+    pulse_per_revolution: Optional[int] = Field(default=None, title="Pulse per revolution")
 
 
 class Arena(MousePlatform):
diff --git a/src/aind_data_schema/core/metadata.py b/src/aind_data_schema/core/metadata.py
@@ -21,7 +21,7 @@
     model_validator,
 )
 
-from aind_data_schema.base import AindCoreModel, is_dict_corrupt, AwareDatetimeWithDefault
+from aind_data_schema.base import AindCoreModel, AwareDatetimeWithDefault
 from aind_data_schema.core.acquisition import Acquisition
 from aind_data_schema.core.data_description import DataDescription
 from aind_data_schema.core.instrument import Instrument
@@ -72,7 +72,7 @@ class Metadata(AindCoreModel):
 
     _DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/metadata.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.1.2"]] = Field(default="1.1.2")
+    schema_version: SkipValidation[Literal["1.2.1"]] = Field(default="1.2.1")
     id: UUID = Field(
         default_factory=uuid4,
         alias="_id",
@@ -144,13 +144,11 @@ def validate_core_fields(cls, value, info: ValidationInfo):
         field_name = info.field_name
         field_class = [f for f in get_args(cls.model_fields[field_name].annotation) if inspect.isclass(f)][0]
 
-        # If the input is a json object, we will try to create the field
         if isinstance(value, dict):
             try:
-                core_model = field_class.model_validate_json(value)
-            # If a validation error is raised,
-            # we will construct the field without validation.
-            except ValidationError:
+                core_model = field_class.model_validate(value)
+            except ValidationError as e:
+                logging.warning(f"Error in validating {field_name}: {e}")
                 core_model = field_class.model_construct(**value)
         else:
             core_model = value
@@ -203,7 +201,8 @@ def validate_metadata(self):
                 model_contents = model.model_dump()
                 try:
                     model_class(**model_contents)
-                except ValidationError:
+                except ValidationError as e:
+                    logging.warning(f"Error in {field_name}: {e}")
                     metadata_status = MetadataStatus.INVALID
         # For certain required fields, like subject, if they are not present,
         # mark the metadata record as missing
@@ -319,10 +318,7 @@ def create_metadata_json(
     core_fields = dict()
     for key, value in core_jsons.items():
         if key in CORE_FILES and value is not None:
-            if is_dict_corrupt(value):
-                logging.warning(f"Provided {key} is corrupt! It will be ignored.")
-            else:
-                core_fields[key] = value
+            core_fields[key] = value
     # Create Metadata object and convert to JSON
     # If there are any validation errors, still create it
     # but set MetadataStatus as Invalid
diff --git a/src/aind_data_schema/core/procedures.py b/src/aind_data_schema/core/procedures.py
diff --git a/src/aind_data_schema/core/rig.py b/src/aind_data_schema/core/rig.py
diff --git a/src/aind_data_schema/core/session.py b/src/aind_data_schema/core/session.py
diff --git a/src/aind_data_schema/utils/schema_version_bump.py b/src/aind_data_schema/utils/schema_version_bump.py
diff --git a/tests/test_base.py b/tests/test_base.py
diff --git a/tests/test_bump_schema_versions.py b/tests/test_bump_schema_versions.py
diff --git a/tests/test_metadata.py b/tests/test_metadata.py

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",`
`3`		`- "schema_version": "1.0.4",`
	`3`	`+ "schema_version": "1.1.1",`
`4`	`4`	`"rig_id": "323_EPHYS1_20231003",`
`5`	`5`	`"modification_date": "2023-10-03",`
`6`	`6`	`"mouse_platform": {`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",`
`3`		`- "schema_version": "1.1.1",`
	`3`	`+ "schema_version": "1.1.2",`
`4`	`4`	`"protocol_id": [`
`5`	`5`	`"dx.doi.org/10.57824/protocols.io.bh7kl4n6"`
`6`	`6`	`],`