Merge branch 'dev' into feat_1147_interoception

examples/quality_control.json

@@ -85,7 +85,8 @@
          "tags": null,
          "notes": "",
          "allow_failed_metrics": false,
-         "latest_status": "Pending"
+         "latest_status": "Pending",
+         "created": "2022-11-22T00:00:00Z"
       },
       {
          "modality": {
@@ -140,9 +141,10 @@
             }
          ],
          "tags": null,
-         "notes": null,
+         "notes": "Pass when video_1_num_frames==video_2_num_frames",
          "allow_failed_metrics": false,
-         "latest_status": "Pass"
+         "latest_status": "Pass",
+         "created": "2022-11-22T00:00:00Z"
       },
       {
          "modality": {
@@ -199,7 +201,8 @@
          "tags": null,
          "notes": null,
          "allow_failed_metrics": false,
-         "latest_status": "Pass"
+         "latest_status": "Pass",
+         "created": "2022-11-22T00:00:00Z"
       }
    ],
    "notes": null

examples/quality_control.py

@@ -59,6 +59,7 @@
         QCMetric(name="Probe C drift", value="Low", reference="ecephys-drift-map", status_history=[s]),
     ],
     notes="",
+    created=t,
 )
 
 eval1 = QCEvaluation(
@@ -85,6 +86,8 @@
             status_history=[s],
         ),
     ],
+    notes="Pass when video_1_num_frames==video_2_num_frames",
+    created=t,
 )
 
 eval2 = QCEvaluation(
@@ -97,6 +100,7 @@
         QCMetric(name="ProbeB", value=True, status_history=[s]),
         QCMetric(name="ProbeC", value=True, status_history=[s]),
     ],
+    created=t,
 )
 
 q = QualityControl(evaluations=[eval0, eval1, eval2])

src/aind_data_schema/base.py

@@ -2,6 +2,7 @@
 
 import json
 import re
+import logging
 from pathlib import Path
 from typing import Any, Generic, Optional, TypeVar, get_args
 
@@ -23,6 +24,9 @@
 from aind_data_schema_models.brain_atlas import CCFStructure
 
 
+MAX_FILE_SIZE = 500 * 1024  # 500KB
+
+
 def _coerce_naive_datetime(v: Any, handler: ValidatorFunctionWrapHandler) -> AwareDatetime:
     """Validator to wrap around AwareDatetime to set a default timezone as user's locale"""
     try:
@@ -178,3 +182,7 @@ def write_standard_file(
 
         with open(filename, "w") as f:
             f.write(self.model_dump_json(indent=3))
+
+        # Check that size doesn't exceed the maximum
+        if len(self.model_dump_json(indent=3)) > MAX_FILE_SIZE:
+            logging.warning(f"File size exceeds {MAX_FILE_SIZE / 1024} KB: {filename}")

src/aind_data_schema/components/devices.py

@@ -250,6 +250,7 @@ class LickSensorType(str, Enum):
     """Type of lick sensor"""
 
     CAPACITIVE = "Capacitive"
+    CONDUCTIVE = "Conductive"
     PIEZOELECTIC = "Piezoelectric"
 
 

src/aind_data_schema/core/quality_control.py

@@ -93,6 +93,9 @@ class QCEvaluation(AindModel):
         ),
     )
     latest_status: Status = Field(default=None, title="Evaluation status")
+    created: AwareDatetimeWithDefault = Field(
+        default_factory=lambda: datetime.now(tz=timezone.utc), title="Evaluation creation date"
+    )
 
     def status(self, date: datetime = datetime.now(tz=timezone.utc)) -> Status:
         """DEPRECATED
@@ -132,7 +135,7 @@ def compute_latest_status(self):
         self.latest_status = self.evaluate_status()
         return self
 
-    def evaluate_status(self, date: datetime = datetime.now(tz=timezone.utc)) -> Status:
+    def evaluate_status(self, date: Optional[datetime] = None) -> Status:
         """Loop through all metrics and return the evaluation's status
 
         Any fail -> FAIL
@@ -144,6 +147,9 @@ def evaluate_status(self, date: datetime = datetime.now(tz=timezone.utc)) -> Sta
         Status
             Current status of the evaluation
         """
+        if not date:
+            date = datetime.now(tz=timezone.utc)
+
         latest_metric_statuses = []
 
         for metric in self.metrics:
@@ -202,14 +208,17 @@ def status(
         modality: Union[Modality.ONE_OF, List[Modality.ONE_OF], None] = None,
         stage: Union[Stage, List[Stage], None] = None,
         tag: Union[str, List[str], None] = None,
-        date: datetime = datetime.now(tz=timezone.utc),
+        date: Optional[datetime] = None,
     ) -> Status:
         """Loop through all evaluations and return the overall status
 
         Any FAIL -> FAIL
         If no fails, then any PENDING -> PENDING
         All PASS -> PASS
         """
+        if not date:
+            date = datetime.now(tz=timezone.utc)
+
         if not modality and not stage and not tag:
             eval_statuses = [evaluation.evaluate_status(date=date) for evaluation in self.evaluations]
         else:

tests/test_base.py

@@ -9,7 +9,14 @@
 from pydantic import ValidationError, create_model, SkipValidation
 from typing import Literal
 
-from aind_data_schema.base import AindGeneric, AwareDatetimeWithDefault, is_dict_corrupt, AindModel, AindCoreModel
+from aind_data_schema.base import (
+    AindGeneric,
+    AwareDatetimeWithDefault,
+    is_dict_corrupt,
+    AindModel,
+    AindCoreModel,
+    MAX_FILE_SIZE,
+)
 from aind_data_schema.core.subject import Subject
 from aind_data_schema_models.brain_atlas import CCFStructure
 
@@ -151,6 +158,20 @@ class Modelv2(AindCoreModel):
         # this is to ensure you can't get a bumped schema_version without passing validation
         self.assertRaises(ValidationError, lambda: Modelv1(**v2_from_v1.model_dump()))
 
+    @patch("builtins.open", new_callable=mock_open)
+    @patch("logging.warning")
+    def test_write_standard_file_size_warning(self, mock_logging_warning: MagicMock, mock_open: MagicMock):
+        """Tests that a warning is logged if the file size exceeds MAX_FILE_SIZE"""
+
+        s = Subject.model_construct()
+        s.subject_id = "s" * (MAX_FILE_SIZE + 1000)
+        s.write_standard_file(output_directory=Path("dir"), suffix=".foo.bar")
+
+        mock_open.assert_has_calls([call(Path("dir/subject.foo.bar"), "w")])
+        mock_logging_warning.assert_called_once_with(
+            f"File size exceeds {MAX_FILE_SIZE / 1024} KB: dir/subject.foo.bar"
+        )
+
 
 if __name__ == "__main__":
     unittest.main()

tests/test_quality_control.py

@@ -23,7 +23,7 @@ def test_constructors(self):
             stage=Stage.PROCESSING,
             metrics=[
                 QCMetric(
-                    name="Multiple values example",
+                    name="Dict example",
                     value={"stuff": "in_a_dict"},
                     status_history=[
                         QCStatus(evaluator="Bob", timestamp=datetime.fromisoformat("2020-10-10"), status=Status.PASS)
@@ -56,7 +56,7 @@ def test_overall_status(self):
             stage=Stage.PROCESSING,
             metrics=[
                 QCMetric(
-                    name="Multiple values example",
+                    name="Dict example",
                     value={"stuff": "in_a_dict"},
                     status_history=[
                         QCStatus(evaluator="Bob", timestamp=datetime.fromisoformat("2020-10-10"), status=Status.PASS)
@@ -298,7 +298,7 @@ def test_multi_session(self):
             stage=Stage.PROCESSING,
             metrics=[
                 QCMetric(
-                    name="Multiple values example",
+                    name="Dict example",
                     value={"stuff": "in_a_dict"},
                     status_history=[
                         QCStatus(evaluator="Automated", timestamp=t0, status=Status.PASS),
@@ -318,7 +318,7 @@ def test_multi_session(self):
                 stage=Stage.PROCESSING,
                 metrics=[
                     QCMetric(
-                        name="Multiple values example",
+                        name="Dict with evaluated assets list",
                         value={"stuff": "in_a_dict"},
                         status_history=[
                             QCStatus(evaluator="Automated", timestamp=t0, status=Status.PASS),
@@ -328,7 +328,6 @@ def test_multi_session(self):
                 ],
             )
 
-        print(context.exception)
         self.assertTrue(
             "is in a single-asset QCEvaluation and should not have evaluated_assets" in repr(context.exception)
         )
@@ -341,7 +340,7 @@ def test_multi_session(self):
                 stage=Stage.MULTI_ASSET,
                 metrics=[
                     QCMetric(
-                        name="Multiple values example",
+                        name="Missing evaluated assets",
                         value={"stuff": "in_a_dict"},
                         status_history=[
                             QCStatus(evaluator="Automated", timestamp=t0, status=Status.PASS),