Enh/waterlog

src/aind_slims_api/models/__init__.py

@@ -8,6 +8,8 @@
 from aind_slims_api.models.mouse import SlimsMouseContent
 from aind_slims_api.models.unit import SlimsUnit
 from aind_slims_api.models.user import SlimsUser
+from aind_slims_api.models.waterlog_result import SlimsWaterlogResult
+from aind_slims_api.models.waterlog_water_restriction import SlimsWaterRestrictionEvent
 
 __all__ = [
     "SlimsAttachment",
@@ -16,4 +18,6 @@
     "SlimsMouseContent",
     "SlimsUnit",
     "SlimsUser",
+    "SlimsWaterlogResult",
+    "SlimsWaterRestrictionEvent",
 ]

src/aind_slims_api/models/behavior_session.py

@@ -16,44 +16,22 @@
 class SlimsBehaviorSession(SlimsBaseModel):
     """Model for an instance of the Behavior Session ContentEvent
 
-    Properties
-    ----------
-    mouse_pk : Optional[int]
-        The primary key of the mouse associated with this behavior session.
-    instrument_pk : Optional[int]
-        The primary key of the instrument associated with this behavior session.
-    trainer_pks : Optional[list[int]]
-        The primary keys of the trainers associated with this behavior session.
-    task : Optional[str]
-        Name of the task associated with the session.
-    task_stage : Optional[str]
-        Name of the stage associated with the session.
-    task_schema_version : Optional[str]
-        Version of the task schema.
-    is_curriculum_suggestion : Optional[bool]
-        Whether the session is a curriculum suggestion.
-    date : Optional[datetime]
-        Date of the suggestion.
-    notes : Optional[str]
-        Notes about the session.
-
     Examples
     --------
-    Read a session.
-
     >>> from datetime import datetime
     >>> from aind_slims_api import SlimsClient
-    >>> from aind_slims_api.models import SlimsMouseContent
+    >>> from aind_slims_api import models
     >>> client = SlimsClient()
-    >>> mouse = client.fetch_model(SlimsMouseContent, barcode="00000000")
+    >>> mouse = client.fetch_model(models.SlimsMouseContent, barcode="00000000")
+
+    ### Read
     >>> behavior_sessions = client.fetch_models(SlimsBehaviorSession,
     ...  mouse_pk=mouse.pk, sort=["date"])
     >>> curriculum_attachments = client.fetch_attachments(behavior_sessions[0])
 
-    Write a new session.
-    >>> from aind_slims_api.models import SlimsInstrument, SlimsUser
-    >>> trainer = client.fetch_model(SlimsUser, username="LKim")
-    >>> instrument = client.fetch_model(SlimsInstrument, name="323_EPHYS1_OPTO")
+    ### Write
+    >>> trainer = client.fetch_model(models.SlimsUser, username="LKim")
+    >>> instrument = client.fetch_model(models.SlimsInstrument, name="323_EPHYS1_OPTO")
     >>> added = client.add_model(
     ...  SlimsBehaviorSession(
     ...      mouse_pk=mouse.pk,
@@ -68,14 +46,35 @@ class SlimsBehaviorSession(SlimsBaseModel):
     ...  )
     ... )
 
-    Add a curriculum attachment to the session (Attachment content isn't
-     available immediately.)
+    ### Add a curriculum attachment
+    Attachment content isn't available immediately.
     >>> import json
     >>> attachment_pk = client.add_attachment_content(
     ...  added,
     ...  "curriculum",
     ...  json.dumps({"curriculum_key": "curriculum_value"}),
     ... )
+
+    Properties
+    ----------
+    mouse_pk : Optional[int]
+        The primary key of the mouse associated with this behavior session.
+    instrument_pk : Optional[int]
+        The primary key of the instrument associated with this behavior session.
+    trainer_pks : Optional[list[int]]
+        The primary keys of the trainers associated with this behavior session.
+    task : Optional[str]
+        Name of the task associated with the session.
+    task_stage : Optional[str]
+        Name of the stage associated with the session.
+    task_schema_version : Optional[str]
+        Version of the task schema.
+    is_curriculum_suggestion : Optional[bool]
+        Whether the session is a curriculum suggestion.
+    date : Optional[datetime]
+        Date of the suggestion.
+    notes : Optional[str]
+        Notes about the session.
     """
 
     pk: Optional[int] = Field(

src/aind_slims_api/models/waterlog_result.py

@@ -0,0 +1,125 @@
+"""Contains a model for a waterlog result stored in SLIMS."""
+
+from datetime import datetime
+from typing import Annotated, ClassVar, Optional
+
+from pydantic import Field
+
+from aind_slims_api import __version__
+from aind_slims_api.models.base import SlimsBaseModel
+from aind_slims_api.models.utils import UnitSpec
+
+
+class SlimsWaterlogResult(SlimsBaseModel):
+    """Model for a SLIMS Waterlog Result, the daily water/weight records
+
+    Examples
+    --------
+    >>> from aind_slims_api.core import SlimsClient
+    >>> from aind_slims_api import models
+    >>> client = SlimsClient()
+    >>> mouse = client.fetch_model(models.SlimsMouseContent, barcode="00000000")
+    >>> test_pk = client.fetch_pk("Test", test_name="test_waterlog")
+
+    Write waterlog result.
+    >>> waterlog_result = client.add_model(
+    ...  models.SlimsWaterlogResult(
+    ...   mouse_pk=mouse.pk,
+    ...   date=datetime(2021,1,1),
+    ...   weight_g=20.0,
+    ...   water_earned_ml=5.0,
+    ...   water_supplement_delivered_ml=5.0,
+    ...   water_supplement_recommended_ml=5.0,
+    ...   total_water_ml=10.0,
+    ...   comments="comments",
+    ...   workstation="aibs-computer-id",
+    ...   test_pk=test_pk,
+    ...  )
+    ... )
+
+    Read a waterlog result.
+    >>> waterlog_results = client.fetch_models(
+    ...  models.SlimsWaterlogResult,
+    ...  mouse_pk=mouse.pk,
+    ...  sort=["date"],
+    ... )
+    >>> waterlog_results[-1].weight_g
+    20.0
+    """
+
+    date: datetime = Field(
+        datetime.now(),
+        serialization_alias="rslt_cf_datePerformed",
+        validation_alias="rslt_cf_datePerformed",
+    )
+    operator: Optional[str] = Field(
+        None,
+        serialization_alias="rslt_cf_waterlogOperator",
+        validation_alias="rslt_cf_waterlogOperator",
+    )
+    weight_g: Annotated[float | None, UnitSpec("g")] = Field(
+        None,
+        serialization_alias="rslt_cf_weight",
+        validation_alias="rslt_cf_weight",
+    )
+    water_earned_ml: Annotated[float | None, UnitSpec("ml")] = Field(
+        ...,
+        serialization_alias="rslt_cf_waterEarned",
+        validation_alias="rslt_cf_waterEarned",
+    )
+    water_supplement_delivered_ml: Annotated[float | None, UnitSpec("ml")] = Field(
+        ...,
+        serialization_alias="rslt_cf_waterSupplementDelivered",
+        validation_alias="rslt_cf_waterSupplementDelivered",
+    )
+    water_supplement_recommended_ml: Annotated[float | None, UnitSpec("ml")] = Field(
+        ...,
+        serialization_alias="rslt_cf_waterSupplementRecommended",
+        validation_alias="rslt_cf_waterSupplementRecommended",
+    )
+    total_water_ml: Annotated[float | None, UnitSpec("ml")] = Field(
+        ...,
+        serialization_alias="rslt_cf_totalWater",
+        validation_alias="rslt_cf_totalWater",
+    )
+    comments: Optional[str] = Field(
+        None,
+        serialization_alias="rslt_comments",
+        validation_alias="rslt_comments",
+    )
+    workstation: Optional[str] = Field(
+        None,
+        serialization_alias="rslt_cf_fk_workStation",
+        validation_alias="rslt_cf_fk_workStation",
+    )
+    sw_source: str = Field(
+        "aind-slims-api",
+        serialization_alias="rslt_cf_swSource",
+        validation_alias="rslt_cf_swSource",
+    )
+    sw_version: str = Field(
+        __version__,
+        serialization_alias="rslt_cf_swVersion",
+        validation_alias="rslt_cf_swVersion",
+    )
+    pk: Optional[int] = Field(
+        None,
+        serialization_alias="rslt_pk",
+        validation_alias="rslt_pk",
+    )
+    mouse_pk: Optional[int] = Field(
+        None,
+        serialization_alias="rslt_fk_content",
+        validation_alias="rslt_fk_content",
+    )
+    test_pk: Optional[int] = Field(
+        None,
+        serialization_alias="rslt_fk_test",
+        validation_alias="rslt_fk_test",
+    )
+
+    _slims_table = "Result"
+
+    _base_fetch_filters: ClassVar[dict[str, str]] = {
+        "test_name": "test_waterlog",
+    }

src/aind_slims_api/models/waterlog_water_restriction.py

@@ -0,0 +1,83 @@
+"""Contains a model for a waterlog water restriction event stored in SLIMS."""
+
+from datetime import datetime
+from typing import ClassVar, Optional
+
+from pydantic import Field
+
+from aind_slims_api.models.base import SlimsBaseModel
+
+DEFAULT_WEIGHT_FRACTION = 0.85
+MIN_WEIGHT_FRACTION = 0.75
+MAX_WEIGHT_FRACTION = 1.0
+
+
+class SlimsWaterRestrictionEvent(SlimsBaseModel):
+    """Model for a Water Restriction Event
+
+    Examples
+    --------
+    >>> from aind_slims_api.core import SlimsClient
+    >>> from aind_slims_api import models
+    >>> client = SlimsClient()
+    >>> mouse = client.fetch_model(models.SlimsMouseContent, barcode="00000000")
+
+    ### Write
+    >>> water_restriction_event = client.add_model(
+    ...  models.SlimsWaterRestrictionEvent(
+    ...   mouse_pk=mouse.pk,
+    ...   start_date=datetime(2021,1,1),
+    ...   end_date=datetime(2021,1,2),
+    ...   assigned_by="mochic",
+    ...   target_weight_fraction=0.90,
+    ...  )
+    ... )
+
+    ### Read
+    >>> water_restriction_events = client.fetch_models(
+    ...  models.SlimsWaterRestrictionEvent,
+    ...  mouse_pk=mouse.pk,
+    ...  sort=["start_date"],
+    ... )
+    >>> water_restriction_events[-1].target_weight_fraction
+    0.9
+    """
+
+    start_date: datetime = Field(
+        datetime.now(),
+        serialization_alias="cnvn_cf_startDate",
+        validation_alias="cnvn_cf_startDate",
+    )
+    end_date: Optional[datetime] = Field(
+        None,
+        serialization_alias="cnvn_cf_endDate",
+        validation_alias="cnvn_cf_endDate",
+    )
+    assigned_by: str = Field(
+        ...,
+        serialization_alias="cnvn_cf_assignedBy",
+        validation_alias="cnvn_cf_assignedBy",
+    )
+    target_weight_fraction: float = Field(
+        default=DEFAULT_WEIGHT_FRACTION,
+        serialization_alias="cnvn_cf_targetWeightFraction",
+        validation_alias="cnvn_cf_targetWeightFraction",
+        gt=MIN_WEIGHT_FRACTION,
+        lt=MAX_WEIGHT_FRACTION,
+    )
+    pk: Optional[int] = Field(
+        None,
+        serialization_alias="cnvn_pk",
+        validation_alias="cnvn_pk",
+    )
+    mouse_pk: Optional[int] = Field(
+        None,
+        serialization_alias="cnvn_fk_content",
+        validation_alias="cnvn_fk_content",
+    )
+    cnvn_fk_contentEventType: int = 9  # pk of Water Restriction ContentEvent type
+
+    _slims_table = "ContentEvent"
+    _base_fetch_filters: ClassVar[dict[str, str]] = {
+        "cnvt_name": "Water Restriction",
+    }