coverage

src/aind_slims_api/behavior_session.py

@@ -8,7 +8,7 @@
 
 from pydantic import Field
 
-from aind_slims_api.core import SlimsBaseModel, SlimsClient, SLIMSTABLES
+from aind_slims_api.core import SlimsBaseModel, SlimsClient
 from aind_slims_api.mouse import SlimsMouseContent
 from aind_slims_api.instrument import SlimsInstrument
 from aind_slims_api.user import SlimsUser
@@ -30,7 +30,11 @@ class SlimsBehaviorSessionContentEvent(SlimsBaseModel):
 
     pk: int | None = Field(default=None, alias="cnvn_pk")
     mouse_pk: int | None = Field(
-        default=None, alias="cnvn_fk_content"
+        default=None,
+        alias="cnvn_fk_content",
+        description=(
+            "The primary key of the mouse associated with this behavior session."
+        ),
     )  # used as reference to mouse
     notes: str | None = Field(default=None, alias="cnvn_cf_notes")
     task_stage: str | None = Field(default=None, alias="cnvn_cf_taskStage")
@@ -47,8 +51,8 @@ class SlimsBehaviorSessionContentEvent(SlimsBaseModel):
         default=None, alias="cnvn_cf_softwareVersion")
     date: datetime | None = Field(default=None, alias="cnvn_cf_scheduledDate")
     cnvn_fk_contentEventType: int = 10  # pk of Behavior Session ContentEvent
-    _slims_table: SLIMSTABLES = "ContentEvent"
-    _base_fetch_filters: ClassVar[dict[str, int | str]] = {
+    _slims_table = "ContentEvent"
+    _base_fetch_filters: ClassVar[dict[str, str]] = {
         "cnvt_name": "Behavior Session",
     }
 

src/aind_slims_api/core.py

@@ -97,8 +97,8 @@ class MyModel(SlimsBaseModel):
 
     pk: Optional[int] = None
     json_entity: Optional[dict] = None
-    _slims_table: SLIMSTABLES
-    _base_fetch_filters: ClassVar[dict[str, str | int]] = {}  # use for fetch_models, fetch_model
+    _slims_table: ClassVar[SLIMSTABLES]
+    _base_fetch_filters: ClassVar[dict[str, str]] = {}  # use for fetch_models, fetch_model
 
     @field_validator("*", mode="before")
     def _validate(cls, value, info: ValidationInfo):
@@ -141,11 +141,11 @@ def _serialize(self, field, info):
     # TODO: Add Table - need Record.json_entity['tableName']
 
 
-class Attachment(SlimsBaseModel):
+class SlimsAttachment(SlimsBaseModel):
 
     pk: int = Field(..., alias="attm_pk")
     name: str = Field(..., alias="attm_name")
-    _slims_table: SLIMSTABLES = "Attachment"
+    _slims_table = "Attachment"
 
 
 SlimsBaseModelTypeVar = TypeVar("SlimsBaseModelTypeVar", bound=SlimsBaseModel)
@@ -281,7 +281,7 @@ def fetch_models(
                 ]
         logger.debug("Resolved sort: %s", resolved_sort)
         response = self.fetch(
-            model._slims_table.default,  # TODO: consider changing fetch method
+            model._slims_table,  # TODO: consider changing fetch method
             *args,
             sort=resolved_sort,
             start=start,
@@ -321,15 +321,15 @@ def fetch_model(
     def fetch_attachments(
         self,
         record: SlimsBaseModel,
-    ) -> list[Attachment]:
+    ) -> list[SlimsAttachment]:
         return self._validate_models(
-            Attachment,
+            SlimsAttachment,
             self.db.slims_api.get_entities(
                 f"attachment/{record._slims_table}/{record.pk}"
             )
         )
 
-    def fetch_attachment_content(self, attachment: Attachment) -> Response:
+    def fetch_attachment_content(self, attachment: SlimsAttachment) -> Response:
         return self.db.slims_api.get(f"repo/{attachment.pk}")
 
     @lru_cache(maxsize=None)

src/aind_slims_api/instrument.py

@@ -4,7 +4,7 @@
 
 from pydantic import Field
 
-from aind_slims_api.core import SlimsBaseModel, SLIMSTABLES
+from aind_slims_api.core import SlimsBaseModel
 
 logger = logging.getLogger()
 
@@ -25,7 +25,7 @@ class SlimsInstrument(SlimsBaseModel):
         description="The name of the instrument",
     )
     pk: int = Field(..., alias="nstr_pk")
-    _slims_table: SLIMSTABLES = "Instrument"
+    _slims_table = "Instrument"
 
     # todo add more useful fields
 

src/aind_slims_api/mouse.py

@@ -3,9 +3,9 @@
 import logging
 from typing import Annotated, ClassVar
 
-from pydantic import Field, BeforeValidator, ValidationError
+from pydantic import Field, BeforeValidator
 
-from aind_slims_api.core import SlimsBaseModel, SlimsClient, UnitSpec, SLIMSTABLES
+from aind_slims_api.core import SlimsBaseModel, UnitSpec
 
 logger = logging.getLogger()
 
@@ -30,8 +30,8 @@ class SlimsMouseContent(SlimsBaseModel):
     barcode: str = Field(..., alias="cntn_barCode")
     pk: int = Field(..., alias="cntn_pk")
 
-    _slims_table: SLIMSTABLES = "Content"
-    _base_fetch_filters: ClassVar[dict[str, int | str]] = {
+    _slims_table = "Content"
+    _base_fetch_filters: ClassVar[dict[str, str]] = {
         "cntp_name": "Mouse",
     }
 
@@ -52,37 +52,6 @@ class SlimsMouseContent(SlimsBaseModel):
     # cntn_cf_parentBarcode: SlimsColumn
 
 
-def fetch_mouse_content(
-    client: SlimsClient,
-    mouse_name: str,
-) -> SlimsMouseContent | dict | None:
-    """Fetches mouse information for a mouse with labtracks id {mouse_name}"""
-    mice = client.fetch(
-        "Content",
-        cntp_name="Mouse",
-        cntn_barCode=mouse_name,
-    )
-
-    if len(mice) > 0:
-        mouse_details = mice[0]
-        if len(mice) > 1:
-            logger.warning(
-                f"Warning, Multiple mice in SLIMS with barcode "
-                f"{mouse_name}, using pk={mouse_details.cntn_pk.value}"
-            )
-    else:
-        logger.warning("Warning, Mouse not in SLIMS")
-        return None
-
-    try:
-        mouse = SlimsMouseContent.model_validate(mouse_details)
-    except ValidationError as e:
-        logger.error(f"SLIMS data validation failed, {repr(e)}")
-        return mouse_details.json_entity
-
-    return mouse
-
-
 if __name__ == "__main__":
     from aind_slims_api import testmod
 

src/aind_slims_api/unit.py

@@ -5,7 +5,7 @@
 
 from pydantic import Field
 
-from aind_slims_api.core import SlimsBaseModel, SLIMSTABLES
+from aind_slims_api.core import SlimsBaseModel
 
 logger = logging.getLogger()
 
@@ -17,4 +17,4 @@ class SlimsUnit(SlimsBaseModel):
     abbreviation: Optional[str] = Field("", alias="unit_abbreviation")
     pk: int = Field(..., alias="unit_pk")
 
-    _slims_table: SLIMSTABLES = "Unit"
+    _slims_table = "Unit"

src/aind_slims_api/user.py

@@ -3,7 +3,7 @@
 
 from pydantic import Field
 
-from aind_slims_api.core import SlimsBaseModel, SLIMSTABLES
+from aind_slims_api.core import SlimsBaseModel
 
 
 # TODO: Tighten this up once users are more commonly used
@@ -12,7 +12,7 @@ class SlimsUser(SlimsBaseModel):
 
     >>> from aind_slims_api.core import SlimsClient
     >>> client = SlimsClient()
-    >>> user = client.fetch_model(SlimsUser, "LisaK")
+    >>> user = client.fetch_model(SlimsUser, username="LKim")
     """
 
     username: str = Field(..., alias="user_userName")
@@ -22,7 +22,7 @@ class SlimsUser(SlimsBaseModel):
     email: Optional[str] = Field("", alias="user_email")
     pk: int = Field(..., alias="user_pk")
 
-    _slims_table: SLIMSTABLES = "User"
+    _slims_table = "User"
 
 
 if __name__ == "__main__":