change models to use friendlier names for init (#22)

* change models to use friendlier names for init

* higher res example

* reduce quality back

README.md

@@ -23,7 +23,7 @@ pip install -e .[dev]
 ## Usage
 
 ### VScode
-![](example-usage.gif)
+![Example usage](example-usage.gif)
 
 Requires the [pylance extension](https://marketplace.visualstudio.com/items?itemName=ms-python.vscode-pylance) to be installed for similar functionality.
 

src/aind_slims_api/core.py

@@ -22,7 +22,7 @@
 
 from aind_slims_api import config
 from aind_slims_api.exceptions import SlimsRecordNotFound
-from aind_slims_api.models.attachment import SlimsAttachment
+from aind_slims_api.models import SlimsAttachment
 from aind_slims_api.models.base import SlimsBaseModel
 from aind_slims_api.types import SLIMS_TABLES
 
@@ -105,10 +105,20 @@ def resolve_model_alias(
         model: Type[SlimsBaseModelTypeVar],
         attr_name: str,
     ) -> str:
-        """Given a SlimsBaseModel object, resolve its pk to the actual value"""
+        """Given a SlimsBaseModel object, resolve its pk to the actual value
+
+        Notes
+        -----
+        - Raises ValueError if the alias cannot be resolved
+        - Resolves the validation alias for a given field name
+        """
         for field_name, field_info in model.model_fields.items():
-            if field_name == attr_name and field_info.alias:
-                return field_info.alias
+            if (
+                field_name == attr_name
+                and field_info.validation_alias
+                and isinstance(field_info.validation_alias, str)
+            ):
+                return field_info.validation_alias
         else:
             raise ValueError(f"Cannot resolve alias for {attr_name} on {model}")
 

src/aind_slims_api/models/attachment.py

@@ -11,9 +11,10 @@ class SlimsAttachment(SlimsBaseModel):
     Examples
     --------
     >>> from aind_slims_api import SlimsClient
+    >>> from aind_slims_api import models
     >>> client = SlimsClient()
     >>> rig_metadata_attachment = client.fetch_model(
-    ...  SlimsAttachment,
+    ...  models.SlimsAttachment,
     ...  name="rig323_EPHYS1_OPTO_2024-02-12.json"
     ... )
     >>> rig_metadata = client.fetch_attachment_content(
@@ -23,6 +24,14 @@ class SlimsAttachment(SlimsBaseModel):
     '323_EPHYS1_OPTO_2024-02-12'
     """
 
-    pk: int = Field(..., alias="attm_pk")
-    name: str = Field(alias="attm_name")
+    pk: int = Field(
+        ...,
+        serialization_alias="attm_pk",
+        validation_alias="attm_pk",
+    )
+    name: str = Field(
+        ...,
+        serialization_alias="attm_name",
+        validation_alias="attm_name",
+    )
     _slims_table = "Attachment"

src/aind_slims_api/models/base.py

@@ -18,6 +18,7 @@ class SlimsBaseModel(
     BaseModel,
     from_attributes=True,
     validate_assignment=True,
+    populate_by_name=True,
 ):
     """Pydantic model to represent a SLIMS record.
     Subclass with fields matching those in the SLIMS record.

src/aind_slims_api/models/behavior_session.py

@@ -4,7 +4,7 @@
 
 import logging
 from datetime import datetime
-from typing import ClassVar
+from typing import ClassVar, Optional
 
 from pydantic import Field
 
@@ -16,6 +16,27 @@
 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.
@@ -35,15 +56,15 @@ class SlimsBehaviorSession(SlimsBaseModel):
     >>> instrument = client.fetch_model(SlimsInstrument, name="323_EPHYS1_OPTO")
     >>> added = client.add_model(
     ...  SlimsBehaviorSession(
-    ...      cnvn_fk_content=mouse.pk,
-    ...      cnvn_cf_fk_instrument=instrument.pk,
-    ...      cnvn_cf_fk_trainer=[trainer.pk],
-    ...      cnvn_cf_notes="notes",
-    ...      cnvn_cf_taskStage="stage",
-    ...      cnvn_cf_task="task",
-    ...      cnvn_cf_taskSchemaVersion="0.0.1",
-    ...      cnvn_cf_stageIsOnCurriculum=True,
-    ...      cnvn_cf_scheduledDate=datetime(2021, 1, 2),
+    ...      mouse_pk=mouse.pk,
+    ...      instrument_pk=instrument.pk,
+    ...      trainer_pks=[trainer.pk],
+    ...      notes="notes",
+    ...      task_stage="stage",
+    ...      task="task",
+    ...      task_schema_version="0.0.1",
+    ...      is_curriculum_suggestion=True,
+    ...      date=datetime(2021, 1, 2),
     ...  )
     ... )
 
@@ -57,27 +78,64 @@ class SlimsBehaviorSession(SlimsBaseModel):
     ... )
     """
 
-    pk: int | None = Field(default=None, alias="cnvn_pk")
-    mouse_pk: int | None = Field(
+    pk: Optional[int] = Field(
+        default=None,
+        serialization_alias="cnvn_pk",
+        validation_alias="cnvn_pk",
+    )
+    mouse_pk: Optional[int] = Field(
         default=None,
-        alias="cnvn_fk_content",
+        serialization_alias="cnvn_fk_content",
+        validation_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")
-    instrument: int | None = Field(default=None, alias="cnvn_cf_fk_instrument")
-    trainers: list[int] = Field(default=[], alias="cnvn_cf_fk_trainer")
-    task: str | None = Field(default=None, alias="cnvn_cf_task")
-    is_curriculum_suggestion: bool | None = Field(
-        default=None, alias="cnvn_cf_stageIsOnCurriculum"
+    notes: Optional[str] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_notes",
+        validation_alias="cnvn_cf_notes",
+    )
+    task_stage: Optional[str] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_taskStage",
+        validation_alias="cnvn_cf_taskStage",
+    )
+    instrument_pk: Optional[int] = Field(
+        default=None,
+        serialization_alias="cnvn_fk_instrument",
+        validation_alias="cnvn_fk_instrument",
+    )
+    trainer_pks: Optional[list[int]] = Field(
+        default=[],
+        serialization_alias="cnvn_cf_fk_trainer",
+        validation_alias="cnvn_cf_fk_trainer",
     )
-    task_schema_version: str | None = Field(
-        default=None, alias="cnvn_cf_taskSchemaVersion"
+    task: Optional[str] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_task",
+        validation_alias="cnvn_cf_task",
+    )
+    is_curriculum_suggestion: Optional[bool] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_stageIsOnCurriculum",
+        validation_alias="cnvn_cf_stageIsOnCurriculum",
+    )
+    task_schema_version: Optional[str] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_taskSchemaVersion",
+        validation_alias="cnvn_cf_taskSchemaVersion",
+    )
+    software_version: Optional[str] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_softwareVersion",
+        validation_alias="cnvn_cf_softwareVersion",
+    )
+    date: Optional[datetime] = Field(
+        default=None,
+        serialization_alias="cnvn_cf_scheduledDate",
+        validation_alias="cnvn_cf_scheduledDate",
     )
-    software_version: str | None = Field(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 = "ContentEvent"
     _base_fetch_filters: ClassVar[dict[str, str]] = {

src/aind_slims_api/models/instrument.py

@@ -1,5 +1,7 @@
 """Contains a model for the instrument content, and a method for fetching it"""
 
+from typing import Optional
+
 from pydantic import Field
 
 from aind_slims_api.models.base import SlimsBaseModel
@@ -15,12 +17,18 @@ class SlimsInstrument(SlimsBaseModel):
     >>> instrument = client.fetch_model(SlimsInstrument, name="323_EPHYS1_OPTO")
     """
 
+    # can't use alias for this due to https://github.com/pydantic/pydantic/issues/5893
     name: str = Field(
         ...,
-        alias="nstr_name",
+        serialization_alias="nstr_name",
+        validation_alias="nstr_name",
         description="The name of the instrument",
     )
-    pk: int = Field(..., alias="nstr_pk")
+    pk: Optional[int] = Field(
+        default=None,
+        serialization_alias="nstr_pk",
+        validation_alias="nstr_pk",
+    )
     _slims_table = "Instrument"
 
     # todo add more useful fields

src/aind_slims_api/models/mouse.py

@@ -1,6 +1,6 @@
 """Contains a model for the mouse content, and a method for fetching it"""
 
-from typing import Annotated, ClassVar
+from typing import Annotated, ClassVar, Optional
 
 from pydantic import BeforeValidator, Field
 
@@ -23,14 +23,30 @@ class SlimsMouseContent(SlimsBaseModel):
     """
 
     baseline_weight_g: Annotated[float | None, UnitSpec("g")] = Field(
-        ..., alias="cntn_cf_baselineWeight"
+        ...,
+        serialization_alias="cntn_cf_baselineWeight",
+        validation_alias="cntn_cf_baselineWeight",
+    )
+    point_of_contact: Optional[str] = Field(
+        ...,
+        serialization_alias="cntn_cf_scientificPointOfContact",
+        validation_alias="cntn_cf_scientificPointOfContact",
     )
-    point_of_contact: str | None = Field(..., alias="cntn_cf_scientificPointOfContact")
     water_restricted: Annotated[bool, BeforeValidator(lambda x: x or False)] = Field(
-        ..., alias="cntn_cf_waterRestricted"
+        ...,
+        serialization_alias="cntn_cf_waterRestricted",
+        validation_alias="cntn_cf_waterRestricted",
+    )
+    barcode: str = Field(
+        ...,
+        serialization_alias="cntn_barCode",
+        validation_alias="cntn_barCode",
+    )
+    pk: Optional[int] = Field(
+        default=None,
+        serialization_alias="cntn_pk",
+        validation_alias="cntn_pk",
     )
-    barcode: str = Field(..., alias="cntn_barCode")
-    pk: int = Field(..., alias="cntn_pk")
 
     _slims_table = "Content"
     _base_fetch_filters: ClassVar[dict[str, str]] = {

src/aind_slims_api/models/unit.py

@@ -10,8 +10,20 @@
 class SlimsUnit(SlimsBaseModel):
     """Model for unit information in SLIMS"""
 
-    name: str = Field(..., alias="unit_name")
-    abbreviation: Optional[str] = Field("", alias="unit_abbreviation")
-    pk: int = Field(..., alias="unit_pk")
+    name: str = Field(
+        ...,
+        serialization_alias="unit_name",
+        validation_alias="unit_name",
+    )
+    abbreviation: Optional[str] = Field(
+        "",
+        serialization_alias="unit_abbreviation",
+        validation_alias="unit_abbreviation",
+    )
+    pk: int = Field(
+        ...,
+        serialization_alias="unit_pk",
+        validation_alias="unit_pk",
+    )
 
     _slims_table = "Unit"

src/aind_slims_api/models/user.py

@@ -18,11 +18,35 @@ class SlimsUser(SlimsBaseModel):
     >>> user = client.fetch_model(SlimsUser, username="LKim")
     """
 
-    username: str = Field(..., alias="user_userName")
-    first_name: Optional[str] = Field("", alias="user_firstName")
-    last_name: Optional[str] = Field("", alias="user_lastName")
-    full_name: Optional[str] = Field("", alias="user_fullName")
-    email: Optional[str] = Field("", alias="user_email")
-    pk: int = Field(..., alias="user_pk")
+    username: str = Field(
+        ...,
+        serialization_alias="user_userName",
+        validation_alias="user_userName",
+    )
+    first_name: Optional[str] = Field(
+        "",
+        serialization_alias="user_firstName",
+        validation_alias="user_firstName",
+    )
+    last_name: Optional[str] = Field(
+        "",
+        serialization_alias="user_lastName",
+        validation_alias="user_lastName",
+    )
+    full_name: Optional[str] = Field(
+        "",
+        serialization_alias="user_fullName",
+        validation_alias="user_fullName",
+    )
+    email: Optional[str] = Field(
+        "",
+        serialization_alias="user_email",
+        validation_alias="user_email",
+    )
+    pk: int = Field(
+        ...,
+        serialization_alias="user_pk",
+        validation_alias="user_pk",
+    )
 
     _slims_table = "User"