scene_pipelines.ingestion.mouse

Write helpers for the mouse tables (Strain, Mouse).

Importing this package registers the mouse schema, so it is not re-exported from scene_pipelines.ingestion: labs without mice never import it.

register_mouse

register_mouse(subject_code: str, sex: str, *, lab: DjKey[Lab], date_of_birth: date | None = None, strain: DjKey[Strain] | None = None, genotype: str | None = None, deployment: DjRow[Deployment] | None = None, if_exists: DuplicatePolicy = VERIFY) -> DjKey[Mouse]

Register a mouse by its lab code: the Subject and its Mouse row.

Parameters:

Name	Type	Description	Default
`subject_code`	`str`	Pseudonymous code, unique within `lab`.	required
`sex`	`str`	`"M"`, `"F"` or `"U"` (unknown).	required
`lab`	`DjKey[Lab]`	Existing lab primary key, e.g. `{"lab_id": "mlai"}`.	required
`date_of_birth`	`date \| None`	Optional date of birth.	`None`
`strain`	`DjKey[Strain] \| None`	Optional existing `Strain` key (background strain), e.g. `{"strain_name": "C57BL/6J"}`; add a new one first with `ensure_strain`.	`None`
`genotype`	`str \| None`	Optional free-text genotype (transgenic lines, zygosity).	`None`
`deployment`	`DjRow[Deployment] \| None`	Optional deployment row. If omitted, built from `SCENE_DEPLOYMENT_ID` / `SCENE_DEPLOYMENT_LABEL`.	`None`
`if_exists`	`DuplicatePolicy`	Policy applied to the subject and to the mouse row when already registered; see `DuplicatePolicy`.	`VERIFY`

Returns:

Type	Description
`DjKey[Mouse]`	Mouse primary key `{subject_id: ...}` (same as the subject's).

Raises:

Type	Description
`ValueError`	If `subject_code` is not a valid code, the code belongs to a subject of another kind, `strain` does not exist, `deployment` is omitted and `SCENE_DEPLOYMENT_ID` is unset, or `if_exists` rejects an existing subject or mouse.

ensure_strain

ensure_strain(strain: DjRow[Strain], *, deployment: DjRow[Deployment] | None = None, if_exists: DuplicatePolicy = VERIFY) -> DjKey[Strain]

Insert a strain row and stamp the deployment that registered it.

Parameters:

Name	Type	Description	Default
`strain`	`DjRow[Strain]`	Full strain insert dict: `strain_name` in official nomenclature (e.g. `C57BL/6J`, not `B6`) and optional `rrid`.	required
`deployment`	`DjRow[Deployment] \| None`	Optional deployment row. If omitted, built from `SCENE_DEPLOYMENT_ID` / `SCENE_DEPLOYMENT_LABEL`.	`None`
`if_exists`	`DuplicatePolicy`	Policy when `strain_name` is already stored; see `DuplicatePolicy`.	`VERIFY`

Returns:

Type	Description
`DjKey[Strain]`	Strain primary key `{strain_name: ...}`.

Raises:

Type	Description
`ValueError`	If `strain_name` or `rrid` is malformed, the name is stored under another spelling, the `rrid` already belongs to another strain, `deployment` is omitted and `SCENE_DEPLOYMENT_ID` is unset, or `if_exists` rejects the existing row.