Skip to main content

v2

ehr_data record, v2 — canonical aliases.

Adds the appointment/encounter history columns to v1. Consumers and the record registry import from here and never touch the inner module names, mirroring steps/*/v1/__init__.py.

Module​

Submodules​

Functions​

downgrade​

def downgrade(op: Operations) ‑> None:

Migrate ehr_data v2 -> v1 (see the module docstring).

upgrade​

def upgrade(op: Operations) ‑> None:

Migrate ehr_data v1 -> v2 (see the module docstring).

Classes​

ORM​

class ORM(**kwargs):

SQLAlchemy model for the ehr_data cache table.

warning

The primary key is (task_hash, bitfount_patient_id), and task_hash is sha256(f"{pod_name}/{datasource_name}")[:32] — it carries no task configuration. Writes go through session.merge, which overwrites every column on a primary-key match. Two tasks over the same pod and datasource therefore contend for the same row: one configured without fetch_appointments writes NULL appointment columns over a row that a fetching task populated, and the fetching task's next read sees UNKNOWN. Resolving this needs a configuration discriminant column plus cache_filter_fields, i.e. a further version bump and migration.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance's class are allowed. These could be, for example, any mapped columns or relationships.

Ancestors​

Variables​

  • bitfount_patient_id : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • cell_numbers : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • condition_codes_json : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • country : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • date_of_birth : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • ehr_patient_id : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • emails : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • error : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • family_name : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • file_ids_json : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • gender : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • given_name : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • home_numbers : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • last_accessed_at : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • mailing_address : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • medical_record_number : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • next_appointment : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • patient_id : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • patient_metadata_json : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • postal_code : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • previous_appointments_json : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • previous_encounters_json : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • procedure_codes_json : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • processed_at : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • row_number : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • run_id : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • tags : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • task_hash : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]

Record​

class Record(**data: Any):

Stored EHR data record for a single patient.

The background flow extracts patient demographic and code data from the EHR datasource and stores it here. The interactive flow applies code filters against the stored diagnosis_codes, condition_codes, and procedure_codes lists to determine EHR eligibility.

file_ids_json holds all imaging file IDs associated with this patient in the batch. Multiple files for the same patient are accumulated into the list before the row is written, so no file ID is ever silently overwritten. It is None for EHR-only tasks that have no associated imaging files.

error is non-None when EHR extraction failed for this patient.

run_id is the UUID of the run that produced this record (for provenance).

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Variables​

  • static bitfount_patient_id : str
  • static cell_numbers : list[str]
  • static condition_codes_json : list[dict[str, str | None | datetime.datetime | dict[str, str]]] | None
  • static country : str | None
  • static ehr_patient_id : str
  • static emails : list[str]
  • static error : str | None
  • static family_name : str | None
  • static file_ids_json : list[str] | None
  • static gender : str | None
  • static given_name : str | None
  • static home_numbers : list[str]
  • static mailing_address : str | None
  • static medical_record_number : list[str] | None
  • static model_config
  • static next_appointment : str | None
  • static patient_id : str | None
  • static patient_metadata_json : dict[str, typing.Any] | None
  • static postal_code : str | None
  • static previous_appointments_json : list[typing.Any] | None
  • static previous_encounters_json : list[typing.Any] | None
  • static procedure_codes_json : list[dict[str, str | None | datetime.datetime | dict[str, str]]] | None
  • static row_number : int | None
  • static run_id : str | None
  • static task_hash : str