dae.schema2_storage package

Submodules

dae.schema2_storage.schema2_import_storage module

class dae.schema2_storage.schema2_import_storage.Schema2ImportStorage

Bases: ImportStorage

Import logic for data in the Schema 2 format.

BATCH_SIZE = 1000

generate_import_task_graph(project: ImportProject) → TaskGraph

Generate task grap for import of the project into this storage.

static generate_reannotate_task_graph(gpf_instance: GPFInstance, study_dir: str, region_size: int, allow_repeated_attributes: bool, work_dir: Path | None = None, *, full_reannotation: bool = False) → TaskGraph

Generate TaskGraph for reannotation of a given study.

static load_meta(project: ImportProject) → dict[str, str]

Load meta data from the parquet dataset.

dae.schema2_storage.schema2_import_storage.schema2_project_dataset_layout(project: ImportProject) → Schema2DatasetLayout

dae.schema2_storage.schema2_layout module

class dae.schema2_storage.schema2_layout.Schema2DatasetLayout(study: str, pedigree: str, summary: str | None, family: str | None, meta: str, base_dir: str | None = None)

Bases: object

Schema2 dataset layout data class.

base_dir: str | None = None

family: str | None

has_variants() → bool

meta: str

pedigree: str

study: str

summary: str | None

dae.schema2_storage.schema2_layout.create_schema2_dataset_layout(study_dir: str) → Schema2DatasetLayout

Create dataset layout for a given directory.

Used for creating new datasets, where all tables should exist.

dae.schema2_storage.schema2_layout.load_schema2_dataset_layout(study_dir: str, *, has_variants: bool = True) → Schema2DatasetLayout

Create dataset layout for a given directory.

Assumes that the dataset already exists, therefore it should check whether summary and family tables exist.

Module contents