ppktstore.registry package

ppktstore.registry.configure_phenopacket_registry(store_dir: str | ~pathlib.Path | None = None, release_service: ~ppktstore.registry._api.PhenopacketStoreReleaseService = <ppktstore.registry._github.GitHubPhenopacketStoreReleaseService object>, remote_phenopacket_store_service: ~ppktstore.registry._api.RemotePhenopacketStoreService = <ppktstore.registry._github.GitHubRemotePhenopacketStoreService object>) → PhenopacketStoreRegistry

A function for getting default PhenopacketStoreRegistry.

Parameters:

• store_dir – path to the directory for storing the registry data ($HOME/.phenopacket-store if None is provided).

• release_service – the service for getting release tags. By default, the tags are fetched from GitHub REST API.

• remote_phenopacket_store_service – a service for getting Phenopacket Store ZIP release data. By default, the data is obtained from GitHub REST API.

class ppktstore.registry.PhenopacketStoreRegistry(data_dir: Path, release_service: PhenopacketStoreReleaseService, remote_phenopacket_store_service: RemotePhenopacketStoreService)

Bases: object

PhenopacketStoreRegistry manages Phenopacket Store releases on a local system.

The registry fetches a ZIP archive with a specific version of Phenopacket Store (or the latest version) from GitHub and stores it in a data directory. Any subsequent openings of Phenopacket Store will use the local ZIP file.

clear()

Clear all Phenopacket Store releases.

open_phenopacket_store(release: str | None = None) → PhenopacketStoreZipAdaptor

Open Phenopacket Store.

Provides an adaptor object that should be used as a context manager to ensure proper resource cleanup.

Example

Let’s load all phenopackets of the SUOX cohort from the 0.1.18 release of Phenopacket Store:

>>> from ppktstore.registry import configure_phenopacket_registry
>>> registry = configure_phenopacket_registry()
>>> with registry.open_phenopacket_store(release="0.1.18") as ps:
...   phenopackets = list(ps.iter_cohort_phenopackets("SUOX"))
>>> len(phenopackets)
35

Parameters:

release – a str with Phenopacket Store release tag (e.g. 0.1.18) or None if the latest release should be loaded.

resolve_registry_path(release: str | None = None) → Path

Resolve the path of a specific Phenopacket Store release within the registry.

Note, the path points to the location of the release ZIP in the local filesystem. The path may point to a non-existing file, if the load function has not been run yet.

Example

>>> from ppktstore.registry import configure_phenopacket_registry
>>> registry = configure_phenopacket_registry()
>>> registry.resolve_registry_path(release='0.1.18')
pathlib.Path('/home/user/.phenopacket-store/0.1.18.zip')

Parameters:

release – an optional str with the desired PS release (if None, the latest release will be provided).

Returns:

a path to the PS release file.

class ppktstore.registry.PhenopacketStoreReleaseService

Bases: object

PhenopacketStoreReleaseService knows how to fetch the Phenopacket Store release tags (e.g. 0.1.18).

abstractmethod fetch_tags() → Iterable[str]

Fetch sequence of Phenopacket Store release tags.

class ppktstore.registry.RemotePhenopacketStoreService

Bases: object

RemotePhenopacketStoreService knows how to open a typing.BinaryIO for reading content of a particular Phenopacket Store release.

abstractmethod fetch_resource(release: str) → BufferedIOBase

Open a connection for reading bytes of the remote resource.

Parameters:

release – a str with the desired Phenopacket Store release.

Returns:

a binary IO for reading the Phenopacket Store data.

class ppktstore.registry.PhenopacketStoreZipAdaptor(zip_path: Path)

Bases: object

A context manager for handling opening and closing of the Phenopacket Store release ZIP handle.

Phenopackets are loaded in a lazy fashion - no phenopackets are loaded upon store opening.