swh.loader.package.bioconductor.loader module#

class swh.loader.package.bioconductor.loader.BioconductorPackageInfo(url: str, filename: str | None, version: str, name: str, intrinsic_version: str, last_update_date: str | None = None, checksums_str: str = None, *, directory_extrinsic_metadata: List[RawExtrinsicMetadataCore] = [], checksums: Dict[str, str] = {})[source]#

Bases: BasePackageInfo

Method generated by attrs for class BioconductorPackageInfo.

intrinsic_version#: Intrinsic version of the package, independent from the distribution (e.g. 1.18.0-5)

last_update_date#: Last update date of the package. (e.g. 2023-04-25)

EXTID_TYPE: str = 'bioconductor-md5'#

MANIFEST_FORMAT: Template | None = <string.Template object>#: If not None, used by the default extid() implementation to format a manifest, before hashing it to produce an ExtID.

classmethod from_metadata(a_metadata: Dict[str, Any], version: str) → BioconductorPackageInfo[source]#

class swh.loader.package.bioconductor.loader.BioconductorLoader(storage: StorageInterface, url: str, packages: Dict[str, Dict[str, Any]], **kwargs: Any)[source]#

Bases: PackageLoader[BioconductorPackageInfo]

Bioconductor Loader implementation.

Parameters:

url – Origin url (e.g. https://bioconductor.org/packages/a4)

packages –

versioned packages and associated artifacts, example:

{
  "3.16/bioc/1.46.0": {
      "package": "a4",
      "release": "3.16",
      "tar_url": (
          "https://bioconductor.org/packages/3.16/bioc"
          "/src/contrib/a4_1.46.0.tar.gz"
      ),
      "version": "1.46.0",
      "category": "bioc",
      "last_update_date": "2022-11-01",
      "checksums": {
          "md5": "4fe2823df78513c79777d009196856fd"
      }
  },
  # ...
}

visit_type: str = 'bioconductor'#

get_versions() → Sequence[str][source]#: Sort package versions in ascending order and return them.

get_default_version() → str[source]#: Get the latest release version of a bioconductor package

get_package_info(version: str) → Iterator[Tuple[str, BioconductorPackageInfo]][source]#

Given a release version of a package, retrieve the associated: package information for such version.

Parameters:: version – Package version
Returns:: (branch name, package metadata)

build_release(p_info: BioconductorPackageInfo, uncompressed_path: str, directory: bytes) → Release | None[source]#

Build the release from the archive metadata (extrinsic artifact metadata) and the intrinsic metadata.

Parameters:

p_info – Package information
uncompressed_path – Artifact uncompressed path on disk