bioimageio.spec.dataset.v0_3

  1from typing import TYPE_CHECKING, Any, ClassVar, Dict, Literal, Optional, cast
  2
  3from pydantic import model_validator
  4
  5from .._internal.common_nodes import InvalidDescr
  6from .._internal.io import FileDescr as FileDescr
  7from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
  8from .._internal.io_basics import Sha256 as Sha256
  9from .._internal.url import HttpUrl as HttpUrl
 10from ..generic.v0_3 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 11from ..generic.v0_3 import Author as Author
 12from ..generic.v0_3 import BadgeDescr as BadgeDescr
 13from ..generic.v0_3 import BioimageioConfig as BioimageioConfig
 14from ..generic.v0_3 import CiteEntry as CiteEntry
 15from ..generic.v0_3 import Config as Config
 16from ..generic.v0_3 import DeprecatedLicenseId as DeprecatedLicenseId
 17from ..generic.v0_3 import (
 18    DocumentationSource,
 19    GenericDescrBase,
 20    LinkedResourceBase,
 21    _author_conv,  # pyright: ignore[reportPrivateUsage]
 22    _maintainer_conv,  # pyright: ignore[reportPrivateUsage]
 23)
 24from ..generic.v0_3 import Doi as Doi
 25from ..generic.v0_3 import LicenseId as LicenseId
 26from ..generic.v0_3 import LinkedResource as LinkedResource
 27from ..generic.v0_3 import Maintainer as Maintainer
 28from ..generic.v0_3 import OrcidId as OrcidId
 29from ..generic.v0_3 import RelativeFilePath as RelativeFilePath
 30from ..generic.v0_3 import ResourceId as ResourceId
 31from ..generic.v0_3 import Uploader as Uploader
 32from ..generic.v0_3 import Version as Version
 33from .v0_2 import DatasetDescr as DatasetDescr02
 34
 35
 36class DatasetId(ResourceId):
 37    pass
 38
 39
 40class DatasetDescr(GenericDescrBase):
 41    """A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
 42    processing.
 43    """
 44
 45    implemented_type: ClassVar[Literal["dataset"]] = "dataset"
 46    if TYPE_CHECKING:
 47        type: Literal["dataset"] = "dataset"
 48    else:
 49        type: Literal["dataset"]
 50
 51    id: Optional[DatasetId] = None
 52    """bioimage.io-wide unique resource identifier
 53    assigned by bioimage.io; version **un**specific."""
 54
 55    parent: Optional[DatasetId] = None
 56    """The description from which this one is derived"""
 57
 58    source: Optional[HttpUrl] = None
 59    """"URL to the source of the dataset."""
 60
 61    @model_validator(mode="before")
 62    @classmethod
 63    def _convert(cls, data: Dict[str, Any], /) -> Dict[str, Any]:
 64        if (
 65            data.get("type") == "dataset"
 66            and isinstance(fv := data.get("format_version"), str)
 67            and fv.startswith("0.2.")
 68        ):
 69            old = DatasetDescr02.load(data)
 70            if isinstance(old, InvalidDescr):
 71                return data
 72
 73            return cast(
 74                Dict[str, Any],
 75                (cls if TYPE_CHECKING else dict)(
 76                    attachments=(
 77                        []
 78                        if old.attachments is None
 79                        else [FileDescr(source=f) for f in old.attachments.files]
 80                    ),
 81                    authors=[
 82                        _author_conv.convert_as_dict(a) for a in old.authors
 83                    ],  # pyright: ignore[reportArgumentType]
 84                    badges=old.badges,
 85                    cite=[
 86                        {"text": c.text, "doi": c.doi, "url": c.url} for c in old.cite
 87                    ],  # pyright: ignore[reportArgumentType]
 88                    config=old.config,  # pyright: ignore[reportArgumentType]
 89                    covers=old.covers,
 90                    description=old.description,
 91                    documentation=cast(DocumentationSource, old.documentation),
 92                    format_version="0.3.0",
 93                    git_repo=old.git_repo,  # pyright: ignore[reportArgumentType]
 94                    icon=old.icon,
 95                    id=None if old.id is None else DatasetId(old.id),
 96                    license=old.license,  # type: ignore
 97                    links=old.links,
 98                    maintainers=[
 99                        _maintainer_conv.convert_as_dict(m) for m in old.maintainers
100                    ],  # pyright: ignore[reportArgumentType]
101                    name=old.name,
102                    source=old.source,
103                    tags=old.tags,
104                    type=old.type,
105                    uploader=old.uploader,
106                    version=old.version,
107                    **(old.model_extra or {}),
108                ),
109            )
110
111        return data
112
113
114class LinkedDataset(LinkedResourceBase):
115    """Reference to a bioimage.io dataset."""
116
117    id: DatasetId
118    """A valid dataset `id` from the bioimage.io collection."""