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# Source code for pystac.extensions.scientific

    """Implements the :stac-ext:`Scientific Citation Extension <scientific>`.

    For a description of Digital Object Identifiers (DOIs), see the DOI Handbook:

    https://doi.org/10.1000/182
    """

    from __future__ import annotations

    from typing import Any, Generic, Literal, TypeVar, cast

    import pystac
    from pystac.extensions.base import (
        ExtensionManagementMixin,
        PropertiesExtension,
        SummariesExtension,
    )
    from pystac.extensions.hooks import ExtensionHooks
    from pystac.utils import StringEnum, map_opt

    #: Generalized version of :class:`~pystac.Collection` or :class:`~pystac.Item`
    T = TypeVar("T", pystac.Collection, pystac.Item)

    SCHEMA_URI: str = "https://stac-extensions.github.io/scientific/v1.0.0/schema.json"
    PREFIX: str = "sci:"

    # Field names
    DOI_PROP: str = PREFIX + "doi"
    CITATION_PROP: str = PREFIX + "citation"
    PUBLICATIONS_PROP: str = PREFIX + "publications"

    DOI_URL_BASE = "https://doi.org/"

    # Link rel type.

    class ScientificRelType(StringEnum):
        """A list of rel types defined in the Scientific Citation Extension.

        See the :stac-ext:`Scientific Citation Extension Relation types
        <scientific#relation-types>` documentation for details.
        """

        CITE_AS = "cite-as"
        """Used to indicate a link to the publication referenced by the ``sci:doi``
        field."""

    def doi_to_url(doi: str) -> str:
        """Converts a DOI to the corresponding URL."""
        from urllib import parse

        return DOI_URL_BASE + parse.quote(doi)

    class Publication:
        """Helper for Publication entries."""

        citation: str | None
        doi: str | None

        def __init__(self, doi: str | None, citation: str | None) -> None:
            self.doi = doi
            self.citation = citation

        def __eq__(self, other: Any) -> bool:
            if not isinstance(other, Publication):
                return NotImplemented

            return self.doi == other.doi and self.citation == other.citation

        def __repr__(self) -> str:
            return f"<Publication doi={self.doi} target={self.citation}>"

        def to_dict(self) -> dict[str, str | None]:
            import copy

            return copy.deepcopy({"doi": self.doi, "citation": self.citation})

        @staticmethod
        def from_dict(d: dict[str, str]) -> Publication:
            return Publication(d.get("doi"), d.get("citation"))

        def get_link(self) -> pystac.Link | None:
            """Gets a :class:`~pystac.Link` for the DOI for this publication. If
            :attr:`Publication.doi` is ``None``, this method will also return ``None``."""
            if self.doi is None:
                return None
            return pystac.Link(ScientificRelType.CITE_AS, doi_to_url(self.doi))

    def remove_link(links: list[pystac.Link], doi: str | None) -> None:
        if doi is None:
            return
        url = doi_to_url(doi)
        for i, a_link in enumerate(links):
            if a_link.rel != ScientificRelType.CITE_AS:
                continue
            if a_link.target == url:
                del links[i]
                break

    class ScientificExtension(
        Generic[T],
        PropertiesExtension,
        ExtensionManagementMixin[pystac.Item | pystac.Collection],
    ):
        """An abstract class that can be used to extend the properties of an
        :class:`~pystac.Item` or a :class:`pystac.Collection` with properties from the
        :stac-ext:`Scientific Citation Extension <scientific>`. This class is generic over
        the type of STAC Object to be extended (e.g. :class:`~pystac.Item`,
        :class:`~pystac.Collection`).

        To create a concrete instance of :class:`ScientificExtension`, use the
        :meth:`ScientificExtension.ext` method. For example:

        .. code-block:: python

           >>> item: pystac.Item = ...
           >>> sci_ext = ScientificExtension.ext(item)
        """

        name: Literal["sci"] = "sci"
        obj: pystac.STACObject

        def __init__(self, obj: pystac.STACObject) -> None:
            self.obj = obj

        def apply(
            self,
            doi: str | None = None,
            citation: str | None = None,
            publications: list[Publication] | None = None,
        ) -> None:
            """Applies scientific extension properties to the extended
            :class:`~pystac.Item`.

            Args:
                doi : Optional DOI string for the item.  Must not be a DOI link.
                citation : Optional human-readable reference.
                publications : Optional list of relevant publications
                    referencing and describing the data.
            """
            self.doi = doi
            self.citation = citation
            self.publications = publications

        @property
        def doi(self) -> str | None:
            """Get or sets the DOI for the item.

            This MUST NOT be a DOIs link. For all DOI names respective DOI links SHOULD be
            added to the links section.
            """
            return self._get_property(DOI_PROP, str)

        @doi.setter
        def doi(self, v: str | None) -> None:
            if DOI_PROP in self.properties:
                if v == self.properties[DOI_PROP]:
                    return
                remove_link(self.obj.links, self.properties[DOI_PROP])

            if v is not None:
                self.properties[DOI_PROP] = v
                url = doi_to_url(v)
                self.obj.add_link(pystac.Link(ScientificRelType.CITE_AS, url))

        @property
        def citation(self) -> str | None:
            """Get or sets the recommended human-readable reference (citation) to be used by
            publications citing the data.

            No specific citation style is suggested, but the citation should contain all
            information required to find the publication distinctively.
            """
            return self._get_property(CITATION_PROP, str)

        @citation.setter
        def citation(self, v: str | None) -> None:
            self._set_property(CITATION_PROP, v)

        @property
        def publications(self) -> list[Publication] | None:
            """Get or sets the list of relevant publications referencing and describing the
            data."""
            return map_opt(
                lambda pubs: [Publication.from_dict(pub) for pub in pubs],
                self._get_property(PUBLICATIONS_PROP, list[dict[str, Any]]),
            )

        @publications.setter
        def publications(self, v: list[Publication] | None) -> None:
            self._set_property(
                PUBLICATIONS_PROP, map_opt(lambda pubs: [pub.to_dict() for pub in pubs], v)
            )
            if v is not None:
                for pub in v:
                    pub_link = pub.get_link()
                    if pub_link is not None:
                        self.obj.add_link(pub_link)

        # None for publication will clear all.

        def remove_publication(self, publication: Publication | None = None) -> None:
            """Removes the given :class:`Publication` from the extended
            :class:`~pystac.Item`. If the ``publication`` argument is ``None``, all
            publications will be removed from the :class:`~pystac.Item`."""
            if PUBLICATIONS_PROP not in self.properties:
                return

            if not publication:
                pubs = self.publications
                if pubs is not None:
                    for one_pub in pubs:
                        remove_link(self.obj.links, one_pub.doi)

                del self.properties[PUBLICATIONS_PROP]
                return

            # One publication and link to remove
            remove_link(self.obj.links, publication.doi)
            to_remove = publication.to_dict()
            self.properties[PUBLICATIONS_PROP].remove(to_remove)

            if not self.properties[PUBLICATIONS_PROP]:
                del self.properties[PUBLICATIONS_PROP]

        @classmethod
        def get_schema_uri(cls) -> str:
            return SCHEMA_URI

        @classmethod
        def ext(cls, obj: T, add_if_missing: bool = False) -> ScientificExtension[T]:
            """Extends the given STAC Object with properties from the :stac-ext:`Scientific
            Extension <scientific>`.

            This extension can be applied to instances of :class:`~pystac.Item` or
            :class:`~pystac.Collection`.

            Raises:

                pystac.ExtensionTypeError : If an invalid object type is passed.
            """
            if isinstance(obj, pystac.Collection):
                cls.ensure_has_extension(obj, add_if_missing)
                return cast(ScientificExtension[T], CollectionScientificExtension(obj))
            if isinstance(obj, pystac.Item):
                cls.ensure_has_extension(obj, add_if_missing)
                return cast(ScientificExtension[T], ItemScientificExtension(obj))
            else:
                raise pystac.ExtensionTypeError(cls._ext_error_message(obj))

        @classmethod
        def summaries(
            cls, obj: pystac.Collection, add_if_missing: bool = False
        ) -> SummariesScientificExtension:
            """Returns the extended summaries object for the given collection."""
            cls.ensure_has_extension(obj, add_if_missing)
            return SummariesScientificExtension(obj)

    class CollectionScientificExtension(ScientificExtension[pystac.Collection]):
        """A concrete implementation of :class:`ScientificExtension` on an
        :class:`~pystac.Collection` that extends the properties of the Item to include
        properties defined in the :stac-ext:`Scientific Citation Extension <scientific>`.

        This class should generally not be instantiated directly. Instead, call
        :meth:`ScientificExtension.ext` on an :class:`~pystac.Collection` to extend it.
        """

        collection: pystac.Collection
        """The :class:`~pystac.Collection` being extended."""

        properties: dict[str, Any]
        """The :class:`~pystac.Collection` properties, including extension properties."""

        links: list[pystac.Link]
        """The list of :class:`~pystac.Link` objects associated with the
        :class:`~pystac.Collection` being extended, including links added by this extension.
        """

        def __init__(self, collection: pystac.Collection):
            self.collection = collection
            self.properties = collection.extra_fields
            self.links = collection.links
            super().__init__(self.collection)

        def __repr__(self) -> str:
            return "<CollectionScientificExtension Collection id={}>".format(
                self.collection.id
            )

    class ItemScientificExtension(ScientificExtension[pystac.Item]):
        """A concrete implementation of :class:`ScientificExtension` on an
        :class:`~pystac.Item` that extends the properties of the Item to include
        properties defined in the :stac-ext:`Scientific Citation Extension
        <scientific>`.

        This class should generally not be instantiated directly. Instead, call
        :meth:`ScientificExtension.ext` on an :class:`~pystac.Item` to extend it.
        """

        item: pystac.Item
        """The :class:`~pystac.Item` being extended."""

        properties: dict[str, Any]
        """The :class:`~pystac.Item` properties, including extension properties."""

        links: list[pystac.Link]
        """The list of :class:`~pystac.Link` objects associated with the
        :class:`~pystac.Item` being extended, including links added by this extension.
        """

        def __init__(self, item: pystac.Item):
            self.item = item
            self.properties = item.properties
            self.links = item.links
            super().__init__(self.item)

        def __repr__(self) -> str:
            return f"<ItemScientificExtension Item id={self.item.id}>"

    class SummariesScientificExtension(SummariesExtension):
        """A concrete implementation of :class:`~pystac.extensions.base.SummariesExtension`
        that extends the ``summaries`` field of a :class:`~pystac.Collection` to include
        properties defined in the :stac-ext:`Scientific Citation Extension <scientific>`.
        """

        @property
        def citation(self) -> list[str] | None:
            """Get or sets the summary of :attr:`ScientificExtension.citation` values
            for this Collection.
            """
            return self.summaries.get_list(CITATION_PROP)

        @citation.setter
        def citation(self, v: list[str] | None) -> None:
            self._set_summary(CITATION_PROP, v)

        @property
        def doi(self) -> list[str] | None:
            """Get or sets the summary of :attr:`ScientificExtension.citation` values
            for this Collection.
            """
            return self.summaries.get_list(DOI_PROP)

        @doi.setter
        def doi(self, v: list[str] | None) -> None:
            self._set_summary(DOI_PROP, v)

    class ScientificExtensionHooks(ExtensionHooks):
        schema_uri: str = SCHEMA_URI
        prev_extension_ids = {"scientific"}
        stac_object_types = {pystac.STACObjectType.COLLECTION, pystac.STACObjectType.ITEM}

    SCIENTIFIC_EXTENSION_HOOKS: ExtensionHooks = ScientificExtensionHooks()