pystac-ext-scientific 1.0.0__tar.gz

pystac_ext_scientific-1.0.0/.gitignore

@@ -0,0 +1,163 @@
+*.pyc
+*.egg-info
+*.eggs
+.DS_Store
+data
+config.json
+stdout*
+/integration*
+.idea
+.vscode
+.actrc
+
+
+# Sphinx documentation
+.ipynb_checkpoints/
+
+docs/tutorials/pystac-example*
+docs/tutorials/spacenet-stac/
+docs/tutorials/spacenet-cog-stac/
+docs/tutorials/data/
+docs/quickstart_stac/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# asv environments
+.asv

pystac_ext_scientific-1.0.0/PKG-INFO

@@ -0,0 +1,37 @@
+Metadata-Version: 2.4
+Name: pystac-ext-scientific
+Version: 1.0.0
+Summary: Scientific extension for PySTAC
+Project-URL: Documentation, https://pystac.readthedocs.io
+Project-URL: Repository, https://github.com/stac-utils/pystac
+Project-URL: Issues, https://github.com/stac-utils/pystac/issues
+Project-URL: Changelog, https://github.com/stac-utils/pystac/blob/main/CHANGELOG.md
+Project-URL: Discussions, https://github.com/radiantearth/stac-spec/discussions/categories/stac-software
+License: Apache-2.0
+Keywords: STAC,catalog,imagery,pystac,raster,scientific
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Requires-Dist: pystac-core
+Description-Content-Type: text/markdown
+
+# pystac-ext-scientific
+
+[PySTAC](https://pypi.org/project/pystac/) extension package for the [Scientific Citation Extension](https://github.com/stac-extensions/scientific).
+This extension provides fields for linking STAC items and collections to scientific publications, including DOIs and bibliographic citations.
+
+## Supported versions
+
+- [v1.0.0](https://stac-extensions.github.io/scientific/v1.0.0/schema.json)
+
+## Versioning
+
+This package's version corresponds to the version of the extension specification it targets.
+When we release updates to the package code without changing the target extension version, we use [post releases](https://packaging.python.org/en/latest/discussions/versioning/#post-releases), e.g. `1.0.0.post1`.

pystac_ext_scientific-1.0.0/README.md

@@ -0,0 +1,13 @@
+# pystac-ext-scientific
+
+[PySTAC](https://pypi.org/project/pystac/) extension package for the [Scientific Citation Extension](https://github.com/stac-extensions/scientific).
+This extension provides fields for linking STAC items and collections to scientific publications, including DOIs and bibliographic citations.
+
+## Supported versions
+
+- [v1.0.0](https://stac-extensions.github.io/scientific/v1.0.0/schema.json)
+
+## Versioning
+
+This package's version corresponds to the version of the extension specification it targets.
+When we release updates to the package code without changing the target extension version, we use [post releases](https://packaging.python.org/en/latest/discussions/versioning/#post-releases), e.g. `1.0.0.post1`.

pystac_ext_scientific-1.0.0/pyproject.toml

@@ -0,0 +1,36 @@
+[project]
+name = "pystac-ext-scientific"
+description = "Scientific extension for PySTAC"
+readme = "README.md"
+version = "1.0.0"
+authors = []
+maintainers = []
+keywords = ["pystac", "imagery", "raster", "catalog", "STAC", "scientific"]
+license = { text = "Apache-2.0" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: Apache Software License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+requires-python = ">=3.10"
+dependencies = ["pystac-core"]
+
+[project.urls]
+Documentation = "https://pystac.readthedocs.io"
+Repository = "https://github.com/stac-utils/pystac"
+Issues = "https://github.com/stac-utils/pystac/issues"
+Changelog = "https://github.com/stac-utils/pystac/blob/main/CHANGELOG.md"
+Discussions = "https://github.com/radiantearth/stac-spec/discussions/categories/stac-software"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["pystac"]

pystac_ext_scientific-1.0.0/pystac/extensions/scientific.py

@@ -0,0 +1,360 @@
+"""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()