destiny_sdk 0.5.1__py3-none-any.whl → 0.6.0__py3-none-any.whl

destiny_sdk/__init__.py

@@ -8,6 +8,7 @@ from . import (
     imports,
     references,
     robots,
+    search,
     visibility,
 )
 
@@ -19,5 +20,6 @@ __all__ = [
     "imports",
     "references",
     "robots",
+    "search",
     "visibility",
 ]

destiny_sdk/core.py

@@ -2,7 +2,9 @@
 
 from typing import Self
 
-from pydantic import BaseModel
+from pydantic import BaseModel, Field
+
+from destiny_sdk.search import SearchResultPage, SearchResultTotal
 
 # These are non-standard newline characters that are not escaped by model_dump_json().
 # We want jsonl files to have empirical new lines so they can be streamed line by line.
@@ -47,3 +49,14 @@ class _JsonlFileInputMixIn(BaseModel):
         :rtype: Self
         """
         return cls.model_validate_json(jsonl)
+
+
+class SearchResultMixIn(BaseModel):
+    """A mixin class for models that represent search results."""
+
+    total: SearchResultTotal = Field(
+        description="The total number of results matching the search criteria.",
+    )
+    page: SearchResultPage = Field(
+        description="Information about the page of results.",
+    )

destiny_sdk/labs/__init__.py

@@ -0,0 +1,10 @@
+"""
+Experimental DESTINY SDK.
+
+The DESTINY SDK-labs provides experimental features
+for interacting with DESTINY repository.
+"""
+
+from . import references
+
+__all__ = ["references"]

destiny_sdk/labs/references.py

@@ -0,0 +1,154 @@
+"""
+Extended Reference SDK.
+
+Extended Reference class for the Destiny SDK
+with added experimental convenience methods and properties.
+"""
+
+from collections.abc import Generator
+from typing import cast
+
+from pydantic import BaseModel, Field
+
+from destiny_sdk.enhancements import (
+    Annotation,
+    AnnotationType,
+    BibliographicMetadataEnhancement,
+    EnhancementType,
+)
+from destiny_sdk.identifiers import ExternalIdentifierType
+from destiny_sdk.references import Reference
+
+
+class LabsReference(BaseModel):
+    """Experimental presenter class for Reference with added convenience methods."""
+
+    reference: Reference = Field(
+        ...,
+        description="The core Reference object",
+    )
+
+    def _get_id(self, identifier_type: ExternalIdentifierType) -> str | int | None:
+        """Fetch an identifier matching the given identifier_type."""
+        for identifier in self.reference.identifiers or []:
+            if identifier.identifier_type == identifier_type:
+                return identifier.identifier
+        return None
+
+    @property
+    def openalex_id(self) -> str | None:
+        """Return an OpenAlex ID for the reference."""
+        return cast(
+            str | None, self._get_id(identifier_type=ExternalIdentifierType.OPEN_ALEX)
+        )
+
+    @property
+    def doi(self) -> str | None:
+        """Return a DOI for the reference."""
+        return cast(
+            str | None, self._get_id(identifier_type=ExternalIdentifierType.DOI)
+        )
+
+    @property
+    def pubmed_id(self) -> int | None:
+        """Return a pubmed ID for the reference."""
+        return cast(
+            int | None, self._get_id(identifier_type=ExternalIdentifierType.PM_ID)
+        )
+
+    @property
+    def abstract(self) -> str | None:
+        """Return an abstract for the reference."""
+        for enhancement in self.reference.enhancements or []:
+            if enhancement.content.enhancement_type == EnhancementType.ABSTRACT:
+                return enhancement.content.abstract
+        return None
+
+    @property
+    def publication_year(self) -> int | None:
+        """Return a publication year for the reference."""
+        for meta in self.it_bibliographics():
+            if meta.publication_year is not None:
+                return meta.publication_year
+        return None
+
+    @property
+    def title(self) -> str | None:
+        """The title of the reference. If multiple are present, return first one."""
+        for meta in self.it_bibliographics():
+            if meta.title is not None:
+                return meta.title
+        return None
+
+    def it_bibliographics(
+        self,
+    ) -> Generator[BibliographicMetadataEnhancement, None, None]:
+        """Iterate bibliographic enhancements."""
+        for enhancement in self.reference.enhancements or []:
+            if enhancement.content.enhancement_type == EnhancementType.BIBLIOGRAPHIC:
+                yield enhancement.content
+
+    def it_annotations(
+        self,
+        source: str | None = None,
+        annotation_type: AnnotationType | None = None,
+        scheme: str | None = None,
+        label: str | None = None,
+    ) -> Generator[Annotation, None, None]:
+        """
+        Iterate annotation enhancements for the given filters.
+
+        :param source: Optional filter for Enhancement.source
+        :param annotation_type: Optional filter for
+                                AnnotationEnhancement.annotation_type
+        :param scheme: Optional filter for Annotation.scheme
+        :param label: Optional filter for Annotation.label
+        """
+        for enhancement in self.reference.enhancements or []:
+            if enhancement.content.enhancement_type == EnhancementType.ANNOTATION:
+                if source is not None and enhancement.source != source:
+                    continue
+                for annotation in enhancement.content.annotations:
+                    if (
+                        annotation_type is not None
+                        and annotation.annotation_type != annotation_type
+                    ):
+                        continue
+                    if scheme is not None and annotation.scheme != scheme:
+                        continue
+                    if label is not None and annotation.label != label:
+                        continue
+                    yield annotation
+
+    def has_bool_annotation(
+        self,
+        source: str | None = None,
+        scheme: str | None = None,
+        label: str | None = None,
+        expected_value: bool = True,  # noqa: FBT001, FBT002
+    ) -> bool | None:
+        """
+        Check if a specific annotation exists and is true.
+
+        :param source: Optional filter for Enhancement.source
+        :param scheme: Optional filter for Annotation.scheme
+        :param label: Optional filter for Annotation.label
+        :param expected_value: Specify expected boolean annotation value
+        :return: Returns the boolean value for the first annotation matching
+                 the filters or None if nothing is found.
+        """
+        if scheme is None and label is None:
+            msg = "Please use at least one of the optional scheme or label filters."
+            raise AssertionError(msg)
+
+        found_annotation = False
+        for annotation in self.it_annotations(
+            source=source,
+            annotation_type=AnnotationType.BOOLEAN,
+            scheme=scheme,
+            label=label,
+        ):
+            if annotation.value == expected_value:
+                return True
+            found_annotation = True
+        return False if found_annotation else None

destiny_sdk/references.py

@@ -4,7 +4,7 @@ from typing import Self
 
 from pydantic import UUID4, BaseModel, Field, TypeAdapter
 
-from destiny_sdk.core import _JsonlFileInputMixIn
+from destiny_sdk.core import SearchResultMixIn, _JsonlFileInputMixIn
 from destiny_sdk.enhancements import Enhancement, EnhancementFileInput
 from destiny_sdk.identifiers import ExternalIdentifier
 from destiny_sdk.visibility import Visibility
@@ -65,3 +65,11 @@ class ReferenceFileInput(_JsonlFileInputMixIn, BaseModel):
         default=None,
         description="A list of enhancements for the reference",
     )
+
+
+class ReferenceSearchResult(SearchResultMixIn, BaseModel):
+    """A search result for references."""
+
+    references: list[Reference] = Field(
+        description="The references returned by the search.",
+    )

destiny_sdk/search.py

@@ -0,0 +1,52 @@
+"""Models for search queries and results."""
+
+from pydantic import BaseModel, Field
+
+
+class SearchResultTotal(BaseModel):
+    """Information about the total number of search results."""
+
+    count: int = Field(
+        description="The total number of results matching the search criteria.",
+    )
+    is_lower_bound: bool = Field(
+        description="Whether the count is a lower bound (true) or exact (false).",
+    )
+
+
+class SearchResultPage(BaseModel):
+    """Information about the page of search results."""
+
+    count: int = Field(
+        description="The number of results on this page.",
+    )
+    number: int = Field(
+        description="The page number of results returned, indexed from 1.",
+    )
+
+
+class AnnotationFilter(BaseModel):
+    """An annotation filter for search queries."""
+
+    scheme: str = Field(
+        description="The annotation scheme to filter by.",
+    )
+    label: str | None = Field(
+        None,
+        description="The annotation label to filter by.",
+    )
+    score: float | None = Field(
+        None,
+        description="The minimum score for the annotation filter.",
+        ge=0.0,
+        le=1.0,
+    )
+
+    def serialize(self) -> str:
+        """Serialize the annotation filter to a string."""
+        annotation = self.scheme
+        if self.label:
+            annotation += f"/{self.label}"
+        if self.score is not None:
+            annotation += f"@{self.score}"
+        return annotation

{destiny_sdk-0.5.1.dist-info → destiny_sdk-0.6.0.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: destiny_sdk
-Version: 0.5.1
+Version: 0.6.0
 Summary: A software development kit (sdk) to support interaction with the DESTINY repository
-Author-email: Adam Hamilton <adam@futureevidence.org>, Andrew Harvey <andrew@futureevidence.org>, Daniel Breves <daniel@futureevidence.org>, Jack Walmisley <jack@futureevidence.org>
+Author-email: Adam Hamilton <adam@futureevidence.org>, Andrew Harvey <andrew@futureevidence.org>, Daniel Breves <daniel@futureevidence.org>, Jack Walmisley <jack@futureevidence.org>, Tim Repke <tim.repke@pik-potsdam.de>
 License-Expression: Apache-2.0
 License-File: LICENSE
 Requires-Python: ~=3.12
@@ -14,6 +14,7 @@ Requires-Dist: pytest-asyncio<2,>=1.0.0
 Requires-Dist: pytest-httpx<0.36,>=0.35.0
 Requires-Dist: pytest<9,>=8.4.0
 Requires-Dist: python-jose<4,>=3.4.0
+Provides-Extra: labs
 Description-Content-Type: text/markdown
 
 # DESTINY SDK
@@ -34,6 +35,13 @@ pip install destiny-sdk
 uv add destiny-sdk
 ```
 
+Some labs functionality may require extra dependencies - these can be installed by:
+
+```sh
+pip install destiny-sdk[labs]
+uv add destiny-sdk --extra labs
+```
+
 ## Development
 
 ### Dependencies

{destiny_sdk-0.5.1.dist-info → destiny_sdk-0.6.0.dist-info}/RECORD

@@ -1,17 +1,20 @@
-destiny_sdk/__init__.py,sha256=gmmrceJX84T4msk_GSm_OjTQvCpHFZRjnlUK5_7IODE,356
+destiny_sdk/__init__.py,sha256=NdSlsPQyDF3TW30_JzbvYMRBRA9iT677iTRWWCMdYOA,382
 destiny_sdk/auth.py,sha256=bY72ywZEcG_67YBd9PrwgWTXkCf58rhLvVEXrtXbWtA,6247
 destiny_sdk/client.py,sha256=fTBtuq5emT8ieNtCuCY8Y6xAKZJDLq8sG1WOvmjLz-I,4971
-destiny_sdk/core.py,sha256=_FwDaczKTSaUSV_qfcnLhkBbZagh4ayFpN0qUwJ03-o,1448
+destiny_sdk/core.py,sha256=PYCYpY72MHXo7iQMHtnXcnCOGn6CUsbYoykHvtQl4Oc,1857
 destiny_sdk/enhancements.py,sha256=SkIlIlWKBN7Z-aXpQiy22SXrU7zVnKxaRb4F5yaFsO8,11503
 destiny_sdk/identifiers.py,sha256=1N2cszBmnQoUeKm54-7MUTO-zTDuvW8U9OjTeAmhWvo,7182
 destiny_sdk/imports.py,sha256=b-rh-dt3NsyLGxqmVzIzKaHiXhbw-3wtAaBN-ZW-i1E,5940
 destiny_sdk/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-destiny_sdk/references.py,sha256=Dx-WKcv9gNJkKU9n52AYoEey7siTHR5_wBVBKSHND6Q,2321
+destiny_sdk/references.py,sha256=3Y8gBMTSyZY35S3pB1bnVHMai9RRiGeoGZysNvSo7kk,2553
 destiny_sdk/robots.py,sha256=I_ZvMxwST52e8ovhv0-gPbOB3P9tptbRG0LrkNNOqKo,13463
+destiny_sdk/search.py,sha256=LIPj_h0yMnav_Stp4qRLg1PvZa6h3BV4N2bXwAYZDqA,1447
 destiny_sdk/visibility.py,sha256=8D44Q868YdScAt6eAFgXXrhonozXnv_Qa5w5yEGMPX8,577
+destiny_sdk/labs/__init__.py,sha256=H4RFPyeelqZ56PagnWPX-JZeWlxPnCZoYHtr4c9SU9Q,180
+destiny_sdk/labs/references.py,sha256=iZisRgGZ5c7X7uTFoe6Q0AwwFMa4yJbIoPUVv_hvOiU,5589
 destiny_sdk/parsers/__init__.py,sha256=d5gS--bXla_0I7e_9wTBnGWMXt2U8b-_ndeprTPe1hk,149
 destiny_sdk/parsers/eppi_parser.py,sha256=rEOtt_5Kp3oktFlzRTLZ2x4_7aQ9-ba3FYpkaEnpnvs,5521
-destiny_sdk-0.5.1.dist-info/METADATA,sha256=eKznxYvVJhW-IVlA16LHzJ2QtpzfG3RyBKk9e-x_o8w,2440
-destiny_sdk-0.5.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-destiny_sdk-0.5.1.dist-info/licenses/LICENSE,sha256=6QURU4gvvTjVZ5rfp5amZ6FtFvcpPhAGUjxF5WSZAHI,9138
-destiny_sdk-0.5.1.dist-info/RECORD,,
+destiny_sdk-0.6.0.dist-info/METADATA,sha256=_xLg34LzOiBZmcjmg6-P6bTKmHIBnArl-0k-Qndftwc,2657
+destiny_sdk-0.6.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+destiny_sdk-0.6.0.dist-info/licenses/LICENSE,sha256=6QURU4gvvTjVZ5rfp5amZ6FtFvcpPhAGUjxF5WSZAHI,9138
+destiny_sdk-0.6.0.dist-info/RECORD,,