basic kg API service setup w participant and biosample

dependencies.py

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+from fastapi import Header, HTTPException
+
+
+async def get_token_header(x_token: str = Header()):
+    if x_token != "test-token":
+        raise HTTPException(status_code=400, detail="X-Token header invalid")
+
+
+async def get_query_token(token: str):
+    if token != "sooyoung":
+        raise HTTPException(status_code=400, detail="No Sooyoung token provided")

main.py

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+from fastapi import Depends, FastAPI
+
+from dependencies import get_query_token, get_token_header
+# from internal import admin
+from routers import biosamples, participants
+
+import uvicorn
+from fastapi_sqlalchemy import DBSessionMiddleware, db
+import os
+from dotenv import load_dotenv
+
+load_dotenv('.env')
+
+app = FastAPI(dependencies=[Depends(get_query_token)])
+
+
+app.include_router(participants.router)
+app.include_router(biosamples.router)
+# app.include_router(
+#     admin.router,
+#     prefix="/admin",
+#     tags=["admin"],
+#     dependencies=[Depends(get_token_header)],
+#     responses={418: {"description": "I'm a teapot"}},
+# )
+
+# to avoid csrftokenError
+app.add_middleware(DBSessionMiddleware, db_url=os.environ['DATABASE_URL'])
+
+@app.get("/")
+async def root():
+    return {"message": "Knowledge Graph API"}
+
+
+# To run locally
+if __name__ == '__main__':
+    uvicorn.run(app, host='0.0.0.0', port=8000)

models/annotations.py

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+from pydantic import BaseModel
+
+
+class Annotations(BaseModel):
+    name: str

models/assay.py

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+from pydantic import BaseModel
+
+
+class Assay(BaseModel):
+    name: str

models/atlas.py

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+from pydantic import BaseModel
+
+
+class Atlas(BaseModel):
+    type: Spatial, Dimensional

models/biosample.py

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+from dandischema import DandiBaseModel
+
+
+class BioSample(DandiBaseModel):
+    """Description of the sample that was studied"""
+
+    identifier: Identifier = Field(nskey="schema")
+    sampleType: SampleType = Field(
+        description="Identifier for the sample characteristics (e.g., from OBI, Encode).",
+        nskey="dandi",
+    )
+    assayType: Optional[List[AssayType]] = Field(
+        None, description="Identifier for the assay(s) used (e.g., OBI).", nskey="dandi"
+    )
+    anatomy: Optional[List[Anatomy]] = Field(
+        None,
+        description="Identifier for what organ the sample belongs "
+                    "to. Use the most specific descriptor from sources such as UBERON.",
+        nskey="dandi",
+    )
+
+    wasDerivedFrom: Optional[List["BioSample"]] = Field(
+        None,
+        description="Describes the hierarchy of sample derivation or aggregation.",
+        nskey="prov",
+    )
+    wasAttributedTo: Optional[List[Participant]] = Field(
+        None,
+        description="Participant(s) or Subject(s) associated with this sample.",
+        nskey="prov",
+    )
+    sameAs: Optional[List[Identifier]] = Field(None, nskey="schema")
+    hasMember: Optional[List[Identifier]] = Field(None, nskey="prov")
+
+    _ldmeta = {
+        "rdfs:subClassOf": ["schema:Thing", "prov:Entity"],
+        "rdfs:label": "Information about the biosample.",
+        "nskey": "dandi",
+    }

models/cell.py

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+from pydantic import BaseModel
+
+
+class Cell(BaseModel):
+    location: str
+    cellType: CellType

models/cellbygene.py

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+from pydantic import BaseModel
+
+
+class CellbyGene(BaseModel):
+    cell: Cell

models/celltype.py

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+from pydantic import BaseModel
+
+
+class CellType(BaseModel):
+    name: str

models/instrument.py

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+from pydantic import BaseModel
+
+
+class Instrument(BaseModel):
+    name: str

models/location.py

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+from pydantic import BaseModel
+
+
+class Location(BaseModel):
+    photo: Photo
+    coordinates: [str, str]
+    atlasMap: dict(Atlas)
+    atlas: Atlas
+    overlappingLabels: [str, str]

models/participant.py

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+from dandischema import DandiBaseModel
+
+
+class Participant(DandiBaseModel):
+    """Description about the Participant or Subject studied.
+    The Participant or Subject can be any individual or synthesized Agent. The
+    properties of the Participant or Subject refers to information at the timepoint
+    when the Participant or Subject engaged in the production of data being described.
+    """
+
+    identifier: Identifier = Field(nskey="schema")
+    altName: Optional[List[Identifier]] = Field(None, nskey="dandi")
+
+    strain: Optional[StrainType] = Field(
+        None,
+        description="Identifier for the strain of the participant or subject.",
+        nskey="dandi",
+    )
+    cellLine: Optional[Identifier] = Field(
+        None,
+        description="Cell line associated with the participant or subject.",
+        nskey="dandi",
+    )
+    vendor: Optional[Organization] = Field(None, nskey="dandi")
+    age: Optional[PropertyValue] = Field(
+        None,
+        description="A representation of age using ISO 8601 duration. This "
+                    "should include a valueReference if anything other than "
+                    "date of birth is used.",
+        nskey="dandi",
+        rangeIncludes="schema:Duration",
+    )
+
+    sex: Optional[SexType] = Field(
+        None,
+        description="Identifier for sex of the participant or subject if "
+                    "available. (e.g. from OBI)",
+        nskey="dandi",
+    )
+    genotype: Optional[Union[List[GenotypeInfo], Identifier]] = Field(
+        None,
+        description="Genotype descriptor of participant or subject if available",
+        nskey="dandi",
+    )
+    species: Optional[SpeciesType] = Field(
+        None,
+        description="An identifier indicating the taxonomic classification of "
+                    "the participant or subject.",
+        nskey="dandi",
+    )
+    disorder: Optional[List[Disorder]] = Field(
+        None,
+        description="Any current diagnosed disease or disorder associated with "
+                    "the participant or subject.",
+        nskey="dandi",
+    )
+
+    relatedParticipant: Optional[List[RelatedParticipant]] = Field(
+        None,
+        description="Information about related participants or subjects in a "
+                    "study or across studies.",
+        nskey="dandi",
+    )
+    sameAs: Optional[List[Identifier]] = Field(
+        None,
+        description="An identifier to link participants or subjects across datasets.",
+        nskey="schema",
+    )
+
+    _ldmeta = {
+        "rdfs:subClassOf": ["prov:Agent"],
+        "rdfs:label": "Information about the participant or subject.",
+        "nskey": "dandi",
+    }

models/participant.yaml

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+id: https://bican.org/examples/participant
+name: participant
+prefixes:
+  linkml: https://w3id.org/linkml/
+imports:
+  - linkml:types
+default_range: string
+
+classes:
+  Participant:
+    attributes:
+      identifier:
+      altName:
+      strain:
+      cellLine:
+      vendor:
+      age:
+      sex:
+      genotype:
+      species:
+      disorder:
+      relatedParticipant:
+      sameAs:

models/protocol.py

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+from pydantic import BaseModel
+
+
+class Protocol(BaseModel):
+    name: str

models/provenance.py

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+from pydantic import BaseModel
+
+
+class Provenance(BaseModel):
+    name: str