Merge branch 'staging' into issue-222-coord-lookup

server/curfu/main.py

@@ -22,6 +22,17 @@
 from curfu.version import __version__ as curfu_version
 
 fastapi_app = FastAPI(
+    title="Fusion Curation API",
+    description="Provide data functions to support [VICC Fusion Curation interface](fusion-builder.cancervariants.org/).",
+    contact={
+        "name": "Alex H. Wagner",
+        "email": "[email protected]",
+        "url": "https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab",
+    },
+    license={
+        "name": "MIT",
+        "url": "https://github.com/cancervariants/fusion-curation/blob/main/LICENSE",
+    },
     version=curfu_version,
     swagger_ui_parameters={"tryItOutEnabled": True},
     docs_url="/docs",
@@ -63,7 +74,7 @@ def serve_react_app(app: FastAPI) -> FastAPI:
     )
     templates = Jinja2Templates(directory=BUILD_DIR.as_posix())
 
-    @app.get("/{full_path:path}")
+    @app.get("/{full_path:path}", include_in_schema=False)
     async def serve_react_app(request: Request, full_path: str) -> TemplateResponse:
         """Add arbitrary path support to FastAPI service.
 

server/curfu/routers/complete.py

@@ -4,7 +4,12 @@
 from fastapi import APIRouter, Query, Request
 
 from curfu import MAX_SUGGESTIONS, LookupServiceError
-from curfu.schemas import AssociatedDomainResponse, ResponseDict, SuggestGeneResponse
+from curfu.schemas import (
+    AssociatedDomainResponse,
+    ResponseDict,
+    RouteTag,
+    SuggestGeneResponse,
+)
 
 router = APIRouter()
 
@@ -14,6 +19,7 @@
     operation_id="suggestGene",
     response_model=SuggestGeneResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.COMPLETION],
 )
 def suggest_gene(request: Request, term: str = Query("")) -> ResponseDict:
     """Provide completion suggestions for term provided by user.
@@ -52,6 +58,7 @@ def suggest_gene(request: Request, term: str = Query("")) -> ResponseDict:
     operation_id="suggestDomain",
     response_model=AssociatedDomainResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.COMPLETION],
 )
 def suggest_domain(request: Request, gene_id: str = Query("")) -> ResponseDict:
     """Provide possible domains associated with a given gene to be selected by a user.

server/curfu/routers/constructors.py

@@ -12,6 +12,7 @@
     GetDomainResponse,
     RegulatoryElementResponse,
     ResponseDict,
+    RouteTag,
     TemplatedSequenceElementResponse,
     TxSegmentElementResponse,
 )
@@ -25,6 +26,7 @@
     operation_id="buildGeneElement",
     response_model=GeneElementResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 def build_gene_element(request: Request, term: str = Query("")) -> GeneElementResponse:
     """Construct valid gene element given user-provided term.
@@ -48,6 +50,7 @@ def build_gene_element(request: Request, term: str = Query("")) -> GeneElementRe
     operation_id="buildTranscriptSegmentElementECT",
     response_model=TxSegmentElementResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 async def build_tx_segment_ect(
     request: Request,
@@ -85,6 +88,7 @@ async def build_tx_segment_ect(
     operation_id="buildTranscriptSegmentElementGCT",
     response_model=TxSegmentElementResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 async def build_tx_segment_gct(
     request: Request,
@@ -132,6 +136,7 @@ async def build_tx_segment_gct(
     operation_id="buildTranscriptSegmentElementGCG",
     response_model=TxSegmentElementResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 async def build_tx_segment_gcg(
     request: Request,
@@ -179,6 +184,7 @@ async def build_tx_segment_gcg(
     operation_id="buildTemplatedSequenceElement",
     response_model=TemplatedSequenceElementResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 def build_templated_sequence_element(
     request: Request, start: int, end: int, sequence_id: str, strand: str
@@ -215,6 +221,7 @@ def build_templated_sequence_element(
     operation_id="getDomain",
     response_model=GetDomainResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 def build_domain(
     request: Request,
@@ -260,6 +267,7 @@ def build_domain(
     operation_id="getRegulatoryElement",
     response_model=RegulatoryElementResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.CONSTRUCTORS],
 )
 def build_regulatory_element(
     request: Request, element_class: RegulatoryClass, gene_name: str

server/curfu/routers/demo.py

@@ -31,6 +31,7 @@
     GeneElement,
     LinkerElement,
     MultiplePossibleGenesElement,
+    RouteTag,
     TemplatedSequenceElement,
     TranscriptSegmentElement,
     UnknownGeneElement,
@@ -156,6 +157,7 @@ def clientify_fusion(fusion: Fusion, fusor_instance: FUSOR) -> ClientFusion:
     operation_id="alkDemo",
     response_model=DemoResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.DEMOS],
 )
 def get_alk(request: Request) -> DemoResponse:
     """Retrieve ALK assayed fusion.
@@ -176,6 +178,7 @@ def get_alk(request: Request) -> DemoResponse:
     operation_id="ewsr1Demo",
     response_model=DemoResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.DEMOS],
 )
 def get_ewsr1(request: Request) -> DemoResponse:
     """Retrieve EWSR1 assayed fusion.
@@ -196,6 +199,7 @@ def get_ewsr1(request: Request) -> DemoResponse:
     operation_id="bcrAbl1Demo",
     response_model=DemoResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.DEMOS],
 )
 def get_bcr_abl1(request: Request) -> DemoResponse:
     """Retrieve BCR-ABL1 categorical fusion.
@@ -216,6 +220,7 @@ def get_bcr_abl1(request: Request) -> DemoResponse:
     operation_id="tpm3Ntrk1Demo",
     response_model=DemoResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.DEMOS],
 )
 def get_tpm3_ntrk1(request: Request) -> DemoResponse:
     """Retrieve TPM3-NTRK1 assayed fusion.
@@ -236,6 +241,7 @@ def get_tpm3_ntrk1(request: Request) -> DemoResponse:
     operation_id="tpm3PdgfrbDemo",
     response_model=DemoResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.DEMOS],
 )
 def get_tpm3_pdgfrb(request: Request) -> DemoResponse:
     """Retrieve TPM3-PDGFRB assayed fusion.
@@ -256,6 +262,7 @@ def get_tpm3_pdgfrb(request: Request) -> DemoResponse:
     operation_id="ighMycDemo",
     response_model=DemoResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.DEMOS],
 )
 def get_igh_myc(request: Request) -> DemoResponse:
     """Retrieve IGH-MYC assayed fusion.

server/curfu/routers/lookup.py

@@ -2,7 +2,7 @@
 from fastapi import APIRouter, Query, Request
 
 from curfu import LookupServiceError
-from curfu.schemas import NormalizeGeneResponse, ResponseDict
+from curfu.schemas import NormalizeGeneResponse, ResponseDict, RouteTag
 
 router = APIRouter()
 
@@ -12,6 +12,7 @@
     operation_id="normalizeGene",
     response_model=NormalizeGeneResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.LOOKUP],
 )
 def normalize_gene(request: Request, term: str = Query("")) -> ResponseDict:
     """Normalize gene term provided by user.

server/curfu/routers/meta.py

@@ -3,14 +3,17 @@
 from fastapi import APIRouter
 from fusor import __version__ as fusor_version
 
-from curfu.schemas import ServiceInfoResponse
+from curfu.schemas import RouteTag, ServiceInfoResponse
 from curfu.version import __version__ as curfu_version
 
 router = APIRouter()
 
 
 @router.get(
-    "/api/service_info", operation_id="serviceInfo", response_model=ServiceInfoResponse
+    "/api/service_info",
+    operation_id="serviceInfo",
+    response_model=ServiceInfoResponse,
+    tags=[RouteTag.META],
 )
 def get_service_info() -> ServiceInfoResponse:
     """Return service info."""

server/curfu/routers/nomenclature.py

@@ -18,7 +18,7 @@
 from pydantic import ValidationError
 
 from curfu import logger
-from curfu.schemas import NomenclatureResponse, ResponseDict
+from curfu.schemas import NomenclatureResponse, ResponseDict, RouteTag
 
 router = APIRouter()
 
@@ -28,6 +28,7 @@
     operation_id="regulatoryElementNomenclature",
     response_model=NomenclatureResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.NOMENCLATURE],
 )
 def generate_regulatory_element_nomenclature(
     request: Request, regulatory_element: Dict = Body()
@@ -69,6 +70,7 @@ def generate_regulatory_element_nomenclature(
     operation_id="txSegmentNomenclature",
     response_model=NomenclatureResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.NOMENCLATURE],
 )
 def generate_tx_segment_nomenclature(tx_segment: Dict = Body()) -> ResponseDict:
     """Build transcript segment element nomenclature.
@@ -96,6 +98,7 @@ def generate_tx_segment_nomenclature(tx_segment: Dict = Body()) -> ResponseDict:
     operation_id="templatedSequenceNomenclature",
     response_model=NomenclatureResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.NOMENCLATURE],
 )
 def generate_templated_seq_nomenclature(
     request: Request, templated_sequence: Dict = Body()
@@ -136,6 +139,7 @@ def generate_templated_seq_nomenclature(
     operation_id="geneNomenclature",
     response_model=NomenclatureResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.NOMENCLATURE],
 )
 def generate_gene_nomenclature(gene_element: Dict = Body()) -> ResponseDict:
     """Build gene element nomenclature.
@@ -170,6 +174,7 @@ def generate_gene_nomenclature(gene_element: Dict = Body()) -> ResponseDict:
     operation_id="fusionNomenclature",
     response_model=NomenclatureResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.NOMENCLATURE],
 )
 def generate_fusion_nomenclature(
     request: Request, fusion: Dict = Body()

server/curfu/routers/utilities.py

@@ -15,6 +15,7 @@
     CoordsUtilsResponse,
     GetTranscriptsResponse,
     GetGeneTranscriptsResponse,
+    RouteTag,
     SequenceIDResponse,
 )
 from curfu.sequence_services import InvalidInputError, get_strand
@@ -28,6 +29,7 @@
     operation_id="getMANETranscripts",
     response_model=GetTranscriptsResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.UTILITIES],
 )
 def get_mane_transcripts(request: Request, term: str) -> Dict:
     """Get MANE transcripts for gene term.
@@ -83,6 +85,7 @@ async def get_transcripts_for_gene(request: Request, gene: str) -> Dict:
     operation_id="getGenomicCoords",
     response_model=CoordsUtilsResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.UTILITIES],
 )
 async def get_genome_coords(
     request: Request,
@@ -155,6 +158,7 @@ async def get_genome_coords(
     operation_id="getExonCoords",
     response_model=CoordsUtilsResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.UTILITIES],
 )
 async def get_exon_coords(
     request: Request,
@@ -214,6 +218,7 @@ async def get_exon_coords(
     operation_id="getSequenceId",
     response_model=SequenceIDResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.UTILITIES],
 )
 async def get_sequence_id(request: Request, sequence: str) -> SequenceIDResponse:
     """Get GA4GH sequence ID and aliases given sequence sequence ID
@@ -263,6 +268,7 @@ async def get_sequence_id(request: Request, sequence: str) -> SequenceIDResponse
     description="Given a known accession identifier, retrieve sequence data and return"
     "as a FASTA file",
     response_class=FileResponse,
+    tags=[RouteTag.UTILITIES],
 )
 async def get_sequence(
     request: Request,

server/curfu/routers/validate.py

@@ -4,7 +4,7 @@
 from fastapi import APIRouter, Body, Request
 from fusor.exceptions import FUSORParametersException
 
-from curfu.schemas import ResponseDict, ValidateFusionResponse
+from curfu.schemas import ResponseDict, RouteTag, ValidateFusionResponse
 
 router = APIRouter()
 
@@ -14,6 +14,7 @@
     operation_id="validateFusion",
     response_model=ValidateFusionResponse,
     response_model_exclude_none=True,
+    tags=[RouteTag.VALIDATORS],
 )
 def validate_fusion(request: Request, fusion: Dict = Body()) -> ResponseDict:
     """Validate proposed Fusion object. Return warnings if invalid.

server/curfu/schemas.py

@@ -1,4 +1,5 @@
 """Provide schemas for FastAPI responses."""
+from enum import Enum
 from typing import Dict, List, Literal, Optional, Tuple, Union
 
 from cool_seq_tool.schemas import GenomicData
@@ -323,3 +324,17 @@ class DemoResponse(Response):
     """Response model for demo fusion object retrieval endpoints."""
 
     fusion: Union[ClientAssayedFusion, ClientCategoricalFusion]
+
+
+class RouteTag(str, Enum):
+    """Define tags for API routes."""
+
+    UTILITIES = "Utilities"
+    CONSTRUCTORS = "Constructors"
+    VALIDATORS = "Validators"
+    COMPLETION = "Completion"
+    NOMENCLATURE = "Nomenclature"
+    DEMOS = "Demos"
+    META = "Meta"
+    SERVICE = "Service"
+    LOOKUP = "Lookup"