Rapid help and blast url redirect and api schema changes

README.md

@@ -9,11 +9,16 @@ The resolver service generates new Ensembl website urls for different features b
  `$ mv sample-env .env`
 
  `$  docker-compose -f docker-compose.yml up`
- 
+
  ### Deploy the app and run docker-compose:
  Some urls that are available after deployment on your local machine:
 
  http://localhost:8001/id/ENSG00000127720
 
  http://localhost:8001/id/ENSG00000127720.3
+
 ### Run unit tests:
+```
+cd app
+python -m unittest tests.test_rapid
+```

app/api/models/resolver.py

@@ -36,3 +36,6 @@ class MetadataResult(BaseModel):
 
 class ResolvedPayload(MetadataResult):
     resolved_url: str
+
+class ResolvedURLResponse(BaseModel):
+    resolved_url: str

app/api/resources/rapid_view.py

@@ -2,6 +2,7 @@
 from fastapi import APIRouter, Request, HTTPException, Query
 from fastapi.responses import RedirectResponse
 import logging
+from api.models.resolver import ResolvedURLResponse
 from core.logging import InterceptHandler
 from core.config import ENSEMBL_URL
 from api.utils.metadata import get_genome_id_from_assembly_accession_id
@@ -12,12 +13,24 @@
 router = APIRouter()
 
 
+@router.get("/info/{subpath:path}", name="Resolve rapid help page")
+async def resolve_rapid_help(request: Request, subpath: str = ""):
+    help_page_url = f"{ENSEMBL_URL}/help"
+    return resolved_response(help_page_url, request)
+
+
+@router.get("/Blast", name="Resolve rapid blast page")
+async def resolve_rapid_blast(request: Request):
+    blast_page_url = f"{ENSEMBL_URL}/blast"
+    return resolved_response(blast_page_url, request)
+
+
 # Resolve rapid urls
-@router.get("/{species_url_name}/", name="Rapid Species Resources")
+@router.get("/{species_url_name}", name="Rapid Species Resources")
 @router.get("/{species_url_name}/{subpath:path}", name="Rapid Species Resources")
 async def resolve_species(
     request: Request, species_url_name: str, subpath: str = "", r: str = Query(None)
-) -> RedirectResponse:
+):
     assembly_accession_id = format_assembly_accession(species_url_name)
 
     if assembly_accession_id is None:
@@ -35,7 +48,7 @@ async def resolve_species(
             query_params = parse_qs(query_string, separator=";")
 
             url = construct_url(genome_id, subpath, query_params)
-            return RedirectResponse(url)
+            return resolved_response(url, request)
         else:
             raise HTTPException(status_code=404, detail="Genome not found")
 
@@ -52,4 +65,10 @@ async def resolve_species(
 
 @router.get("/", name="Rapid Home")
 async def resolve_home(request: Request):
-    return RedirectResponse(ENSEMBL_URL)
+    return resolved_response(ENSEMBL_URL, request)
+
+
+def resolved_response(url: str, request: Request):
+    if "application/json" in request.headers.get("accept"):
+        return ResolvedURLResponse(resolved_url=url)
+    return RedirectResponse(url=url, status_code=301)

app/static/APISpecification.yaml

@@ -8,13 +8,15 @@ info:
 servers:
   - url: https://resolver.ensembl.org
 tags:
-  - name: resolver
+  - name: Resolver
     description: Resolver API resolves external urls to Ensembl
+  - name: Rapid Resolver
+    description: Resolver API to resolve rapid site urls to Ensembl
 paths:
   /id/{stable_id}:
     get:
       tags:
-        - resolver
+        - Resolver
       summary: Resolve stable ID with optional query params
       description: Resolves to a beta url when a stable id wih optional query params provided
       parameters:
@@ -32,7 +34,7 @@ paths:
           required: false
           schema:
             type: string
-            enum: [gene, transcript, variant]
+            enum: [ gene, transcript, variant ]
             example:
               gene
         - name: app
@@ -41,7 +43,7 @@ paths:
           required: false
           schema:
             type: string
-            enum: [genome-browser, entity-viewer]
+            enum: [ genome-browser, entity-viewer ]
             example:
               genome-browser
         - name: gca
@@ -100,8 +102,158 @@ paths:
           $ref: '#/components/responses/404'
         '500':
           $ref: '#/components/responses/500'
+  /rapid:
+    get:
+      summary: Resolve rapid site url
+      description: Resolves to Ensembl site url (home page).
+      tags:
+        - Rapid Resolver
+      responses:
+        '301':
+          $ref: '#/components/responses/301'
+        '200':
+          $ref: '#/components/responses/200'
+        '400':
+          $ref: '#/components/responses/400'
+        '404':
+          $ref: '#/components/responses/404'
+        '500':
+          $ref: '#/components/responses/500'
+  /rapid/Blast:
+    get:
+      summary: Resolve rapid site blast url
+      description: Resolves to Ensembl site blast url.
+      tags:
+        - Rapid Resolver
+      responses:
+        '301':
+          $ref: '#/components/responses/301'
+        '200':
+          $ref: '#/components/responses/200'
+        '400':
+          $ref: '#/components/responses/400'
+        '404':
+          $ref: '#/components/responses/404'
+        '500':
+          $ref: '#/components/responses/500'
+  /rapid/{species_url_name}:
+    get:
+      summary: Resolve rapid site url with species url name (with assembly accession)
+      description: Resolves to Ensembl site url with the species url name provided.
+      tags:
+        - Rapid Resolver
+      parameters:
+        - name: species_url_name
+          in: path
+          description: Species name with assembly accession
+          required: true
+          schema:
+            type: string
+            example: Camarhynchus_parvulus_GCA_902806625.1
+      responses:
+        '301':
+          $ref: '#/components/responses/301'
+        '200':
+          $ref: '#/components/responses/200'
+        '422':
+          $ref: '#/components/responses/422'
+        '400':
+          $ref: '#/components/responses/400'
+        '404':
+          $ref: '#/components/responses/404'
+        '500':
+          $ref: '#/components/responses/500'
+  /rapid/{species_url_name}/{subpath}:
+    get:
+      summary: Resolve rapid site url with species url name and subpath
+      description: Resolves to Ensembl site url with the species url name and subpath provided.
+      tags:
+        - Rapid Resolver
+      parameters:
+        - name: species_url_name
+          in: path
+          description: Species name with assembly accession
+          required: true
+          schema:
+            type: string
+            example: Camarhynchus_parvulus_GCA_902806625.1
+        - name: subpath
+          in: path
+          description: Additional path under species_url_name
+          required: true
+          schema:
+            type: string
+            example: Location/View
+        - name: r
+          in: query
+          required: false
+          description: Region string
+          schema:
+            type: string
+            example: 2:361680-384534
+      responses:
+        '301':
+          $ref: '#/components/responses/301'
+        '200':
+          $ref: '#/components/responses/200'
+        '422':
+          $ref: '#/components/responses/422'
+        '400':
+          $ref: '#/components/responses/400'
+        '404':
+          $ref: '#/components/responses/404'
+        '500':
+          $ref: '#/components/responses/500'
+  /rapid/info/{subpath}:
+    get:
+      summary: Resolve rapid site help and docs url
+      description: Resolves to Ensembl site help page url.
+      tags:
+        - Rapid Resolver
+      parameters:
+        - name: subpath
+          in: path
+          required: true
+          schema:
+            type: string
+            example: index.html
+      responses:
+        '301':
+          $ref: '#/components/responses/301'
+        '200':
+          $ref: '#/components/responses/200'
+        '400':
+          $ref: '#/components/responses/400'
+        '404':
+          $ref: '#/components/responses/404'
+        '500':
+          $ref: '#/components/responses/500'
 components:
+  headers:
+    Location:
+      description: Ensembl URL
+      schema:
+        type: string
   responses:
+    200:
+      description: OK
+      headers:
+        Location:
+          $ref: '#/components/headers/Location'
+      content:
+        application/json:
+          schema:
+            type: object
+            properties:
+              resolved_url:
+                type: string
+                description: Resolved URL to the Ensembl site
+    301:
+      description: Redirect to resolved URL
+      headers:
+        Location:
+          $ref: '#/components/headers/Location'
+      content: { }
     400:
       description: Bad Request. Missing stable id in the url
       content:
@@ -122,13 +274,19 @@ components:
         application/json:
           schema:
             example: '{"status_code": 404, "details": "Not found"}'
+    422:
+      description: Unprocessable Content
+      content:
+        application/json:
+          schema:
+            example: '{"status_code": 422, "detail": "Unable to process input accession ID"}'
     500:
       description: Internal server error
       content:
         text/plain:
           schema:
             type: string
-            example: 
+            example:
               Internal server error
         application/json:
           schema: