resolve rapid species home (#10)

jyobhai · web-flow · commit 8247a97dfcf3 · 2025-01-02T16:16:02.000Z
diff --git a/app/api/resources/rapid_view.py b/app/api/resources/rapid_view.py
@@ -0,0 +1,55 @@
+from urllib.parse import parse_qs
+from fastapi import APIRouter, Request, HTTPException, Query
+from fastapi.responses import RedirectResponse
+import logging
+from core.logging import InterceptHandler
+from core.config import ENSEMBL_URL
+from api.utils.metadata import get_genome_id_from_assembly_accession_id
+from api.utils.rapid import construct_url, format_assembly_accession
+
+logging.getLogger().handlers = [InterceptHandler()]
+
+router = APIRouter()
+
+
+# Resolve rapid urls
+@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:
+        raise HTTPException(
+            status_code=422, detail="Unable to process input accession ID"
+        )
+    try:
+        genome_object = get_genome_id_from_assembly_accession_id(assembly_accession_id)
+
+        if genome_object and genome_object != {}:
+            genome_id = genome_object["genome_tag"] or genome_object["genome_uuid"]
+
+            # Extract specific parameters because Ensembl url uses ; instead of &
+            query_string = request.scope["query_string"].decode()
+            query_params = parse_qs(query_string, separator=";")
+
+            url = construct_url(genome_id, subpath, query_params)
+            return RedirectResponse(url)
+        else:
+            raise HTTPException(status_code=404, detail="Genome not found")
+
+    except HTTPException as e:
+        logging.debug(e)
+        raise HTTPException(
+            status_code=e.status_code, detail="Unexpected error occured"
+        )
+
+    except Exception as e:
+        logging.debug(f"Unexpected error occurred: {e}")
+        raise HTTPException(status_code=500, detail="Unexpected error occurred")
+
+
+@router.get("/", name="Rapid Home")
+async def resolve_home(request: Request):
+    return RedirectResponse(ENSEMBL_URL)
diff --git a/app/api/resources/routes.py b/app/api/resources/routes.py
@@ -17,8 +17,9 @@
 
 from fastapi import APIRouter
 
-from api.resources import resolver_view
+from api.resources import resolver_view, rapid_view
 
 router = APIRouter()
 
 router.include_router(resolver_view.router, tags=["resolver"], prefix="/id")
+router.include_router(rapid_view.router, tags=["rapid"], prefix="/rapid")
diff --git a/app/api/utils/metadata.py b/app/api/utils/metadata.py
@@ -23,9 +23,26 @@ def get_metadata(matches: List[SearchMatch] = []):
                 )
         except requests.exceptions.HTTPError as HTTPError:
             logger.error(f"HTTPError: {HTTPError}")
-            return None
+            raise HTTPError
         except Exception as e:
             logger.exception(e)
-            return None
+            raise e
 
     return metadata_results
+
+
+def get_genome_id_from_assembly_accession_id(accession_id: str):
+    try:
+        session = requests.Session()
+        metadata_api_url = (
+            f"{ENSEMBL_URL}/api/metadata/genomeid?assembly_accession_id={accession_id}"
+        )
+        with session.get(url=metadata_api_url) as response:
+            response.raise_for_status()
+            return response.json()
+    except requests.exceptions.HTTPError as HTTPError:
+        logger.error(f"HTTPError: {HTTPError}")
+        raise HTTPError
+    except Exception as e:
+        logger.exception(e)
+        raise e
diff --git a/app/api/utils/rapid.py b/app/api/utils/rapid.py
@@ -0,0 +1,77 @@
+from loguru import logger
+import requests
+from core.config import ENSEMBL_URL, NCBI_DATASETS_URL
+import re
+
+
+def get_assembly_accession_from_ncbi(accession_id: str):
+    try:
+        session = requests.Session()
+        ncbi_dataset_api_url = (
+            f"{NCBI_DATASETS_URL}/genome/accession/{accession_id}/dataset_report"
+        )
+
+        with session.get(url=ncbi_dataset_api_url) as response:
+            response.raise_for_status()
+            response_json = response.json()
+            if response_json and response_json["reports"]:
+                return response_json["reports"][0]
+            else:
+                return None
+
+    except requests.exceptions.HTTPError as HTTPError:
+        logger.error(f"HTTPError: {HTTPError}")
+        raise HTTPError
+    except Exception as e:
+        logger.exception(e)
+        raise e
+
+
+def format_assembly_accession(species_url_name: str):
+    if re.search("_GCA_|_GCF_", species_url_name):
+        _, accession_id = re.split("_GCA_|_GCF_", species_url_name)
+
+        prefix = "GCA_"
+        if re.search("GCF", species_url_name):
+            prefix = "GCF_"
+
+        assembly_accession_id = prefix + accession_id
+
+        # RefSeqs have GCF prefix but version could be different. So fetch it from ncbi
+        if assembly_accession_id.endswith("rs"):
+            trimmed_assembly_accession_id = re.sub("rs$", "", assembly_accession_id)
+            ncbi_dataset_report = get_assembly_accession_from_ncbi(
+                trimmed_assembly_accession_id
+            )
+
+            if ncbi_dataset_report:
+                assembly_accession_id = ncbi_dataset_report["paired_accession"]
+            else:
+                logger.error("HTTPError: {HTTPError}")
+                return None
+        return assembly_accession_id
+    else:
+        return None
+
+
+def construct_url(genome_id, subpath, query_params):
+    location = query_params.get("r", [None])[0]
+    gene_id = query_params.get("g", [None])[0]
+
+    if subpath == "" or re.search("Info/Index", subpath, re.IGNORECASE):
+        return f"{ENSEMBL_URL}/species/{genome_id}"
+    elif re.search("Location", subpath):
+        return f"{ENSEMBL_URL}/genome-browser/{genome_id}?focus=location:{location}"
+    elif re.search("Gene", subpath):
+        if re.search("Gene/Compara_Homolog", subpath):
+            return (
+                f"{ENSEMBL_URL}/entity-viewer/{genome_id}/gene:{gene_id}?view=homology"
+            )
+        return f"{ENSEMBL_URL}/entity-viewer/{genome_id}/gene:{gene_id}"
+    elif re.search("Transcript", subpath):
+        if re.search("Domains|ProteinSummary", subpath):
+            return (
+                f"{ENSEMBL_URL}/entity-viewer/{genome_id}/gene:{gene_id}?view=protein"
+            )
+        return f"{ENSEMBL_URL}/entity-viewer/{genome_id}/gene:{gene_id}"
+    return ENSEMBL_URL
diff --git a/app/core/config.py b/app/core/config.py
@@ -36,6 +36,10 @@
 )
 DEFAULT_APP = config("DEFAULT_APP", cast=str, default="entity-viewer")
 ENSEMBL_URL = config("ENSEMBL_URL", cast=str, default="https://beta.ensembl.org")
+NCBI_DATASETS_URL = config(
+    "NCBI_DATASETS_URL", cast=str, default="https://api.ncbi.nlm.nih.gov/datasets/v2"
+)
+
 DEBUG: bool = config("DEBUG", cast=bool, default=False)
 PROJECT_NAME: str = config("PROJECT_NAME", default="Ensembl Web Resolver")
 ALLOWED_HOSTS: list[str] = config(
diff --git a/app/tests/test_rapid.py b/app/tests/test_rapid.py
@@ -0,0 +1,157 @@
+import unittest
+from unittest.mock import patch
+from fastapi.testclient import TestClient
+from core.config import ENSEMBL_URL
+from main import app
+
+
+class TestRapid(unittest.TestCase):
+    def setUp(self):
+        self.client = TestClient(app)
+        self.api_prefix = ""
+        self.mock_rapid_api_url = "/rapid"
+        self.species_url_name = "Human_GCA_123.1"
+        self.species_url_name_refseq = "DogRefSeq_GCA_123.1rs"
+
+        self.mock_genome_id_response1 = {
+            "genome_uuid": "genome_uuid1",
+            "release_version": 110,
+            "genome_tag": "",
+        }
+
+        self.mock_genome_id_response2 = {
+            "genome_uuid": "genome_uuid2",
+            "release_version": 110,
+            "genome_tag": "xyz",
+        }
+
+        self.mock_ncbi_accession = "GCF_000001405.40"
+
+        self.mock_resolved_url = {
+            "genome1": f"{ENSEMBL_URL}/species/genome_uuid1",
+            "genome2": f"{ENSEMBL_URL}/species/xyz",
+        }
+
+    # Test species home page
+    @patch("api.resources.rapid_view.get_genome_id_from_assembly_accession_id")
+    def test_rapid_species_home_success(
+        self, mock_get_genome_id_from_assembly_accession_id
+    ):
+
+        # test web-metadata-api response without genome_tag
+        mock_get_genome_id_from_assembly_accession_id.return_value = (
+            self.mock_genome_id_response1
+        )
+
+        response = self.client.get(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/",
+            follow_redirects=False,
+        )
+
+        self.assertEqual(response.status_code, 307)  # Temporary Redirect
+        self.assertIn("location", response.headers)
+        self.assertEqual(
+            response.headers["location"], self.mock_resolved_url["genome1"]
+        )
+
+        # test web-metadata-api response with genome_tag
+        mock_get_genome_id_from_assembly_accession_id.return_value = (
+            self.mock_genome_id_response2
+        )
+
+        response = self.client.get(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/",
+            follow_redirects=False,
+        )
+
+        self.assertEqual(response.status_code, 307)  # Temporary Redirect
+        self.assertIn("location", response.headers)
+        self.assertEqual(
+            response.headers["location"], self.mock_resolved_url["genome2"]
+        )
+
+    # Test Region in detail page
+    @patch("api.resources.rapid_view.get_genome_id_from_assembly_accession_id")
+    def test_rapid_species_location_success(
+        self, mock_get_genome_id_from_assembly_accession_id
+    ):
+
+        # test web-metadata-api response without genome_tag
+        mock_get_genome_id_from_assembly_accession_id.return_value = (
+            self.mock_genome_id_response1
+        )
+
+        response = self.client.get(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/Location/View",
+            params={"r": "1:1000-2000"},
+            follow_redirects=False,
+        )
+
+        self.assertEqual(response.status_code, 307)  # Redirect
+        self.assertIn(
+            f"{ENSEMBL_URL}/genome-browser/genome_uuid1?focus=location:1:1000-2000",
+            response.headers["location"],
+        )
+
+    # Test Gene pages
+    @patch("api.resources.rapid_view.get_genome_id_from_assembly_accession_id")
+    def test_rapid_species_gene_compara_homolog(
+        self, mock_get_genome_id_from_assembly_accession_id
+    ):
+        mock_get_genome_id_from_assembly_accession_id.return_value = (
+            self.mock_genome_id_response1
+        )
+
+        response = self.client.get(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/Gene/Compara_Homolog",
+            params={"g": "GENE123"},
+            follow_redirects=False,
+        )
+
+        self.assertEqual(response.status_code, 307)  # Redirect
+        self.assertIn(
+            f"{ENSEMBL_URL}/entity-viewer/genome_uuid1/gene:GENE123?view=homology",
+            response.headers["location"],
+        )
+
+    # Test 404
+    @patch("api.resources.rapid_view.get_genome_id_from_assembly_accession_id")
+    def test_rapid_species_404_not_found(
+        self, mock_get_genome_id_from_assembly_accession_id
+    ):
+        mock_get_genome_id_from_assembly_accession_id.return_value = {}
+
+        response = self.client.get(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/Invalid_GCA"
+        )
+        self.assertEqual(response.status_code, 404)
+
+    # Test invalid url entity
+    def test_rapid_species_422_unprocessable_entity(self):
+        response = self.client.get(f"{self.mock_rapid_api_url}/Invalid_Name/")
+        self.assertEqual(response.status_code, 422)
+
+    # Test POST
+    def test_rapid_species_post_method_not_allowed(self):
+        response = self.client.post(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/"
+        )
+        self.assertEqual(response.status_code, 405)
+
+    # Test 500
+    @patch("api.resources.rapid_view.get_genome_id_from_assembly_accession_id")
+    def test_rapid_species_500_internal_server_error(
+        self, mock_get_genome_id_from_assembly_accession_id
+    ):
+        mock_get_genome_id_from_assembly_accession_id.return_value = (
+            self.mock_genome_id_response1
+        )
+
+        mock_get_genome_id_from_assembly_accession_id.side_effect = Exception(
+            "Unexpected error"
+        )
+
+        response = self.client.get(
+            f"{self.mock_rapid_api_url}/{self.species_url_name}/"
+        )
+        self.assertEqual(response.status_code, 500)
diff --git a/sample-env b/sample-env
@@ -3,3 +3,4 @@ ENSEMBL_SEARCH_HUB_API=https://beta.ensembl.org/api/search/stable-id
 DEFAULT_APP=entity-viewer
 ENSEMBL_URL=http://beta.ensembl.org
 DEBUG=true
+NCBI_DATASETS_URL=https://api.ncbi.nlm.nih.gov/datasets/v2
