Fix liftover

CHANGELOG.md

@@ -19,6 +19,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Updated color scheme for variant assessment badges that were hard to see in light mode, notably Risk Factor (#5318)
 - Avoid page timeout by skipping HGVS validations in ClinVar multistep submission for non-MANE transcripts from variants in build 38 (#5302)
 - Sashimi view page displaying an error message when Ensembl REST API (LiftOver) is not available (#5322)
+- Refactored the liftover functionality to avoid using the old Ensembl REST API (#5326)
 
 ## [4.98]
 ### Added

scout/utils/ensembl_rest_clients.py

@@ -10,23 +10,18 @@
 LOG = logging.getLogger(__name__)
 
 HEADERS = {"Content-type": "application/json"}
-RESTAPI_37 = "https://grch37.rest.ensembl.org"
-RESTAPI_38 = "https://rest.ensembl.org"
+RESTAPI_URL = "https://rest.ensembl.org"
 
 
 class EnsemblRestApiClient:
     """A class handling requests and responses to and from the Ensembl REST APIs.
-    Endpoints for human build 37: https://grch37.rest.ensembl.org
-    Endpoints for human build 38: http://rest.ensembl.org/
+    Endpoint: http://rest.ensembl.org/
     Documentation: https://github.com/Ensembl/ensembl-rest/wiki
     doi:10.1093/bioinformatics/btu613
     """
 
-    def __init__(self, build="37"):
-        if build == "38":
-            self.server = RESTAPI_38
-        else:
-            self.server = RESTAPI_37
+    def __init__(self):
+        self.server = RESTAPI_URL
 
     def build_url(self, endpoint, params=None):
         """Build an url to query ensembml"""
@@ -63,18 +58,11 @@ def send_request(url) -> Optional[dict]:
             flash(error)
         return data
 
-    def liftover(self, build, chrom, start, end=None):
+    def liftover(
+        self, build: str, chrom: str, start: int, end: Optional[int] = None
+    ) -> Optional[dict]:
         """Perform variant liftover using Ensembl REST API
-
-        Args:
-            build(str): genome build: "37" or "38"
-            chrom(str): 1-22,X,Y,MT,M
-            start(int): start coordinate
-            stop(int): stop coordinate or None
-
-        Returns:
-            mappings(list of dict): example:
-                example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
+        example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
         """
 
         build = "GRCh38" if "38" in str(build) else "GRCh37"

tests/server/blueprints/alignviewers/test_alignviewers_controllers.py

@@ -5,6 +5,7 @@
 
 from scout.server.blueprints.alignviewers import controllers
 from scout.server.extensions import config_igv_tracks, store
+from scout.utils.ensembl_rest_clients import RESTAPI_URL
 
 
 @responses.activate
@@ -15,7 +16,7 @@ def test_make_sashimi_tracks_variant_38(app, case_obj, ensembl_liftover_response
     test_variant = store.variant_collection.find_one({"hgnc_symbols": ["POT1"]})
 
     # GIVEN a patched response from Ensembl liftover API
-    url = f'https://grch37.rest.ensembl.org/map/human/GRCh37/{test_variant["chromosome"]}:{test_variant["position"]}..{test_variant["end"]}/GRCh38?content-type=application/json'
+    url = f'{RESTAPI_URL}/map/human/GRCh37/{test_variant["chromosome"]}:{test_variant["position"]}..{test_variant["end"]}/GRCh38?content-type=application/json'
     responses.add(
         responses.GET,
         url,
@@ -56,7 +57,7 @@ def test_make_sashimi_tracks_variant_37(app, case_obj, ensembl_liftover_response
     test_variant = store.variant_collection.find_one({"hgnc_symbols": ["POT1"]})
 
     # GIVEN a patched response from Ensembl liftover API
-    url = f'https://grch37.rest.ensembl.org/map/human/GRCh37/{test_variant["chromosome"]}:{test_variant["position"]}..{test_variant["end"]}/GRCh38?content-type=application/json'
+    url = f'{RESTAPI_URL}/map/human/GRCh37/{test_variant["chromosome"]}:{test_variant["position"]}..{test_variant["end"]}/GRCh38?content-type=application/json'
     responses.add(
         responses.GET,
         url,

tests/server/blueprints/alignviewers/test_alignviewers_views.py

@@ -2,6 +2,8 @@
 import responses
 from flask import session, url_for
 
+from scout.utils.ensembl_rest_clients import RESTAPI_URL
+
 
 def test_remote_static_no_auth(app):
     """Test endpoint that serves alignment files as non-logged user"""
@@ -152,7 +154,7 @@ def test_sashimi_igv(app, user_obj, case_obj, variant_obj, ensembl_liftover_resp
     # GIVEN a mocked response from the Ensembl liftover service
     chromosome = variant_obj["chromosome"]
     position = variant_obj["position"]
-    mocked_liftover_url = f"https://grch37.rest.ensembl.org/map/human/GRCh37/{chromosome}:{position}..{position}/GRCh38?content-type=application/json"
+    mocked_liftover_url = f"{RESTAPI_URL}/map/human/GRCh37/{chromosome}:{position}..{position}/GRCh38?content-type=application/json"
     responses.add(
         responses.GET,
         mocked_liftover_url,

tests/server/blueprints/variant/test_variant_views.py

@@ -3,9 +3,9 @@
 
 import responses
 from flask import url_for
-from flask_login import current_user
 
 from scout.server.extensions import store
+from scout.utils.ensembl_rest_clients import RESTAPI_URL
 
 
 @responses.activate
@@ -24,7 +24,7 @@ def test_marrvel_link_38(app, case_obj):
     store.variant_collection.insert_one(test_variant)
 
     # GIVEN that the variant can be lifted over to build 37
-    url = f"https://grch37.rest.ensembl.org/map/human/GRCh38/{test_variant['chromosome']}:{test_variant['position']}..{test_variant['position']}/GRCh37?content-type=application/json"
+    url = f"{RESTAPI_URL}/map/human/GRCh38/{test_variant['chromosome']}:{test_variant['position']}..{test_variant['position']}/GRCh37?content-type=application/json"
 
     liftover_mappings = {
         "mappings": [

tests/utils/conftest.py

@@ -49,21 +49,15 @@ def fixture_ensembl_biomart_xml_query():
 
 
 @pytest.fixture
-def ensembl_biomart_client_37():
+def ensembl_biomart_client():
     """Return a client to the ensembl biomart, build 37"""
     return ensembl_rest_clients.EnsemblBiomartClient("37")
 
 
 @pytest.fixture
-def ensembl_rest_client_37():
-    """Return a client to the ensembl rest api, build 37"""
-    return ensembl_rest_clients.EnsemblRestApiClient("37")
-
-
-@pytest.fixture
-def ensembl_rest_client_38():
-    """Return a client to the ensembl rest api, build 38"""
-    return ensembl_rest_clients.EnsemblRestApiClient("38")
+def ensembl_rest_client():
+    """Return a client to the Ensembl REST API."""
+    return ensembl_rest_clients.EnsemblRestApiClient()
 
 
 @pytest.fixture

tests/utils/test_ensembl_rest_clients.py

@@ -4,53 +4,33 @@
 from requests.exceptions import MissingSchema
 from requests.models import Response
 
-from scout.utils.ensembl_rest_clients import RESTAPI_37
+from scout.utils.ensembl_rest_clients import RESTAPI_URL
 
 
 @responses.activate
-def test_liftover(ensembl_rest_client_37, ensembl_liftover_response):
+def test_liftover(ensembl_rest_client, ensembl_liftover_response):
     """Test send request for coordinates liftover"""
     # GIVEN a patched response from Ensembl
-    url = f"{RESTAPI_37}/map/human/GRCh37/X:1000000..1000100/GRCh38?content-type=application/json"
+    url = f"{RESTAPI_URL}/map/human/GRCh37/X:1000000..1000100/GRCh38?content-type=application/json"
     responses.add(
         responses.GET,
         url,
         json=ensembl_liftover_response,
         status=200,
     )
-    client = ensembl_rest_client_37
+    client = ensembl_rest_client
     # WHEN sending the liftover request the function should return a mapped locus
     mapped_coords = client.liftover("37", "X", 1000000, 1000100)
     assert mapped_coords[0]["mapped"]
 
 
-@responses.activate
-def test_send_gene_request(ensembl_gene_response, ensembl_rest_client_37):
-    """Test send request with correct params and endpoint"""
-    url = f"{RESTAPI_37}/overlap/id/ENSG00000103591?feature=gene"
-    client = ensembl_rest_client_37
-    responses.add(
-        responses.GET,
-        url,
-        json=ensembl_gene_response,
-        status=200,
-    )
-    data = client.send_request(url)
-
-    # get all gene for the ensembl gene, They should be a list of items
-    assert data[0]["assembly_name"] == "GRCh37"
-    assert data[0]["external_name"] == "AAGAB"
-    assert data[0]["start"]
-    assert data[0]["end"]
-
-
-def test_send_request_fakey_url(mock_app, ensembl_rest_client_37, mocker):
+def test_send_request_fakey_url(mock_app, ensembl_rest_client, mocker):
     """Test the Ensembl REST client with an URL that is raising missing schema error."""
 
     # GIVEN a completely invalid URL
     url = "fakeyurl"
     # GIVEN a patched Ensembl client
-    client = ensembl_rest_client_37
+    client = ensembl_rest_client
     mocker.patch("requests.get", side_effect=MissingSchema("Invalid URL"))
 
     # THEN the client should return no content
@@ -59,12 +39,12 @@ def test_send_request_fakey_url(mock_app, ensembl_rest_client_37, mocker):
         assert data is None
 
 
-def test_send_request_unavaailable(mock_app, ensembl_rest_client_37, mocker):
+def test_send_request_unavaailable(mock_app, ensembl_rest_client, mocker):
     """Test the Ensembl REST client with an URL that is not available (500 error)."""
 
-    url = f"{RESTAPI_37}/fakeyurl"
+    url = f"{RESTAPI_URL}/fakeyurl"
     # GIVEN a patched Ensembl client
-    client = ensembl_rest_client_37
+    client = ensembl_rest_client
 
     # GIVEN a mocked 550 response from Ensembl
     mock_response = Response()