Error message when requests to Ensembl (liftover) fail (#5322)

* Warning message when requests to Ensembl (liftover) fail

* Some fixes

* Update CHANGELOG.md

Co-authored-by: Daniel Nilsson <[email protected]>

* Remove debug message

* Displayed as error anyway, which is fine

* Fix changelog

* Update tests/utils/test_ensembl_rest_clients.py

Co-authored-by: Daniel Nilsson <[email protected]>

* Update tests/utils/test_ensembl_rest_clients.py

Co-authored-by: Daniel Nilsson <[email protected]>

* Remove as err in the client code

* Add referece to the PRs on changelog items

---------

Co-authored-by: Chiara Rasi <[email protected]>
Co-authored-by: Daniel Nilsson <[email protected]>

Author: 3 people

CHANGELOG.md

@@ -6,19 +6,19 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
 ## [unreleased]
 ### Added
-- De novo assembly alignment file load and display
-- Paraphase bam-let alignment file load and display
-- Parsing and showing ClinVar somatic oncogenicity anontations, when available
-### Changed
-- Allow ACMG criteria strength modification to Very strong/Stand-alone
-- Mocked the Ensembl liftover service in igv tracks tests
-### Fixed
-- Re-enable display of case and individual specific tracks (pre-computed coverage, UPD, zygosity)
-- Disable 2-color mode in IGV.js by default, since it obscures variant proportion of reads. Can be manually enabled.
-- Institute settings reset
-- Updated color scheme for variant assessment badges that were hard to see in light mode, notably Risk Factor
-- Avoid page timeout by skipping HGVS validations in ClinVar multistep submission for non-MANE transcripts from variants in build 38
-
+- De novo assembly alignment file load and display (#5284)
+- Paraphase bam-let alignment file load and display (#5284)
+- Parsing and showing ClinVar somatic oncogenicity anontations, when available (#5304)
+### Changed
+- Allow ACMG criteria strength modification to Very strong/Stand-alone (#5297)
+- Mocked the Ensembl liftover service in igv tracks tests (#5319)
+### Fixed
+- Re-enable display of case and individual specific tracks (pre-computed coverage, UPD, zygosity) (#5300)
+- Disable 2-color mode in IGV.js by default, since it obscures variant proportion of reads. Can be manually enabled (#5311)
+- Institute settings reset (#5309)
+- 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)
 
 ## [4.98]
 ### Added

scout/utils/ensembl_rest_clients.py

@@ -1,9 +1,11 @@
 """Code for talking to ensembl rest API"""
 
 import logging
+from typing import Optional
 from urllib.parse import urlencode
 
 import requests
+from flask import flash
 
 LOG = logging.getLogger(__name__)
 
@@ -34,7 +36,7 @@ def build_url(self, endpoint, params=None):
         return "".join([self.server, endpoint])
 
     @staticmethod
-    def send_request(url):
+    def send_request(url) -> Optional[dict]:
         """Sends the actual request to the server and returns the response
 
         Accepts:
@@ -43,19 +45,22 @@ def send_request(url):
         Returns:
             data(dict): dictionary from json response
         """
-        data = {}
+        error = None
+        data = None
         try:
             response = requests.get(url, headers=HEADERS)
-            if response.status_code == 404:
-                LOG.info("Request failed for url %s\n", url)
-                response.raise_for_status()
-            data = response.json()
-        except requests.exceptions.MissingSchema as err:
-            LOG.info("Request failed for url %s: Error: %s\n", url, err)
-            data = err
-        except requests.exceptions.HTTPError as err:
-            LOG.info("Request failed for url %s: Error: %s\n", url, err)
-            data = err
+            if response.status_code not in [404, 500]:
+
+                data = response.json()
+            else:
+                error = f"Ensembl request failed with code:{response.status_code} for url {url}"
+        except requests.exceptions.MissingSchema:
+            error = f"Ensembl request failed with MissingSchema error for url {url}"
+        except requests.exceptions.HTTPError:
+            error = f"Ensembl request failed with HTTPError error for url {url}"
+
+        if error:
+            flash(error)
         return data
 
     def liftover(self, build, chrom, start, end=None):

tests/utils/test_ensembl_rest_clients.py

@@ -1,16 +1,17 @@
 """Tests for ensembl rest api"""
 
 import responses
-from requests.exceptions import HTTPError, MissingSchema
+from requests.exceptions import MissingSchema
+from requests.models import Response
 
-REST_CLIENT_37_URL = "https://grch37.rest.ensembl.org"
+from scout.utils.ensembl_rest_clients import RESTAPI_37
 
 
 @responses.activate
 def test_liftover(ensembl_rest_client_37, ensembl_liftover_response):
     """Test send request for coordinates liftover"""
     # GIVEN a patched response from Ensembl
-    url = f"{REST_CLIENT_37_URL}/map/human/GRCh37/X:1000000..1000100/GRCh38?content-type=application/json"
+    url = f"{RESTAPI_37}/map/human/GRCh37/X:1000000..1000100/GRCh38?content-type=application/json"
     responses.add(
         responses.GET,
         url,
@@ -26,7 +27,7 @@ def test_liftover(ensembl_rest_client_37, ensembl_liftover_response):
 @responses.activate
 def test_send_gene_request(ensembl_gene_response, ensembl_rest_client_37):
     """Test send request with correct params and endpoint"""
-    url = f"{REST_CLIENT_37_URL}/overlap/id/ENSG00000103591?feature=gene"
+    url = f"{RESTAPI_37}/overlap/id/ENSG00000103591?feature=gene"
     client = ensembl_rest_client_37
     responses.add(
         responses.GET,
@@ -43,37 +44,37 @@ def test_send_gene_request(ensembl_gene_response, ensembl_rest_client_37):
     assert data[0]["end"]
 
 
-@responses.activate
-def test_send_request_fakey_url(ensembl_rest_client_37):
-    """Successful requests are tested by other tests in this file.
-    This test will trigger errors instead.
-    """
+def test_send_request_fakey_url(mock_app, ensembl_rest_client_37, mocker):
+    """Test the Ensembl REST client with an URL that is raising missing schema error."""
+
     # GIVEN a completely invalid URL
     url = "fakeyurl"
-    # GIVEN a client
+    # GIVEN a patched Ensembl client
     client = ensembl_rest_client_37
-    responses.add(
-        responses.GET,
-        url,
-        body=MissingSchema(),
-        status=404,
-    )
-    data = client.send_request(url)
-    assert isinstance(data, MissingSchema)
+    mocker.patch("requests.get", side_effect=MissingSchema("Invalid URL"))
 
+    # THEN the client should return no content
+    with mock_app.test_request_context():
+        data = client.send_request(url)
+        assert data is None
 
-@responses.activate
-def test_send_request_wrong_url(ensembl_rest_client_37):
-    """Successful requests are tested by other tests in this file.
-    This test will trigger errors instead.
-    """
-    url = f"{REST_CLIENT_37_URL}/fakeyurl"
+
+def test_send_request_unavaailable(mock_app, ensembl_rest_client_37, mocker):
+    """Test the Ensembl REST client with an URL that is not available (500 error)."""
+
+    url = f"{RESTAPI_37}/fakeyurl"
+    # GIVEN a patched Ensembl client
     client = ensembl_rest_client_37
-    responses.add(
-        responses.GET,
-        url,
-        body=HTTPError(),
-        status=404,
-    )
-    data = client.send_request(url)
-    assert isinstance(data, HTTPError)
+
+    # GIVEN a mocked 550 response from Ensembl
+    mock_response = Response()
+    mock_response.status_code = 500  # Simulate 500 Internal Server Error
+    mock_response._content = b"Internal Server Error"  # Optional: Set error content
+
+    # Mock `requests.get` to return the mock response
+    mocker.patch("scout.utils.ensembl_rest_clients.requests.get", return_value=mock_response)
+
+    with mock_app.test_request_context():
+        # THEN the client should return no content
+        data = client.send_request(url)
+        assert data is None