Merge branch 'main' into melter_interact

CHANGELOG.md

@@ -9,6 +9,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Add a toggle for melter rerun monitoring of cases
 - Add an option to export cases with rerun monitoring enabled
 ### Changed
+- Start Scout also when loqusdbapi is not reachable
 ### Fixed
 - Gene panel crashing on edit action
 

scout/server/blueprints/variant/controllers.py

@@ -2,7 +2,7 @@
 from base64 import b64encode
 from datetime import date
 
-from flask import url_for
+from flask import flash, url_for
 from flask_login import current_user
 
 from scout.constants import (
@@ -401,6 +401,15 @@ def observations(store, loqusdb, case_obj, variant_obj):
     Returns:
         obs_data(dict)
     """
+    institute_id = variant_obj["institute"]
+    institute_obj = store.institute(institute_id)
+    loqusdb_id = institute_obj.get("loqusdb_id") or "default"
+    if loqusdb.loqusdb_settings[loqusdb_id]["version"] is None:
+        flash("Could not connect to the preselected loqusdb instance", "danger")
+        return {
+            "total": "N/A",
+        }
+
     chrom = variant_obj["chromosome"]
     end_chrom = variant_obj.get("end_chrom", chrom)
     pos = variant_obj["position"]
@@ -426,10 +435,6 @@ def observations(store, loqusdb, case_obj, variant_obj):
         "variant_type": variant_obj.get("sub_category", "").upper(),
         "category": category,
     }
-
-    institute_id = variant_obj["institute"]
-    institute_obj = store.institute(institute_id)
-    loqusdb_id = institute_obj.get("loqusdb_id") or "default"
     obs_data = loqusdb.get_variant(variant_query, loqusdb_id=loqusdb_id)
 
     if not obs_data:

scout/server/config.py

@@ -48,6 +48,7 @@
 #    "default" : {"binary_path": "/miniconda3/envs/loqus2.5/bin/loqusdb", "config_path": "/home/user/settings/loqus_default.yaml"},
 #    "loqus_api" : {"api_url": "http://127.0.0.1:9000"},
 # }
+
 #
 # Cloud IGV tracks can be configured here to allow users to enable them on their IGV views.
 # CLOUD_IGV_TRACKS = [

scout/server/extensions/loqus_extension.py

@@ -93,13 +93,18 @@ def init_app(self, app):
                 setting["version"] = "2.5"
             else:
                 setting["version"] = self.get_instance_version(setting)
-            self.version_check(setting)
-
-        self.loqus_ids = self.loqusdb_settings.keys()
-        LOG.debug(f"LoqusDB setup: {self.__repr__()}")
+            try:
+                self.version_check(setting)
+            except EnvironmentError as env_ex:
+                LOG.warning(env_ex)
+            self.loqus_ids = self.loqusdb_settings.keys()
+            LOG.debug(f"LoqusDB setup: {self.__repr__()}")
 
     def version_check(self, loqusdb_settings):
         """Check if a compatible version is used otherwise raise an error"""
+        if loqusdb_settings["version"] is None:
+            raise EnvironmentError("LoqusDB instance not available")
+
         if not loqusdb_settings["version"] >= "2.5":
             LOG.info("Please update your loqusdb version to >=2.5")
             raise EnvironmentError("Only compatible with loqusdb version >= 2.5")
@@ -127,9 +132,6 @@ def get_api_loqus_version(api_url):
             return None
         json_resp = api_get("".join([api_url, "/"]))
         version = json_resp.get("content", {}).get("loqusdb_version")
-        if version is None:
-            raise ConfigError(f"LoqusDB API url '{api_url}' did not return a valid response.")
-
         return version
 
     def get_exec_loqus_version(self, loqusdb_id=None):

tests/server/conftest.py

@@ -20,6 +20,14 @@ class LoqusdbMock:
     def __init__(self):
         self.nr_cases = 130
         self.variants = {"1_169898014_T_C": {"families": ["vitalmouse"]}}
+        self.loqusdb_settings = {
+            "default": {
+                "api_url": "http://127.0.0.1:9000",
+                "instance_type": "api",
+                "id": "default",
+                "version": "2.5",
+            }
+        }
 
     def case_count(self):
         return self.nr_cases

tests/server/extensions/test_loqusdb_api_extension.py

@@ -17,10 +17,9 @@ def test_get_api_loqus_version_no_connection(loqus_api_app):
     """Test function that returns the version of the LoqusDB API when the API is not available"""
 
     # When the get_api_loqus_version function is invoked for a non-reachable API
-    # THEN it should raise ConfigError
+    # THEN it should set the loqus version to None
     with loqus_api_app.app_context():
-        with pytest.raises(ConfigError):
-            assert loqusdb.get_api_loqus_version(api_url="test_url")
+        assert loqusdb.get_api_loqus_version(api_url="test_url") == None
 
 
 def test_get_api_loqus_version(loqus_api_app, monkeypatch):

tests/server/extensions/test_loqusdb_exe_extension.py

@@ -183,28 +183,6 @@ def mockcommand(*args):
         assert 0 == loqusdb.case_count(variant_category="snv")
 
 
-def test_loqusdb_exe_wrong_version(monkeypatch, loqus_exe, loqus_config):
-    """Test creating a loqus extension when loqusDB version is too old."""
-
-    # Given a mocked loqus exe instance returning a loqus version older than 2.5
-    def mockcommand(*args):
-        return "2.4"
-
-    monkeypatch.setattr(loqus_extension, "execute_command", mockcommand)
-
-    # WHEN instantiating an adapter
-    with pytest.raises(EnvironmentError):
-        # Then the app should not be created because of EnvironmentError
-        app = create_app(
-            config=dict(
-                LOQUSDB_SETTINGS={
-                    "binary_path": loqus_exe,
-                    "loqusdb_config": loqus_config,
-                }
-            )
-        )
-
-
 def test_init_app_loqus_list(monkeypatch, loqus_exe, loqus_config):
     """Test creating a Loqus extension from a list of config params"""