Merge branch 'show_mane_on_variant_summary' of https://github.com/Cli…

…nical-Genomics/scout into show_mane_on_variant_summary

CHANGELOG.md

@@ -13,6 +13,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - In the diagnoses page genes associated with a disease are displayed using hgnc symbol instead of hgnc id
 - Refactor view route to allow navigation directly to unique variant document id, improve permissions check
 - Do not show MANE and MANE Plus Clinical transcripts annotated from VEP (saved in variants)but collect this info from the transcripts database collection
+- Refactor view route to allow navigation directly to unique case id (in particular for gens)
 ### Fixed
 - Refactored code in cases blueprints and variant_events adapter (set diseases for partial causative variants) to use "disease" instead of "omim" to encompass also ORPHA terms
 - Refactored code in `scout/parse/omim.py` and `scout/parse/disease_terms.py` to use "disease" instead of "phenotype" to differentiate from HPO terms

scout/server/blueprints/cases/views.py

@@ -74,9 +74,29 @@ def index():
 
 
 @cases_bp.route("/<institute_id>/<case_name>")
+@cases_bp.route("/case/case_id/<case_id>")
 @templated("cases/case.html")
-def case(institute_id, case_name):
-    """Display one case."""
+def case(
+    case_name: Optional[str] = None,
+    institute_id: Optional[str] = None,
+    case_id: Optional[str] = None,
+):
+    """Display one case.
+    Institute and display_name pairs uniquely specify a case.
+    So do case_id, but we still call institute_and_case again to fetch institute
+    and reuse its user access verification.
+    """
+
+    if case_id:
+        case_obj = store.case(case_id=case_id, projection={"display_name": 1, "owner": 1})
+
+        if not case_obj:
+            flash("Case {} does not exist in database!".format(case_id))
+            return abort(404)
+
+        case_name = case_obj.get("display_name")
+        institute_id = case_obj.get("owner")
+
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     if not case_obj:
         flash("Case {} does not exist in database!".format(case_name))

tests/server/blueprints/cases/test_cases_views.py

@@ -350,6 +350,7 @@ def test_case_custom_images(app, institute_obj, case_obj):
     with app.test_client() as client:
         # GIVEN that the user could be logged in
         resp = client.get(url_for("auto_login"))
+        assert resp.status_code == 200
 
         # WHEN case page is loaded
         resp = client.get(
@@ -365,6 +366,26 @@ def test_case_custom_images(app, institute_obj, case_obj):
             assert bytes(f"{section_name}-accordion", "utf-8") in dta
 
 
+def test_case_by_id(app, case_obj):
+    """Test that cases can be retrieved using case_id only"""
+    # GIVEN an initialized app
+    with app.test_client() as client:
+        # GIVEN that the user could be logged in
+        resp = client.get(url_for("auto_login"))
+        assert resp.status_code == 200
+
+        # WHEN case page is loaded
+        resp = client.get(
+            url_for(
+                "cases.case",
+                case_id=case_obj["_id"],
+            )
+        )
+
+        # THEN it should return a valid page
+        assert resp.status_code == 200
+
+
 def test_case_outdated_panel(app, institute_obj, case_obj):
     """Test case displaying an outdated panel warning badge"""
 
@@ -385,6 +406,7 @@ def test_case_outdated_panel(app, institute_obj, case_obj):
     with app.test_client() as client:
         # GIVEN that the user could be logged in
         resp = client.get(url_for("auto_login"))
+        assert resp.status_code == 200
 
         # WHEN case page is loaded
         resp = client.get(
@@ -423,7 +445,7 @@ def test_case_sma(app, case_obj, institute_obj):
         assert resp.status_code == 200
 
 
-def test_case_fusion(app, adapter, fusion_case_obj, institute_obj):
+def test_case_fusion(app, fusion_case_obj, institute_obj):
     """Test the RNA fusion case page."""
 
     # GIVEN an initialized app