Report ccv score/temperature on case report

CHANGELOG.md

@@ -6,6 +6,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
 ## [unreleased]
 ### Added
+- CCV score / temperature on case reports
 - ACMG SNV classification form also accessible from SV variant page
 - Simplify updating of the PanelApp Green panel from all source types in the command line interactive session
 ### Changed

scout/server/blueprints/cases/controllers.py

@@ -63,6 +63,7 @@
     institute_and_case,
 )
 from scout.utils.acmg import get_acmg_temperature
+from scout.utils.ccv import get_ccv_temperature
 
 LOG = logging.getLogger(__name__)
 
@@ -632,6 +633,26 @@ def add_bayesian_acmg_classification(variant_obj: dict):
         variant_obj["bayesian_acmg"] = get_acmg_temperature(terms)
 
 
+def add_bayesian_ccv_classification(variant_obj: dict):
+    """Append info to display the CCV VUS Bayesian score / temperature.
+    Criteria have a term and a modifier field on the db document
+    that are joined together in a string to conform to a regular
+    CCV term format. A set of such terms are passed on for evaluation
+    to the same function as the CCV classification form uses.
+    """
+    variant_ccv_classifications = list(
+        store.get_ccv_evaluations_case_specific(document_id=variant_obj["_id"])
+    )
+    if variant_ccv_classifications:
+        terms = set()
+        for criterium in variant_ccv_classifications[0].get("ccv_criteria", []):
+            term = criterium.get("term")
+            if criterium.get("modifier"):
+                term += f"_{criterium.get('modifier')}"
+            terms.add(term)
+        variant_obj["bayesian_ccv"] = get_ccv_temperature(terms)
+
+
 def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dict, data: dict):
     """Gather evaluated variants info to include in case report."""
 
@@ -646,6 +667,7 @@ def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dic
             if case_key == "partial_causatives":
                 var_obj["phenotypes"] = case_obj["partial_causatives"][var_id]
             add_bayesian_acmg_classification(var_obj)
+            add_bayesian_ccv_classification(var_obj)
             evaluated_variants_by_type[eval_category].append(
                 _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
             )
@@ -687,6 +709,7 @@ def _append_evaluated_variant_by_type(
         if variant_key in var_obj and var_obj[variant_key] is not None:
 
             add_bayesian_acmg_classification(var_obj)
+            add_bayesian_ccv_classification(var_obj)
 
             evaluated_variants_by_type[eval_category].append(
                 _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -658,7 +658,7 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
         </tr>
       </table>
       <table id="panel-table" class="table table-sm" style="background-color: transparent">
-        <thead>
+        <thead style="text-align:center;">
           <tr>
             <th>Rank</th>
             <th>Score</th>
@@ -674,7 +674,7 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
             {% endif %}
           </tr>
         </thead>
-        <tbody>
+        <tbody style="text-align:center;">
           <tr>
             <td>{{variant.variant_rank}}</td>
             <td>{{variant.rank_score}}</td>
@@ -715,7 +715,7 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
             {% endif %}
             <td>
               {% if variant.acmg_classification %}
-                <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['code'] }}</span>
+                <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['label']}}">{{variant.acmg_classification['label'] }}</span>
               {% else %}
                 -
               {% endif %}
@@ -730,10 +730,17 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
             {% if cancer %}
             <td>
               {% if variant.ccv_classification %}
-                <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['code']}}">{{variant.ccv_classification['code'] }}</span>
+                <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['label']}}">{{variant.ccv_classification['label'] }}</span>
               {% else %}
                 -
               {% endif %}
+              {% if variant.bayesian_ccv %}
+                 <span class="badge rounded-pill bg-{{variant.bayesian_ccv.temperature_class}}">Score {{variant.bayesian_ccv.points|string}} <span class='fa {{variant.bayesian_ccv.temperature_icon}}'></span>
+                 {% if variant.bayesian_ccv.point_classification == "VUS" %}
+                 {{variant.bayesian_ccv.temperature}}
+                {% endif %}
+                </span>
+              {% endif %}
             </td>
             {% endif %}
           </tr>

scout/utils/ccv.py

@@ -146,15 +146,7 @@ def get_ccv_temperature(ccv_terms: set) -> Optional[dict]:
     }
 
     if not ccv_terms:
-        points = 0
-        point_classification = "uncertain_significance"
-        return {
-            "points": points,
-            "temperature": TEMPERATURE_STRINGS[points].get("label"),
-            "temperature_class": TEMPERATURE_STRINGS[points].get("color"),
-            "temperature_icon": TEMPERATURE_STRINGS[points].get("icon"),
-            "point_classification": CCV_COMPLETE_MAP[point_classification].get("short"),
-        }
+        return {}
 
     points = get_ccv_points(ccv_terms)