Sanger feedback

CHANGELOG.md

@@ -7,6 +7,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 ## [unreleased]
 ### Added
 - Pydantic validation of image paths provided in case load config file
+- Sanger recipient may send an alert to the user which ordered the verification when a variant is flagged as true positive
 ### Changed
 - Revel score, Revel rank score and SpliceAI values are also displayed in Causatives and Validated variants tables
 - Remove unused functions and tests

scout/adapter/mongo/user.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import logging
+from typing import Optional
 
 import pymongo
 from pymongo.errors import DuplicateKeyError
@@ -100,3 +101,16 @@ def delete_user(self, email):
         LOG.info("Deleting user %s", email)
         result = self.user_collection.delete_one({"email": email})
         return result
+
+    def update_users_verified_positives(
+        self, user_id: str, variant_info: dict, add: bool = True
+    ) -> Optional[dict]:
+        """Update the list of links to the variants for which the user has ordered verification and turned out to be true positives."""
+        if add:
+            return self.user_collection.find_one_and_update(
+                {"_id": user_id}, {"$addToSet": {"validated_positive_variants": variant_info}}
+            )
+        else:
+            return self.user_collection.find_one_and_update(
+                {"_id": user_id}, {"$pull": {"validated_positive_variants": variant_info}}
+            )

scout/adapter/mongo/variant_events.py

@@ -1,6 +1,6 @@
 import logging
 from collections import Counter
-from typing import Any, Dict, List
+from typing import Dict, List, Optional
 
 import pymongo
 
@@ -214,6 +214,22 @@ def sanger_ordered(
         sanger_ordered = [item for item in results]
         return sanger_ordered
 
+    def sanger_ordered_by(self, institute_id: str, case_id: str, variant_id: str) -> Optional[str]:
+        """retrieve the id of a user which ordered the Sanger verification of a variant."""
+
+        query = {
+            "verb": "sanger",
+            "institute": institute_id,
+            "case": case_id,
+            "variant_id": variant_id,
+        }
+        projection = {"_id": 0, "user_id": 1}
+        result: dict = self.event_collection.find_one(
+            query, projection, sort=[("created_at", pymongo.DESCENDING)]
+        )
+        if result:
+            return result["user_id"]
+
     def validated(
         self, institute_id: str = None, user_id: str = None, case_id: str = None
     ) -> List[Dict[str, List]]:

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

@@ -704,5 +704,17 @@ <h5 class="modal-title" id="exampleModalLabel">Edit synopsis</h5>
 $('[data-bs-toggle=sidebar-collapse]').click(function() {
   SidebarCollapse();
 });
+
+// Allows a Sanger recipient to notify the user who ordered a Sanger verification that it was a true positive
+function validate_action(validated_option) {
+  if (validated_option != "True positive"){
+    document.getElementById('validation_form').submit();
+  }
+  const sanger_recipients = {{ institute.sanger_recipients | tojson }};
+  if ( sanger_recipients.includes("{{current_user.email}}") ){
+    var myModal = new bootstrap.Modal(document.getElementById('validationModal'))
+    myModal.show();
+  }
+}
 </script>
 {% endblock %}

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

@@ -553,17 +553,7 @@ <h6>No pinned variants</h6>
                 </div>
               </div>
               <div class="col-5">
-              <form action="{{ url_for('cases.mark_validation',
-                                         institute_id=variant.institute,
-                                         case_name=case.display_name,
-                                         variant_id=variant._id) }}"
-                      method="POST" accept-charset="utf-8">
-                  <select class="form-control form-control-sm" onchange="this.form.submit()" name="type">
-                    {% for type in ('Not validated', 'True positive', 'False positive') %}
-                      <option value="{{ type }}" {% if type == variant.validation %}selected{% endif %}>{{ type }}</option>
-                    {% endfor %}
-                  </select>
-                </form>
+              {{ validation_macro(variant, case) }}
               </div>
             <div class="col-2">
               {{ remove_form(url_for('cases.pin_variant',
@@ -583,6 +573,43 @@ <h6>No pinned variants</h6>
   </div>
 {% endmacro %}
 
+
+{% macro validation_macro(variant, case) %}
+ <form action="{{ url_for('cases.mark_validation', institute_id=variant.institute, case_name=case.display_name, variant_id=variant._id) }}" method="POST" accept-charset="utf-8" id="validation_form">
+  <select class="form-control form-control-sm" onchange="validate_action(this.value);" name="type">
+    {% for type in ('Not validated', 'True positive', 'False positive') %}
+      <option value="{{ type }}" {% if type == variant.validation %}selected{% endif %}>{{ type }}</option>
+    {% endfor %}
+  </select>
+ </form>
+
+<div class="modal fade" tabindex="-1" id="validationModal">
+  <div class="modal-dialog">
+    <div class="modal-content">
+      <div class="modal-header">
+        <h5 class="modal-title">Positive validation notification</h5>
+        <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
+      </div>
+      <form action="{{ url_for('cases.mark_validation', institute_id=variant.institute, case_name=case.display_name, variant_id=variant._id) }}" method="POST" accept-charset="utf-8">
+        <input type="hidden" name="type" value="True positive"/>
+        <div class="modal-body">
+          <p>The variant is being marked as a true positive.</p>
+          <input class="form-check-input" type="checkbox" value="yes" name="notify_user" id="notify_user" checked>
+          <label class="form-check-label" for="notify_user">
+            Notify user which ordered verification
+          </label>
+        </div>
+        <div class="modal-footer">
+          <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Dismiss</button>
+          <button type="submit" class="btn btn-primary">Save changes</button>
+        </div>
+      </form>
+    </div>
+  </div>
+</div>
+{% endmacro %}
+
+
 {% macro matching_causatives(other_causatives, institute, case, default=False) %}
     <div data-bs-toggle='tooltip' class="panel-heading" title="If there are any variants in this case
       that have been marked as causative in another case for this insitute. {% if default %}Variants in default panels for the case only.{% endif %}">

scout/server/blueprints/cases/views.py

@@ -675,6 +675,20 @@ def mark_validation(institute_id, case_name, variant_id):
         variant_id=variant_id,
     )
     store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
+    if request.form.get("notify_user"):
+        sanger_by: str = store.sanger_ordered_by(
+            institute_id=institute_id, case_id=case_obj["_id"], variant_id=variant_obj["variant_id"]
+        )
+        if sanger_by:
+            variant_info: dict = {
+                "subject": variant_obj["display_name"],
+                "link": link,
+                "case_name": case_name,
+            }
+            store.update_users_verified_positives(
+                user_id=sanger_by, variant_info=variant_info, add=True
+            )
+
     return redirect(request.referrer or link)
 
 

scout/server/blueprints/institutes/controllers.py

@@ -480,6 +480,8 @@ def cases(store, request, institute_id):
     data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
     data["nr_cases"] = sum(data["status_ncases"].values())
     data["sanger_unevaluated"] = get_sanger_unevaluated(store, institute_id, current_user.email)
+    user_obj: dict = store.user(email=current_user.email)
+    data["sanger_positives"] = user_obj.get("validated_positive_variants",[])
 
     case_groups = {status: [] for status in CASE_STATUSES}
     nr_cases = 0

scout/server/blueprints/institutes/templates/overview/cases.html

@@ -249,6 +249,24 @@ <h5 class="modal-title" id="sangerModalLabel">Sanger validations to evaluate:</h
           </div>
         </div>
       {% endif %}
+
+      <!-- Eventual variants the user has ordered verification for and turned out to be true positives -->
+      {% if sanger_positives %}
+        <form action="{{url_for('overview.dismiss_positive_verified_alert')}}" method="POST">
+        <div class="row mt-3">
+          <div class="alert alert-primary">
+            The following variants were verified as true positives:&nbsp;
+            {% for variant in sanger_positives %}
+              <a target="_blank" rel="noopener" href="{{variant.link}}">{{variant.case_name}}/{{variant.subject}}</a>
+              <button class="btn btn-link btn-sm" name="variant_link" value="{{variant.link}}" type="submit"><i class="fa fa-remove text-dark""></i></button>
+              &emsp;&emsp;
+            {% endfor %}
+          </div>
+        </div>
+        </form>
+      {% endif %}
+
+
       <div>
         {% set ordered_statuses = ['prioritized', 'inactive', 'active', 'archived', 'solved', 'ignored'] -%}
         {% for status in ordered_statuses %}

scout/server/blueprints/institutes/views.py

@@ -248,3 +248,17 @@ def institute_users(institute_id):
         return redirect(request.referrer)
     data = controllers.institute(store, institute_id)
     return render_template("/overview/users.html", panel=2, **data)
+
+
+@blueprint.route("/overview/dismiss_positive_verified_alert", methods=["POST"])
+def dismiss_positive_verified_alert():
+    """Removes the alert for a user to go check a variant that was verified as a true positive."""
+    variant_link_to_remove = request.form.get("variant_link")
+    users_verified_positives: list = current_user.validated_positive_variants or []
+    for variant_info in users_verified_positives:
+        if variant_info["link"] == variant_link_to_remove:
+            store.update_users_verified_positives(
+                user_id=current_user._id, variant_info=variant_info, add=False
+            )
+            break
+    return redirect(request.referrer)