Added feature to select multiple rows in results to create same annot…

…ation (#259) (#280)

HISTORY.rst

@@ -32,6 +32,7 @@ End-User Summary
   For this, GRCh38 background data must be imported.
   Kiosk mode does not support GRCh38 yet.
   **This is a breaking change, new data and CLI must be used!**
+- Added feature to select multiple rows in results to create same annotation (#259)
 
 Full Change List
 ================
@@ -65,6 +66,7 @@ Full Change List
 - Setting ``VARFISH_CADD_SUBMISSION_RELEASE`` is called ``VARFISH_CADD_SUBMISSION_VERSION`` now (**breaking change**).
 - ``import_info.tsv`` expected as in data release from ``20210728`` as built from varfish-db-downloader ``1b03e97`` or later.
 - Extending  columns of ``Hgnc`` to upstream update.
+- Added feature to select multiple rows in results to create same annotation (#259)
 
 -------
 v0.23.9

svs/models.py

@@ -430,6 +430,9 @@ def no_flags_set(self):
                 self.flag_candidate,
                 self.flag_final_causative,
                 self.flag_for_validation,
+                self.flag_no_disease_association,
+                self.flag_segregates,
+                self.flag_doesnt_segregate,
                 self.flag_molecular != "empty",
                 self.flag_visual != "empty",
                 self.flag_validation != "empty",

svs/templates/svs/filter_result/header.html

@@ -2,8 +2,9 @@
 
 {# Variant filter table header #}
 <tr>
-  <th style="width:0px; background-color: #f0f0f0;" class="p-0 m-0"></th> {# rank #}
   <th style="width:0px; background-color: #f0f0f0;" class="p-0 m-0"></th> {# fold-out #}
+  <th style="width:0px; background-color: #f0f0f0;" class="p-0 m-0"></th> {# rank #}
+  <th style="width:0px; background-color: #f0f0f0;" class="p-0 m-0"></th> {# checkbox #}
   <th style="width:0px; background-color: #f0f0f0;" class="p-0 m-0"></th> {# bookmark #}
 
   <th style="width: 65px;" class="text-center">SV type / caller</th> {# sv_type + caller #}

svs/templates/svs/filter_result/row_sv.html

@@ -5,7 +5,7 @@
 {% load regmaps_tags %}
 {% load dict %}
 
-<tr class="variant-row {% if not training_mode %}variant-row-{{ first_entry|flag_class }}{% endif %}">
+<tr class="variant-row {% if not training_mode %}variant-row-{{ first_entry|flag_class }}{% endif %}" id="{{ first_entry.case_uuid }}-{{ first_entry.sv_uuid }}">
   {# fold-out #}
   <td class="clickable toggle-variant-details pl-0 pr-0"
       data-url="{% url "svs:sv-details" project=project.sodar_uuid case=object.sodar_uuid sv=first_entry.sv_uuid %}?database={{ database }}&regulatory_general_padding={{ form.cleaned_data|keyvalue:"regulatory_general_padding" }}"
@@ -16,13 +16,16 @@
   <td class="text-nowrap text-right text-muted">
       #{{ forloop.counter }}
   </td>
-
+  {# checkbox #}
+  <td class="pl-0 pr-1">
+    <input type="checkbox" value="{{ first_entry.sv_uuid }}" class="multivar-selector" data-case="{{ first_entry.case_uuid }}">
+  </td>
   {# bookmark #}
   {% if not training_mode %}
   <td class="bookmark pl-0 pr-0 text-nowrap">
     <a style="text-decoration: none" class="variant-bookmark-comment-group" data-sv="{{ first_entry.sv_uuid }}" data-project="{{ project.sodar_uuid }}" data-case="{{ first_entry.case_uuid }}">
-      <img class="text-muted variant-bookmark" src="/icons/fa-{% if first_entry.flag_count %}solid{% else %}regular{% endif %}/bookmark.svg" />
-      <img class="text-muted variant-comment" src="/icons/fa-{% if first_entry.comment_count %}solid{% else %}regular{% endif %}/comment.svg" />
+      <img class="text-muted variant-bookmark" style="filter: invert(54%) sepia(0%) saturate(0%) hue-rotate(321deg) brightness(95%) contrast(89%);" src="/icons/fa-{% if first_entry.flag_count %}solid{% else %}regular{% endif %}/bookmark.svg" />
+      <img class="text-muted variant-comment" style="filter: invert(54%) sepia(0%) saturate(0%) hue-rotate(321deg) brightness(95%) contrast(89%);" src="/icons/fa-{% if first_entry.comment_count %}solid{% else %}regular{% endif %}/comment.svg" />
     </a>
   </td>
   {% endif %}

svs/templates/svs/filter_result/table.html

@@ -22,15 +22,25 @@ <h2>
         {{ rows_by_sv|length|intcomma }} SV calls
         {% if object %}(case has a total of {{ object.num_svs|intcomma }}{% endif %} SV calls)
       </div>
-        <div class="pl-3">
-          Using
-          {% if database == "refseq" %}
-            <strong>RefSeq</strong>
-          {% else %}
-            <strong>ENSEMBL</strong>
-          {% endif %}
-          transcripts.
+      <div class="pl-3">
+        Using
+        {% if database == "refseq" %}
+          <strong>RefSeq</strong>
+        {% else %}
+          <strong>ENSEMBL</strong>
+        {% endif %}
+        transcripts.
+      </div>
+      <div class="dropdown pl-2">
+        <button type="button" id="multiVarButton" class="btn btn-sm btn-outline-secondary dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+          <i class="iconify" data-icon="fluent:bookmark-multiple-16-filled"></i> Multi-Variant Options
+        </button>
+        <div class="dropdown-menu dropdown-menu-left" style="z-index: 1031;">
+          <a class="dropdown-item" id="multivar-bookmark-comment" data-toggle="modal" data-target="#multiVarBookmarkCommentModal">
+            <i class="iconify" data-icon="fluent:bookmark-multiple-16-filled"></i> Flag & Comment
+          </a>
         </div>
+      </div>
     </div>
   </div>
 
@@ -54,5 +64,27 @@ <h2>
     <p>
       Query completed in {{ elapsed_seconds }} sec.
     </p>
+
+    {# Multi-var bookmark and comment modal #}
+    <div class="modal fade" id="multiVarBookmarkCommentModal" aria-hidden="true">
+      <div class="modal-dialog" style="width: 434px" role="document">
+        <div class="modal-content">
+          <div class="modal-header">
+            <h4 class="modal-title" id="multiVarBookmarkCommentModal">Multi-Variant Comments &amp; Flags</h4>
+            <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+              <span aria-hidden="true">&times;</span>
+            </button>
+          </div>
+          <div class="modal-body">
+            <div class="container-fluid" id="multiVarBookmarkCommentModalContent">
+            </div>
+          </div>
+          <div class="modal-footer">
+            <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            <button type="button" class="btn btn-primary save">Save</button>
+          </div>
+        </div>
+      </div>
+    </div>
   </div> <!-- sodar-page-container -->
 {% endif %}

svs/templates/svs/scripts.html

@@ -30,9 +30,11 @@
   let structural_or_small = "structural";
   let variant_flags_url = "{% url 'svs:sv-flags-api' project=project.sodar_uuid case="--abcef--" sv="--bbccee--" %}";
   let variant_comment_url = "{% url 'svs:sv-comment-api' project=project.sodar_uuid case="--abcef--" sv="--bbccee--" %}";
+  let multi_variant_flags_comment_url = "{% url 'svs:multi-sv-flags-comment-api' project=project.sodar_uuid %}";
 </script>
 <script type="text/javascript" src="{% static "js/helpers.js" %}"></script>
 <script type="text/javascript" src="{% static "js/filter_form.js" %}"></script>
 <script type="text/javascript" src="{% static "js/flags_comments.js" %}"></script>
 
 {% include "variants/_variant_flag_form_tpl.html" %}
+{% include "variants/_multi_variant_flag_form_tpl.html" %}

svs/urls.py

@@ -28,6 +28,11 @@
         view=views.StructuralVariantCommentApiView.as_view(),
         name="sv-comment-api",
     ),
+    url(
+        regex=r"^(?P<project>[0-9a-f-]+)/multi-sv-flags-comment",
+        view=views.MultiStructuralVariantFlagsAndCommentApiView.as_view(),
+        name="multi-sv-flags-comment-api",
+    ),
     # Views for variants import job.
     url(
         regex=r"^(?P<project>[0-9a-f-]+)/import/(?P<job>[0-9a-f-]+)/$",

svs/views.py

@@ -8,7 +8,7 @@
 from projectroles.views import LoginRequiredMixin
 from django.db import transaction
 from django.forms import model_to_dict
-from django.http import HttpResponse, Http404
+from django.http import HttpResponse, Http404, JsonResponse
 from django.shortcuts import render, redirect, get_object_or_404, reverse
 from django.utils import timezone
 from django.views import View
@@ -341,10 +341,10 @@ def post(self, *_args, **kwargs):
         if timeline:
             tl_event = timeline.add_event(
                 project=self.get_project(self.request, self.kwargs),
-                app_name="variants",
+                app_name="svs",
                 user=self.request.user,
                 event_name="comment_add",
-                description="add comment for variant %s in case {case}: {text}"
+                description="add comment for structural variant %s in case {case}: {text}"
                 % comment.get_variant_description(),
                 status_type="OK",
             )
@@ -353,6 +353,159 @@ def post(self, *_args, **kwargs):
         return HttpResponse(json.dumps({"result": "OK"}), content_type="application/json")
 
 
+class MultiStructuralVariantFlagsAndCommentApiView(
+    LoginRequiredMixin, LoggedInPermissionMixin, ProjectPermissionMixin, ProjectContextMixin, View,
+):
+    """A view that returns JSON for the ``SmallVariantFlags`` for a variant of a case and allows updates."""
+
+    # TODO: create new permission
+    permission_required = "variants.view_data"
+
+    def get(self, *_args, **_kwargs):
+        get_data = dict(self.request.GET)
+        variant_list = json.loads(get_data.get("variant_list")[0])
+        flags_keys = [
+            "flag_bookmarked",
+            "flag_candidate",
+            "flag_final_causative",
+            "flag_for_validation",
+            "flag_no_disease_association",
+            "flag_segregates",
+            "flag_doesnt_segregate",
+            "flag_visual",
+            "flag_molecular",
+            "flag_validation",
+            "flag_phenotype_match",
+            "flag_summary",
+        ]
+        flags = {i: None for i in flags_keys}
+        flags_interfering = set()
+
+        for variant in reversed(variant_list):
+            case = get_object_or_404(Case, sodar_uuid=variant.get("case"))
+
+            try:
+                flag_data = model_to_dict(self._get_flags_for_variant(variant.get("sv_uuid"), case))
+
+                for flag in flags_keys:
+                    if flags[flag] is None:
+                        flags[flag] = flag_data[flag]
+
+                    if not flags[flag] == flag_data[flag]:
+                        flags_interfering.add(flag)
+
+                    flags[flag] = flag_data[flag]
+
+            except StructuralVariantFlags.DoesNotExist:
+                continue
+
+        results = {
+            "flags": flags,
+            "flags_interfering": sorted(flags_interfering),
+            "variant_list": variant_list,
+        }
+
+        return JsonResponse(results, UUIDEncoder)
+
+    def post(self, *_args, **_kwargs):
+        timeline = get_backend_api("timeline_backend")
+        post_data = dict(self.request.POST)
+        variant_list = post_data.pop("variant_list")[0]
+        post_data.pop("csrfmiddlewaretoken")
+        post_data_clean = {k: v[0] for k, v in post_data.items()}
+        text = post_data_clean.pop("text")
+
+        for variant in json.loads(variant_list):
+            case = get_object_or_404(Case, sodar_uuid=variant.get("case"))
+            sv = StructuralVariant.objects.get(sv_uuid=variant.get("sv_uuid"))
+
+            try:
+                flags = self._get_flags_for_variant(variant.get("sv_uuid"), case)
+
+            except StructuralVariantFlags.DoesNotExist:
+                flags = StructuralVariantFlags(
+                    case=case,
+                    bin=sv.bin,
+                    release=sv.release,
+                    chromosome=sv.chromosome,
+                    start=sv.start,
+                    end=sv.end,
+                    sv_type=sv.sv_type,
+                    sv_sub_type=sv.sv_sub_type,
+                )
+                flags.save()
+
+            form = StructuralVariantFlagsForm({**variant, **post_data_clean}, instance=flags)
+
+            try:
+                flags = form.save()
+
+            except ValueError as e:
+                raise Exception(str(form.errors)) from e
+
+            if timeline:
+                tl_event = timeline.add_event(
+                    project=self.get_project(self.request, self.kwargs),
+                    app_name="svs",
+                    user=self.request.user,
+                    event_name="flags_set",
+                    description="set flags for structural variant %s in case {case}: {extra-flag_values}"
+                    % sv,
+                    status_type="OK",
+                    extra_data={"flag_values": flags.human_readable()},
+                )
+                tl_event.add_object(obj=case, label="case", name=case.name)
+
+            if flags.no_flags_set():
+                flags.delete()
+
+            if text:
+                comment = StructuralVariantComment(
+                    case=case,
+                    user=self.request.user,
+                    bin=sv.bin,
+                    release=sv.release,
+                    chromosome=sv.chromosome,
+                    start=sv.start,
+                    end=sv.end,
+                    sv_type=sv.sv_type,
+                    sv_sub_type=sv.sv_sub_type,
+                    sodar_uuid=uuid.uuid4(),
+                )
+                form = StructuralVariantCommentForm({**variant, "text": text}, instance=comment)
+
+                try:
+                    comment = form.save()
+
+                except ValueError as e:
+                    raise Exception(str(form.errors)) from e
+
+                if timeline:
+                    tl_event = timeline.add_event(
+                        project=self.get_project(self.request, self.kwargs),
+                        app_name="svs",
+                        user=self.request.user,
+                        event_name="comment_add",
+                        description="add comment for structural variant %s in case {case}: {text}"
+                        % comment.get_variant_description(),
+                        status_type="OK",
+                    )
+                    tl_event.add_object(obj=case, label="case", name=case.name)
+                    tl_event.add_object(obj=comment, label="text", name=comment.shortened_text())
+
+        return JsonResponse({"message": "OK", "flags": post_data_clean, "comment": text})
+
+    def _get_flags_for_variant(self, sv_uuid, case):
+        with contextlib.closing(best_matching_flags(get_engine(), case.id, sv_uuid)) as results:
+            result = results.first()
+            if not result:
+                raise StructuralVariantFlags.DoesNotExist()
+            else:
+                return StructuralVariantFlags.objects.get(
+                    case_id=case.id, sodar_uuid=result.flags_uuid
+                )
+
+
 class ImportStructuralVariantsJobDetailView(
     LoginRequiredMixin,
     LoggedInPermissionMixin,