scout-browser 4.85__py3-none-any.whl → 4.86__py3-none-any.whl

scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html

@@ -14,14 +14,11 @@
     <link rel="stylesheet" type="text/css"
           href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/themes/smoothness/jquery-ui.css"/>
 
-    <!-- Font Awesome CSS -->
-    <link rel="stylesheet" type="text/css"
-          href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css"/>
-
     <!-- jQuery JS -->
     <script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
     <script type="text/javascript"
             src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js"></script>
+
     {{ igv_script() }}
 </head>
 
@@ -30,6 +27,11 @@
 </body>
 
 <script type="text/javascript">
+
+  var outLinks = {
+    COSV: "https://cancer.sanger.ac.uk/cosmic/search?q=", // COSMIC variant search
+  };
+
   $(document).ready(function () {
       var div = $("#igvDiv")[0],
               options = {
@@ -146,7 +148,45 @@
                       {% endfor %}
                   ]
               };
-      igv.createBrowser(div, options);
+      igv.createBrowser(div, options)
+      .then(function (browser) {
+          browser.on('trackclick', function (track, popoverData) {
+
+              var markup = "<table class=\"igv-popover-table\">";
+
+              // Don't show a pop-over when there's no data.
+              if (!popoverData || !popoverData.length) {
+                  return false;
+              }
+
+              popoverData.forEach(function (nameValue) {
+
+              if (nameValue.name) {
+
+                  var value = nameValue.value;
+                  for (var key in outLinks) {
+                    if (nameValue.value.toString().startsWith(key) && nameValue.name.toLowerCase() === 'name') {
+                      value = '<a href="' + outLinks[key] + value + '" target="_blank" rel="noopener noreferrer">' + nameValue.value + '</a>';
+                    }
+                  }
+
+                  markup += "<tr><td class=\"igv-popover-td\">"
+                          + "<span class=\"igv-popover-name\">" + nameValue.name + "</span>&nbsp;"
+                          + "<span class=\"igv-popover-value\">" + value + "</span>"
+                          + "</td></tr>";
+                  }
+                  else {
+                      // not a name/value pair
+                      markup += "<tr><td>" + nameValue.toString() + "</td></tr>";
+                  }
+                });
+
+                markup += "</table>";
+
+              // By returning a string from the trackclick handler we're asking IGV to use our custom HTML in its pop-over.
+              return markup;
+          });
+      });
   });
 </script>
 

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

@@ -1,5 +1,5 @@
 {% macro igv_script() %}
   <link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
   <!-- IGV JS-->
-  <script src="https://cdn.jsdelivr.net/npm/igv@2.15.11/dist/igv.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.0.1/dist/igv.min.js"></script>
 {% endmacro %}

scout/server/blueprints/alignviewers/views.py

@@ -91,7 +91,15 @@ def remote_static():
 @alignviewers_bp.route(
     "/<institute_id>/<case_name>/<variant_id>/igv-splice-junctions", methods=["GET"]
 )
-def sashimi_igv(institute_id, case_name, variant_id=None):
+@alignviewers_bp.route(
+    "/<institute_id>/<case_name>/outliers/<omics_variant_id>/igv-splice-junctions", methods=["GET"]
+)
+def sashimi_igv(
+    institute_id: str,
+    case_name: str,
+    variant_id: Optional[str] = None,
+    omics_variant_id: Optional[str] = None,
+):
     """Visualize splice junctions on igv.js sashimi-like viewer for one or more individuals of a case.
     wiki: https://github.com/igvteam/igv.js/wiki/Splice-Junctions
     """
@@ -99,7 +107,7 @@ def sashimi_igv(institute_id, case_name, variant_id=None):
         store, institute_id, case_name
     )  # This function takes care of checking if user is authorized to see resource
 
-    display_obj = controllers.make_sashimi_tracks(case_obj, variant_id)
+    display_obj = controllers.make_sashimi_tracks(case_obj, variant_id, omics_variant_id)
     controllers.set_session_tracks(display_obj)
 
     response = Response(render_template("alignviewers/igv_sashimi_viewer.html", **display_obj))

scout/server/blueprints/cases/controllers.py

@@ -452,6 +452,9 @@ def case(
         "gens_info": gens.connection_settings(case_obj.get("genome_build")),
         "display_rerunner": rerunner.connection_settings.get("display", False),
         "hide_matching": hide_matching,
+        "audits": store.case_events_by_verb(
+            category="case", institute=institute_obj, case=case_obj, verb="filter_audit"
+        ),
     }
 
     return data

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

@@ -1,7 +1,7 @@
 {% extends "layout.html" %}
 {% from "cases/collapsible_actionbar.html" import action_bar, research_modal, reanalysis_modal %}
 {% from "utils.html" import comments_panel, activity_panel, pedigree_panel %}
-{% from "cases/utils.html" import causatives_list, suspects_list, remove_form, matching_causatives, matching_managed_variants, beacon_modal, matchmaker_modal %}
+{% from "cases/utils.html" import causatives_list, suspects_list, remove_form, matching_causatives, matching_managed_variants, beacon_modal, matchmaker_modal, filter_audits %}
 {% from "cases/individuals_table.html" import cancer_individuals_table, individuals_table %}
 {% from "cases/phenotype.html" import hpo_item, cohort_panel, diagnosis_phenotypes, phenotype_groups_panel, add_phenotype_terms_panel, hpo_panel %}
 {% from "cases/gene_panel.html" import genepanels_table, hpo_genelist_panel %}
@@ -119,8 +119,16 @@
         </div>
       </div>
 
+      <div class="row ms-1">
       {{ matching_variants() }}
 
+      {% if audits | count_cursor > 0 %}
+        <div class="card panel-default col-4 ms-5 me-1">
+            {{ filter_audits(audits, true) }}
+        </div>
+      {% endif %}
+      </div>
+
       <div class="card panel-default" >
         <div class="row">
           <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
@@ -258,6 +266,9 @@
         {% if case.vcf_files.vcf_fusion %}
           <a class="btn btn-dark btn-sm text-white" href="{{ url_for('variants.fusion_variants', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">Clinical fusion variants</a>
         {% endif %}
+        {% if case.has_outliers %}
+          <a class="btn btn-dark btn-sm text-white" href="{{ url_for('omics_variants.outliers', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">Clinical WTS outliers</a>
+        {% endif %}
       </div>
     </div>
   </div>
@@ -537,9 +548,9 @@
 {% endmacro %}
 
 {% macro matching_variants() %}
-<div class="card mt-3">
-  <div class="row mt-0 ms-3">
-    <div class="col-sm-12 col-md-12">
+<div class="card mt-3 col-7">
+  <div class="mt-0">
+    <div class="col-md-7">
       <div data-bs-toggle='tooltip' class="panel-heading" title="Check if there are any variants in this case
         marked as causative in another case for this institute, or are on the managed variants list.">
         <strong>
@@ -554,27 +565,27 @@
     {% if hide_matching == false %}
       {% if other_causatives|length > 0 %}
         <div class="row mt-0 ms-3">
-          <div class="col-xs-12 col-md-12">{{ matching_causatives(other_causatives, institute, case) }}</div>
+          <div class="col-md-7">{{ matching_causatives(other_causatives, institute, case) }}</div>
         </div>
       {% endif %}
       {% if default_other_causatives|length > 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-xs-12 col-md-12">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
+          <div class="col-md-7">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
         </div>
       {% endif %}
       {% if managed_variants|length > 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
+          <div class="col-md-7">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
         </div>
       {% endif %}
       {% if default_managed_variants|length > 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
+          <div class="col-md-7">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
         </div>
       {% endif %}
       {% if other_causatives|length == 0 and default_other_causatives|length == 0 and managed_variants|length == 0 and default_managed_variants|length == 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-sm-12 col-md-12">No matching causatives or managed variants found</div>
+          <div class="col-md-7">No matching causatives or managed variants found</div>
         </div>
       {% endif %}
     {% endif %}
@@ -772,5 +783,12 @@ $('#collapse-icon').addClass('fa-angle-double-left');
 $('[data-bs-toggle=sidebar-collapse]').click(function() {
   SidebarCollapse();
 });
+
+function dynamicPhenotypeCheck(source){
+  var checkboxes = document.getElementsByName('hpo_id');
+  for(var i=0, n=checkboxes.length;i<n;i++) {
+    checkboxes[i].checked = source.checked;
+  }
+}
 </script>
 {% endblock %}

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

@@ -1,4 +1,4 @@
-{% from "cases/utils.html" import variant_transcripts %}
+{% from "cases/utils.html" import variant_transcripts, filter_audits %}
 {% from "utils.html" import comments_table, variant_related_comments_table %}
 {% from "variants/components.html" import fusion_variants_header, default_fusion_variant_cells %}
 
@@ -266,22 +266,7 @@
         {% if audits | count_cursor > 0 %}
         <tr>
           <td colspan=2>
-            <table id="audit-table" class="table table-sm" style="background-color: transparent">
-              <thead>
-                <tr>
-                  <th>Filters marked audited for case</th>
-                </tr>
-              </thead>
-              <tbody>
-                 {% set audit_query = namespace() %}
-                 {% for audit in audits %}
-                  {% set audit_query = audit.link|url_args %}
-                  <tr>
-                    <td><strong>{{ audit.subject }} ({{audit_query.variant_type if audit_query.variant_type else "type unavailable -"}} {{ audit_query.category if audit_query.category else "category unavailable"}})</strong> was marked checked by {{ audit.user_name }} on {{audit.created_at.strftime('%Y-%m-%d')}}.</td>
-                  </tr>
-                 {%  endfor %}
-              </tbody>
-            </table>
+            {{filter_audits(audits)}}
           </td>
         </tr>
         {% endif %}

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

@@ -234,16 +234,19 @@
     <form action="{{ url_for('cases.phenotypes_actions', institute_id=institute._id, case_name=case.display_name)+'#phenotypes_panel' }}" method="POST">
 
       <!-- Display and remove added HPO terms -->
-      <div class="row mt-3">
-        <div class="col-12 ms-3">
+      <div class="mt-3">
          {% if "phenotype_terms" in case and case.phenotype_terms|length > 0 %}
            {% for hpo_term in case.phenotype_terms %}
-             {{ hpo_item(hpo_term, case) }}
+             <div class="col-12"> {{ hpo_item(hpo_term, case) }} </div>
            {% endfor %}
+
+          <div class="col-12 mt-3 form-check form-switch">
+            <input type="checkbox" class="form-check-input" id="checkAllPhenotypes" onChange="dynamicPhenotypeCheck(this)" name="checkAllPhenotypes">
+            <label for="checkAllPhenotypes" class="form-check-label">Select all phenotypes</label>
+          </div>
          {% else %}
            <span class="text-mute">No phenotypes added yet</span>
          {% endif %}
-        </div>
       </div>
 
       <div id="phenotypes_panel" class="mt-3">
@@ -284,7 +287,7 @@
 
 {% macro hpo_item(hpo_term, case) %}
   {% if hpo_term %}
-    <input type="checkbox" name="hpo_id" value="{{ hpo_term.phenotype_id }}"
+   <input type="checkbox" name="hpo_id" value="{{ hpo_term.phenotype_id }}"
            {% if case.dynamic_panel_phenotypes and hpo_term.phenotype_id in case.dynamic_panel_phenotypes %} checked {% endif %}>
     {{ hpo_term.feature }}
     <span class="badge bg-info">

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

@@ -324,18 +324,18 @@
     <a href="{{ url_for('variant.cancer_variant',
                    institute_id=variant.institute,
                    case_name=case.display_name,
-                   variant_id=variant._id) }}">
+                   variant_id=variant._id) }}" target="_blank">
     {% else %}
     <a href="{{ url_for('variant.variant',
                    institute_id=variant.institute,
                    case_name=case.display_name,
-                   variant_id=variant._id) }}">
+                   variant_id=variant._id) }}" target="_blank">
     {% endif %}
   {% else %} <!-- structural variants -->
     <a href="{{ url_for('variant.sv_variant',
                               institute_id=variant.institute,
                               case_name=case.display_name,
-                              variant_id=variant._id) }}">
+                              variant_id=variant._id) }}" target="_blank">
   {% endif %}
     {{ pretty_variant(variant) }}
   </a>
@@ -698,3 +698,26 @@
     <span class="fa fa-exclamation-circle text-danger" data-bs-toggle='tooltip' title="Sex is not confirmed."></span>
   {% endif %}
 {% endmacro %}
+
+{% macro filter_audits(audits, edit=none) %}
+<table id="audit-table" class="table table-sm" style="background-color: transparent">
+  <thead>
+    <tr>
+      <th>Filters marked audited for case</th>
+    </tr>
+  </thead>
+  <tbody>
+  {% set audit_query = namespace() %}
+  {% for audit in audits %}
+  {% set audit_query = audit.link|url_args %}
+    <tr>
+      <td class="d-flex align-items-center"><strong>{{ audit.subject }} ({{audit_query.variant_type if audit_query.variant_type else "type unavailable -"}} {{ audit_query.category if audit_query.category else "category unavailable"}})</strong>&nbspwas marked checked by {{ audit.user_name }} on {{audit.created_at.strftime('%Y-%m-%d')}}.
+      {% if edit is true %}
+        <a href="{{ url_for('variants.unaudit_filter', audit_id=audit._id) }}" class="btn btn-link btn-sm" type="submit" data-bs-toggle='tooltip' title="Un-audit filter"><i class="fa fa-times text-danger"></i></a>
+      {% endif %}
+      </td>
+    </tr>
+  {%  endfor %}
+  </tbody>
+</table>
+{% endmacro %}

scout/server/blueprints/clinvar/controllers.py

@@ -442,11 +442,14 @@ def send_api_submission(institute_id, submission_id, key):
     if clinvar_id:  # Check if submission object has already an associated ClinVar ID
         conversion_res["submissionName"] = clinvar_id
 
-    code, submit_res = clinvar_api.submit_json(conversion_res, key)
+    service_url, code, submit_res = clinvar_api.submit_json(conversion_res, key)
 
     if code in [200, 201]:
         clinvar_id = submit_res.json().get("id")
-        flash(f"Submission saved successfully with ID: {clinvar_id}", "success")
+        flash(
+            f"Submission sent to API URL '{service_url}'. Saved successfully with ID: {clinvar_id}",
+            "success",
+        )
 
         # Update ClinVar submission ID with the ID returned from ClinVar
         store.update_clinvar_id(
@@ -459,7 +462,10 @@ def send_api_submission(institute_id, submission_id, key):
         )
 
     else:
-        flash(str(submit_res.json()), "warning")
+        flash(
+            f"Submission sent to API URL '{service_url}'. Returned the following error: {str(submit_res.json())}",
+            "warning",
+        )
 
 
 def clinvar_submission_file(submission_id, csv_type, clinvar_subm_id):

scout/server/blueprints/dashboard/controllers.py

@@ -3,7 +3,7 @@ import logging
 from flask import flash, redirect, request, url_for
 from flask_login import current_user
 
-from scout.constants import CASE_SEARCH_TERMS
+from scout.constants import CASE_SEARCH_TERMS, CASE_TAGS
 from scout.server.extensions import store
 from scout.server.utils import user_institutes
 
@@ -139,8 +139,22 @@ def get_dashboard_info(adapter, data={}, institute_id=None, slice_query=None):
             "count": general_sliced_info["cohort_cases"],
             "percent": general_sliced_info["cohort_cases"] / total_sliced_cases,
         },
+        {
+            "title": "Case status tag",
+            "count": general_sliced_info["tagged_cases"],
+            "percent": general_sliced_info["tagged_cases"] / total_sliced_cases,
+        },
     ]
 
+    for stats_tag in CASE_TAGS.keys():
+        overview.append(
+            {
+                "title": CASE_TAGS[stats_tag]["label"] + " status tag",
+                "count": general_sliced_info[stats_tag + "_cases"],
+                "percent": general_sliced_info[stats_tag + "_cases"] / total_sliced_cases,
+            }
+        )
+
     data["overview"] = overview
 
     return data
@@ -149,6 +163,11 @@ def get_dashboard_info(adapter, data={}, institute_id=None, slice_query=None):
 def get_general_case_info(adapter, institute_id=None, slice_query=None):
     """Return general information about cases
 
+    Count e.g. cases with each kind of case tag, as well as cases that have phenotype, causatives or pinned variants
+    marked or are part of cohorts.
+
+    Gather pedigree information - single, duo, trio or many individuals in case.
+
     Args:
         adapter(adapter.MongoAdapter)
         institute_id(str)
@@ -168,15 +187,24 @@ def get_general_case_info(adapter, institute_id=None, slice_query=None):
         "suspects": 1,
         "cohorts": 1,
         "individuals": 1,
+        "tags": 1,
     }
     cases = adapter.cases(
         owner=institute_id, name_query=name_query, projection=CASE_GENERAL_INFO_PROJECTION
     )
 
-    phenotype_cases = 0
-    causative_cases = 0
-    pinned_cases = 0
-    cohort_cases = 0
+    case_counter_keys = [
+        "phenotype",
+        "causative",
+        "pinned",
+        "cohort",
+        "tagged",
+    ]
+    case_counter_keys.extend(CASE_TAGS.keys())
+
+    case_counter = {}
+    for counter in case_counter_keys:
+        case_counter[counter] = 0
 
     pedigree = {
         1: {"title": "Single", "count": 0},
@@ -191,13 +219,18 @@ def get_general_case_info(adapter, institute_id=None, slice_query=None):
     for total_cases, case in enumerate(cases, 1):
         case_ids.add(case["_id"])
         if case.get("phenotype_terms"):
-            phenotype_cases += 1
+            case_counter["phenotype"] += 1
         if case.get("causatives"):
-            causative_cases += 1
+            case_counter["causative"] += 1
         if case.get("suspects"):
-            pinned_cases += 1
+            case_counter["pinned"] += 1
         if case.get("cohorts"):
-            cohort_cases += 1
+            case_counter["cohort"] += 1
+        if case.get("tags"):
+            case_counter["tagged"] += 1
+            case_tags = case.get("tags")
+            for tag in case_tags:
+                case_counter[tag] += 1
 
         nr_individuals = len(case.get("individuals", []))
         if nr_individuals == 0:
@@ -208,12 +241,10 @@ def get_general_case_info(adapter, institute_id=None, slice_query=None):
             pedigree[nr_individuals]["count"] += 1
 
     general["total_cases"] = total_cases
-    general["phenotype_cases"] = phenotype_cases
-    general["causative_cases"] = causative_cases
-    general["pinned_cases"] = pinned_cases
-    general["cohort_cases"] = cohort_cases
     general["pedigree"] = pedigree
     general["case_ids"] = case_ids
+    for counter in case_counter_keys:
+        general[counter + "_cases"] = case_counter[counter]
 
     return general
 

scout/server/blueprints/dashboard/static/charts.js

@@ -15,12 +15,16 @@ function analysisTypeData(analysis_types) {
     "bkgColors": {
       "WES": "#46bfbd",
       "WGS": "#fdb45c",
-      "PANEL": "#44449B"
+      "PANEL": "#44449B",
+			"PANEL-UMI": "#949fb1",
+			"WTS": "#f7464A"
     },
     "hoverColors": {
       "WES": "#5ad3d1",
       "WGS": "#ffc870",
-      "PANEL": "#353578"
+      "PANEL": "#353578",
+			"PANEL-UMI": "#a8b3c5",
+			"WTS": "#ff5a5e"
     }
   };
   var bkg = [];
@@ -77,7 +81,7 @@ function casesType(cases) {
   var bkg = [];
   var hover = [];
   labels.forEach(function (item, index) {
-    bkg.push(bkgColors[index]);
+		bkg.push(bkgColors[index]);
     hover.push(hoverColors[index]);
   });
   var chart_data = {
@@ -129,52 +133,58 @@ function casesDetailed(overview, all_cases) {
   var bkg = [];
   var hover = [];
   labels.forEach(function (item, index) {
-    bkg.push(bkgColors[index]);
+		ncol = bkgColors.length;
+    bkg.push(bkgColors[index % ncol]);
   });
   var chart_data = {
-    type: "horizontalBar",
+    type: "bar",
     data: {
       labels: labels,
       datasets: [{
         data: overview.map(function (overview) {
           return overview.count * 100 / all_cases;
         }),
+				label: "Case percentage",
         backgroundColor: bkg,
         hoverBackgroundColor: hover
       }]
     },
     options: {
-      tooltips: {
-        callbacks: {
-          label: function label(tooltipItems) {
-            return Math.round(Number(tooltipItems.value) * all_cases / 100);
-          }
-        }
-      },
-      scales: {
-        xAxes: [{
-          ticks: {
-            min: 0,
-            max: 100,
-            callback: function callback(value) {
-              return value + "%";
-            }
-          },
-          scaleLabel: {
-            display: true,
-            labelString: "Case percentage",
-            fontSize: 20
-          }
-        }],
-        yAxes: [{
-          ticks: {
-            fontSize: 20
-          }
-        }]
-      },
-      legend: {
-        display: false
-      }
+			indexAxis: 'y',
+			tooltips: {
+				callbacks: {
+					label: function label(tooltipItems) {
+						return Math.round(Number(tooltipItems.value) * all_cases / 100);
+					}
+				}
+			},
+			scales: {
+				x: {
+					ticks: {
+						min: 0,
+						max: 100,
+						callback: function callback(value) {
+							return value + "%";
+						}
+					},
+					title: {
+						display: true,
+						text: "Case percentage",
+						font: 20
+					}
+				},
+				y: {
+					ticks: {
+						fontSize: 20
+					}
+				}
+			},
+			plugins:
+				{
+					legend: {
+						display: false
+					}
+				}
     }
   };
   return chart_data;

scout/server/blueprints/dashboard/templates/dashboard/dashboard_general.html

@@ -108,7 +108,7 @@
 {% endmacro %}
 
 {% macro cases_stats_panels() %}
-<div class="mt-3" id="cases">
+<div class="mt-3 mb-1" id="cases">
   <div class="row">
     <div class="col-md-8">
         <canvas id="cases-bar-horiz" height="80"></canvas>
@@ -129,7 +129,7 @@
 
 {% block scripts %}
   {{ super() }}
-  <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.8.0/Chart.bundle.min.js" integrity="sha512-60KwWtZOhzgr840mc57MV8JqDZHAws3w61mhK45KsYHmhyNFJKmfg4M7/s2Jsn4PgtQ4Uhr9xItS+HCbGTIRYQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
+  <script src="https://cdn.jsdelivr.net/npm/chart.js@4.4.3/dist/chart.umd.min.js" integrity="sha512-NqRhTU0DQNHNUO0pTx6zPLJ11YhOqj4MRcvv0+amxJk+re07ykGhFuhMmrQpfTRAUx8nQ4EcMuX/m8cz2K8vIQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
   <script src="{{ url_for('dashboard.static', filename='charts.js') }}"></script>
   <script type="text/javascript">
 

scout/server/blueprints/institutes/forms.py

@@ -17,6 +17,7 @@ from scout.constants import CASE_SEARCH_TERMS, PHENOTYPE_GROUPS
 from scout.models.case import STATUS
 
 CASE_SEARCH_KEY = [(value["prefix"], value["label"]) for key, value in CASE_SEARCH_TERMS.items()]
+CATEGORY_CHOICES = [("snv", "SNV"), ("sv", "SV")]
 
 
 class NonValidatingSelectField(SelectField):
@@ -142,6 +143,7 @@ class GeneVariantFiltersForm(FlaskForm):
     """Base FiltersForm for SNVs"""
 
     variant_type = SelectMultipleField(choices=[("clinical", "clinical"), ("research", "research")])
+    category = SelectMultipleField(choices=CATEGORY_CHOICES)
     hgnc_symbols = TagListField(
         "HGNC Symbols (comma-separated, case sensitive)", validators=[validators.InputRequired()]
     )

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

@@ -113,19 +113,21 @@
 {% macro case_row(case) %}
   <tr class="{% if case.status == 'solved' %}causative{% endif %}">
     <td>
-      <a href="{{ url_for('cases.case', institute_id=case.owner, case_name=case.display_name) }}">
+      <a class="me-2"
+         {% if case.individuals|length == 1 %} data-bs-toggle="tooltip" title="{{case.individuals[0].display_name}}" {% endif %}
+         href="{{ url_for('cases.case', institute_id=case.owner, case_name=case.display_name) }}">
         {{ case.display_name }}
       </a>
       {% if case.individuals|length > 1 %}
-      <span class="badge bg-primary">
-        {% for item in case.individuals %}
+        {% for sample in case.individuals %}
+          <span class="badge {{'bg-danger' if sample.phenotype == 2 else 'bg-primary'}}" style="margin:-3px !important;" data-bs-toggle="tooltip" title="{{sample.display_name}}">
           {% if case.track == "cancer" %}
             <span class="fa fa-vial"></span>
           {% else %} <!-- rare disease case -->
             <span class="fa fa-user"></span>
           {% endif %}
+          </span>
         {% endfor %}
-      </span>
       {% endif %}
       {% for user in case.assignees %}
         <span class="badge bg-secondary">{{ user.name }}</span>