scout-browser 4.84__py3-none-any.whl → 4.86__py3-none-any.whl

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

@@ -9,7 +9,7 @@
         <thead class="table-light thead">
           <tr style="cursor: pointer; white-space: nowrap">
             <th>Panel <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by gene panel name"></i></th>
-            <th >Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by default panel"></i></th>
+            <th>Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by if panel is default"></i></th>
             <th>Version <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by panel version"></i></th>
             <th>Genes <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by number of genes"></i></th>
           </tr>
@@ -20,10 +20,10 @@
               <td>
                 <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}">
                   {{ panel.display_name|truncate(30, True) }}
-                  {% if panel.removed %}
-                    <span class="badge bg-danger">Removed</span>
-                  {% endif %}
                 </a>
+                {% if panel.removed %}
+                  <span class="badge bg-danger">Removed</span>
+                {% endif %}
               </td>
               <td >
                 {% if panel.is_default %}
@@ -35,53 +35,39 @@
             </tr>
           {% else %}
             <tr>
-              <td colspan="5">No panels linked to case</td>
+              <td colspan="4">No panels linked to case</td>
             </tr>
           {% endfor %}
         </tbody>
       </table>
     </div>
-    <div class="card-body">
-      <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
-        <div class="row">
-          <label>Change default gene panels</label>
-        </div>
-        <div class="row">
-          <div class="col-8">
-            <select name="panel_ids" class="selectpicker" multiple="multiple" data-style="btn-secondary">
-              {% for panel in case.panels %}
-                <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>{{ panel.display_name }}</option>
-              {% endfor %}
-            </select>
-          </div>
-          <div class="col-4">
-            <button class="btn btn-secondary form-control">Save</button>
-          </div>
-        </div>
-      </form>
-    </div>
+    {{ change_default_panels(case, institute) }}
+
   </div>
 {% endmacro %}
 
 {% macro change_default_panels(case, institute) %}
-  <div class="card panel-default">
-    <div class="panel-heading">Change default gene panels</div>
-    <div class="card-body">
-      <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
-        <div class="row">
-          <div class="col-xs-4">
-            <select name="panel_ids" class="form-control" multiple>
-              {% for panel in case.panels %}
-                <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>{{ panel.display_name }}</option>
-              {% endfor %}
-            </select>
-          </div>
-          <div class="col-xs-4">
-            <button class="btn btn-secondary form-control">Save</button>
-          </div>
+  <div class="card-body">
+    <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
+      <div class="row">
+        <label>Change default gene panels</label>
+      </div>
+
+      <div class="row">
+        <div class="col-8">
+          <select name="panel_ids" class="selectpicker" multiple="multiple" data-style="btn-secondary">
+            {% for panel in case.panels|sort(attribute='display_name')  %}
+              <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>
+                {{ panel.display_name }} {% if panel.removed %} (Removed) {% endif %}
+              </option>
+            {% endfor %}
+          </select>
         </div>
-      </form>
-    </div>
+        <div class="col-4">
+          <button class="btn btn-secondary form-control">Save</button>
+        </div>
+      </div>
+    </form>
   </div>
 {% endmacro %}
 

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>
@@ -676,7 +676,7 @@
               name="{{ button_name if button_name }}"
               value="{{ button_value if button_value }}"
               type="submit">
-        <i class="fa fa-remove text-danger""></i>
+        <i class="fa fa-times text-danger"></i>
       </button>
     </div>
   </form>
@@ -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>

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

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/components.html" import gene_cell, frequency_cell_general %}
+{% from "variants/components.html" import frequency_cell_general, variant_funct_anno_cell, variant_gene_symbols_cell, variant_region_anno_cell %}
 {% from "utils.html" import comments_table %}
 {% from "overview/institute_sidebar.html" import institute_actionbar %}
 {% from "variants/utils.html" import pagination_footer, pagination_hidden_div %}
@@ -39,12 +39,12 @@
 <thead>
         <tr>
           <th scope="col">Case : Score</th>
+          <th scope="col">Var</th>
           <th scope="col">Gene</th>
           <th scope="col">Pop Freq</th>
           <th scope="col">CADD</th>
           <th scope="col">Region</th>
           <th scope="col">Function</th>
-          <th scope="col">HGVS</th>
         </tr>
 </thead>
 <tbody>
@@ -55,20 +55,12 @@
         <tr>
       {% endif %}
             <td class="align-middle">{{ cell_rank(variant) }}</td>
-            <td class="align-middle">{{ gene_cell(variant) }}</td>
+            <td class="align-middle">{{ pretty_link_no_gene(variant) }} </td>
+            <td class="align-middle">{{ variant_gene_symbols_cell(variant) }}</td>
             <td class="align-middle">{{ frequency_cell_general(variant) }}</td>
             <td class="align-middle">{{ cell_cadd(variant) }}</td>
-            <td class="align-middle">
-              {% for annotation in variant.region_annotations %}
-                <div>{{ annotation }}</div>
-              {% endfor %}
-            </td>
-            <td class="align-middle">
-              {% for annotation in variant.functional_annotations %}
-                <div>{{ annotation }}</div>
-              {% endfor %}
-            </td>
-            <td class="align-middle"> {{ (variant.hgvs or '')|url_decode  }}</td>
+            <td class="align-middle">{{ variant_region_anno_cell(variant) }}</td>
+            <td class="align-middle">{{ variant_funct_anno_cell(variant) }}</td>
           </tr>
         {% endfor %}
         {% if form.hgnc_symbols.data == [] %}
@@ -80,7 +72,10 @@
         {% elif variants == [] %}
         <tr>
           <td colspan=7>
-            No variants matching your query in genes: {{form.hgnc_symbols.data|join(", ")}}
+            No variants matching your query in genes: {{form.hgnc_symbols.data|join(", ")}}.
+            {% if "research" not in form.variant_type.data %}
+              Consider a lower rank score threshold or including research variants.
+            {% endif %}
           </td>
         </tr>
         {% endif %}
@@ -92,12 +87,26 @@
 </form>
 {% endmacro %}
 
-{% macro cell_rank(variant) %}
-    <a
-       href="{{ url_for('variant.variant', institute_id=variant.institute,
+
+{% macro pretty_link_no_gene(variant) %}
+  {% if variant.category == "sv" %}
+    <a href="{{ url_for('variant.sv_variant', institute_id=variant.institute,
             case_name=variant.case_display_name, variant_id=variant._id) }}" target="_blank">
-      {{ variant.case_display_name}}
-    </a>
+       {% if hgvs in variant %}
+        {{ variant.hgvs }}
+       {% else %}
+        {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
+       {% endif %}
+  {% else %}
+    <a href="{{ url_for('variant.variant', institute_id=variant.institute,
+            case_name=variant.case_display_name, variant_id=variant._id) }}" target="_blank">
+    {{ (variant.hgvs or '')|url_decode }}
+  {% endif %}
+  </a>
+{% endmacro %}
+
+{% macro cell_rank(variant) %}
+   {{ variant.case_display_name }}
     :
     <span class="badge bg-info">{{ variant.rank_score|int }}</span>
 {% endmacro %}
@@ -123,29 +132,33 @@
           {{ form.hgnc_symbols.label(class="control-label") }}
           {{ form.hgnc_symbols(class="form-control") }}
         </div>
-        <div class="col col-md-3">
-          <label class="control-label">Rank Score ></label>
+        <div class="col col-md-1">
+          <label class="control-label" for="rank_score">Rank Score</label>
           <input type="number" class="form-control" id="rank_score" name="rank_score" min="5" value={{form.rank_score.data}}>
         </div>
-        <div class="col col-md-3">
+        <div class="col col-md-2">
           {{ form.variant_type.label(class="control-label") }}
           {{ form.variant_type(class="form-control", class="selectpicker", data_style="btn-secondary") }}
         </div>
+        <div class="col col-md-2">
+          {{ form.category.label(class="control-label") }}
+          {{ form.category(class="form-control", class="selectpicker", data_style="btn-secondary") }}
+        </div>
       </div>
       <div class="row">
-        <div class="col-md-3">
+        <div class="col-md-6">
           {{ form.phenotype_terms.label(class="control-label") }}
           {{ form.phenotype_terms(class="form-control") }}
         </div>
-        <div class="col-md-3">
+        <div class="col-md-2">
           {{ form.phenotype_groups.label(class="control-label") }}
           {{ form.phenotype_groups(class="form-control") }}
         </div>
-        <div class="col-md-3">
+        <div class="col-md-2">
           {{ form.cohorts.label(class="control-label") }}
           {{ form.cohorts(class="form-control") }}
         </div>
-        <div class="col-md-3">
+        <div class="col-md-2">
           {{ form.similar_case.label(class="control-label") }}
           {{ form.similar_case(class="form-control") }}
         </div>

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

@@ -31,7 +31,7 @@
       <a href="{{ url_for('overview.gene_variants', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start h-100">
           <div class="d-flex w-100 justify-content-start align-items-center">
               <span class="fa fa-search me-3"></span>
-              <span class="menu-collapsed">Search SNVs and INDELs</span>
+              <span class="menu-collapsed">Search SNVs & SVs</span>
           </div>
       </a>