scout-browser 4.88.1__py3-none-any.whl → 4.89__py3-none-any.whl

scout/server/blueprints/cases/controllers.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 import datetime
 import itertools
-import json
 import logging
 import os
 from typing import Dict, List, Set
@@ -21,6 +20,7 @@ from scout.constants import (
     CASE_TAGS,
     CUSTOM_CASE_REPORTS,
     DATE_DAY_FORMATTER,
+    INHERITANCE_PALETTE,
     MITODEL_HEADER,
     MT_COV_STATS_HEADER,
     MT_EXPORT_HEADER,
@@ -41,7 +41,16 @@ from scout.export.variant import export_mt_variants
 from scout.parse.matchmaker import genomic_features, hpo_terms, omim_terms, parse_matches
 from scout.server.blueprints.variant.controllers import variant as variant_decorator
 from scout.server.blueprints.variants.controllers import get_manual_assessments
-from scout.server.extensions import RerunnerError, bionano_access, gens, matchmaker, rerunner, store
+from scout.server.extensions import (
+    RerunnerError,
+    bionano_access,
+    chanjo2,
+    chanjo_report,
+    gens,
+    matchmaker,
+    rerunner,
+    store,
+)
 from scout.server.links import disease_link
 from scout.server.utils import (
     case_has_alignments,
@@ -692,6 +701,7 @@ def case_report_content(store: MongoAdapter, institute_obj: dict, case_obj: dict
         category="case", institute=institute_obj, case=case_obj, verb="filter_audit"
     )
 
+    data["inherit_palette"] = INHERITANCE_PALETTE
     data["manual_rank_options"] = MANUAL_RANK_OPTIONS
     data["genetic_models"] = dict(GENETIC_MODELS)
     data["report_created_at"] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M")
@@ -701,48 +711,6 @@ def case_report_content(store: MongoAdapter, institute_obj: dict, case_obj: dict
     return data
 
 
-def mt_coverage_stats(individuals, ref_chrom="14") -> dict:
-    """Send a request to chanjo report endpoint to retrieve MT vs autosome coverage stats
-
-    Args:
-        individuals(dict): case_obj["individuals"] object
-        ref_chrom(str): reference chromosome (1-22)
-
-    Returns:
-        coverage_stats(dict): a dictionary with mean MT and autosome transcript coverage stats
-    """
-    coverage_stats = {}
-    ind_ids = []
-    for ind in individuals:
-        ind_ids.append(ind["individual_id"])
-
-    # Prepare complete url to Chanjo report chromosome mean coverage calculation endpoint
-    cov_calc_url = url_for("report.json_chrom_coverage", _external=True)
-    # Prepare request data to calculate mean MT coverage
-    data = dict(sample_ids=",".join(ind_ids), chrom="MT")
-    # Send POST request with data to chanjo endpoint
-    resp = requests.post(cov_calc_url, json=data)
-    mt_cov_data = json.loads(resp.text)
-
-    # Change request data to calculate mean autosomal coverage
-    data["chrom"] = str(ref_chrom)  # convert to string if an int is provided
-    # Send POST request with data to chanjo endpoint
-    resp = requests.post(cov_calc_url, json=data)
-    ref_cov_data = json.loads(resp.text)  # mean coverage over the transcripts of ref chrom
-
-    for ind in ind_ids:
-        if not (mt_cov_data.get(ind) and ref_cov_data.get(ind)):
-            continue
-        coverage_info = dict(
-            mt_coverage=round(mt_cov_data[ind], 2),
-            autosome_cov=round(ref_cov_data[ind], 2),
-            mt_copy_number=round((mt_cov_data[ind] / ref_cov_data[ind]) * 2, 2),
-        )
-        coverage_stats[ind] = coverage_info
-
-    return coverage_stats
-
-
 def mt_excel_files(store, case_obj, temp_excel_dir):
     """Collect MT variants and format line of a MT variant report
     to be exported in excel format. Create mt excel files, one for each sample,
@@ -760,9 +728,15 @@ def mt_excel_files(store, case_obj, temp_excel_dir):
     today = datetime.datetime.now().strftime(DATE_DAY_FORMATTER)
     samples = case_obj.get("individuals")
     coverage_stats = None
-    # if chanjo connection is established, include MT vs AUTOSOME coverage stats
-    if current_app.config.get("chanjo_report"):
-        coverage_stats = mt_coverage_stats(samples)
+
+    case_has_chanjo_coverage(case_obj)
+    case_has_chanjo2_coverage(case_obj)
+
+    # Check if coverage and MT copy number stats are available via chanjo2 or chanjo
+    if case_obj.get("chanjo2_coverage"):
+        coverage_stats: Dict[str, dict] = chanjo2.mt_coverage_stats(individuals=samples)
+    elif case_obj.get("chanjo_coverage"):
+        coverage_stats: Dict[str, dict] = chanjo_report.mt_coverage_stats(individuals=samples)
 
     query = {"chrom": "MT"}
     mt_variants = list(

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

@@ -1,5 +1,6 @@
 {% from "cases/utils.html" import variant_transcripts, filter_audits %}
 {% from "utils.html" import comments_table, variant_related_comments_table %}
+{% from "variant/gene_disease_relations.html" import inheritance_badge %}
 {% from "variants/components.html" import fusion_variants_header, default_fusion_variant_cells %}
 
 {% extends "report_base.html" %}
@@ -712,7 +713,9 @@
                 <td>
                   <ul class="p-0" style="list-style-type: none;">
                   {% for disease_term in gene.disease_terms %}
-                    <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{{ disease_term.inheritance }}</span></li>
+                    <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{% if disease_term.source != 'ORPHA' and disease_term.inheritance %}
+                      {% for model in disease_term.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}
+                    {% endif %}</span></li>
                   {% endfor %}
                 </ul>
                 </td>

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

@@ -50,6 +50,25 @@
           </div>
         </div> <!-- end of div class row -->
 
+        <div class="d-flex">
+          {% if case.vcf_files.vcf_snv %}
+          <span class="me-3">
+            <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
+              <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
+              <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+              <span><button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes SMN1 and SMN2">SNVs</button></span>
+            </form>
+          </span>
+          {% endif %}
+          {% if case.vcf_files.vcf_sv %}
+          <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
+            <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
+            <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+            <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button></span>
+          </form>
+          {% endif %}
+        </div>
+
         <div class="row">
           <div class="col-sm-12">{{activity_panel(events)}}</div>
         </div>

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

@@ -86,7 +86,7 @@
     </div>
 
     <!-- If connected to a chanjo or chanjo2 instance, display coverage report -->
-    {% if case.chanjo2_coverage and case.default_genes %}
+    {% if case.chanjo2_coverage %}
       <div href="#" class="bg-dark list-group-item text-white">
         <div class="d-flex flex-row flex-fill bd-highlight">
           <span class="menu-collapsed">Coverage (chanjo2)</span>
@@ -121,11 +121,6 @@
     </div>
     {% endif %}
 
-    <!-- Custom case reports as in constants.CUSTOM_CASE_REPORTS -->
-    {% for _, report_data in report_types.items() %}
-      {{ custom_case_report(institute, case, report_data) }}
-    {% endfor %}
-
     <!-- Delivery reports for old analyses -->
     {% if case.analyses %}
       {% for analysis in case.analyses %}
@@ -134,6 +129,11 @@
         {% endif %}
       {% endfor %}
     {% endif %}
+
+    <!-- Custom case reports as in constants.CUSTOM_CASE_REPORTS -->
+    {% for _, report_data in report_types.items() %}
+      {{ custom_case_report(institute, case, report_data) }}
+    {% endfor %}
 </div>
 <!-- end reports macro -->
 {% endmacro %}
@@ -144,7 +144,7 @@
     <div href="#" class="bg-dark list-group-item text-white">
       <div class="d-flex flex-row bd-highlight mt-1">
         <div>
-          <span class="menu-collapsed">{{report_key|replace("_"," ")|title}}</span>
+          <span class="menu-collapsed">{{report_key|replace("_"," ")|title|upper_na}}</span>
         </div>
         {% if case.get(report_key) is existing %}
           <div>

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

@@ -29,7 +29,7 @@
         <tbody>
           {% for ind in case.individuals %}
             <tr {% if ind.phenotype_human == 'tumor' %} class="bg-danger-light" {% endif %}>
-              <td>{{ ind.display_name }}{% if gens_info.display and ind.analysis_type|upper == "WGS" %}
+              <td>{{ ind.display_name }}{% if gens_info.display %}
                   <a style="font-size: .8rem;" class="btn btn-secondary btn-sm float-end" target="_blank" href="http://{{gens_info.host}}/{{ind.display_name}}?&genome_build={{case.genome_build}}&case_id={{case._id}}&individual_id={{ind.individual_id}}">CN profile</a>
                 {% endif %}</td>
               {% if ind.phenotype_human == "normal" %}

scout/server/blueprints/clinvar/form.py

@@ -55,7 +55,7 @@ class ClinVarVariantForm(FlaskForm):
     clinsig = SelectField(
         "Germline classification", choices=[(item, item) for item in GERMLINE_CLASSIF_TERMS[:5]]
     )
-    clinsig_comment = TextAreaField("Comment on clinical significance")
+    clinsig_comment = TextAreaField("Comment on classification")
     clinsig_cit = TextAreaField("Clinical significance citations (with identifier)")
     last_evaluated = DateField("Date evaluated")
     hpo_terms = MultiCheckboxField("Case-associated HPO terms", choices=[])

scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html

@@ -160,7 +160,7 @@
                   <td>{{subm_variant.clinsig}}</td>
                   <td>{{subm_variant.added_by or "N/A"}}</td>
                   <form id="delete_variant_{{subm_variant._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='variant_data') }}" method="POST">
-                    <td><button type="submit" name="delete_object" value="{{subm_variant._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash fa-lg" aria-hidden="true"></span></button></td>
+                    <td><button type="submit" name="delete_object" value="{{subm_variant._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
                   </form>
                 </tr>
                 <tr>
@@ -217,7 +217,7 @@
                     <td>{{var_key_name[case.linking_id]|truncate(25,true,'..')}}</td>
                     <td>{{case.allele_origin}}</td>
                     <form id="delete_casedata_{{case._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='case_data') }}" method="POST">
-                      <td><button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash fa-lg" aria-hidden="true"></span></button></td>
+                      <td><button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
                     </form>
                   </tr>
                   <tr>

scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html

@@ -209,18 +209,24 @@
                 <legend class="text-dark">Germline Classification</legend>
                 <h3 class="fs-subtitle">Represents a variant-level classification for a disease, rather than an interpretation of the clinical significance of a variant for a specific patient.</h3>
 
+                {% set scout_classif = variant_data.var_obj.classification|replace("_"," ") if variant_data.var_obj.classification else "n.a." %}
+
                 <div class="row">
                   <div class="col-4">
                     <span class="text-dark">Classification in Scout:</span><br>
-                    <span class="badge bg-secondary">{{variant_data.var_obj.classification|replace("_"," ")|upper if variant_data.var_obj.classification else "n.a."}}</span>
+                    <span class="badge bg-secondary">{{ scout_classif|upper }}</span>
                   </div>
                   <div class="col-8">
                     {{variant_data.var_form.clinsig.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required field"><strong>*</strong></span>
-                    {{variant_data.var_form.clinsig(class="form-control, btn-secondary")}}
+                    <select name="clinsig" class="form-control, btn-secondary">
+                      {% for classif, classif_value in variant_data.var_form.clinsig.choices %}
+                        <option value="{{classif_value}}" {% if classif==scout_classif|capitalize %} selected {% endif %}>{{classif}}</option>
+                      {% endfor %}
+                    </select>
                   </div>
                 </div>
                 <br><br><br>
-                {{variant_data.var_form.clinsig_comment.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required only if you select 'drug response' or 'other' as clinical significance"><strong>?</strong></span>
+                {{variant_data.var_form.clinsig_comment.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Optional, but highly encouraged. Free text describing the rationale for the classification."><strong>?</strong></span>
                 {{variant_data.var_form.clinsig_comment(class="form-control, bg-white", placeholder="(optional)")}}
                 <br><br>
                 {{variant_data.var_form.clinsig_cit.label(class="fw-bold, text-dark")}}

scout/server/blueprints/institutes/controllers.py

@@ -10,13 +10,7 @@ from pymongo.cursor import Cursor
 from werkzeug.datastructures import Headers, MultiDict
 
 from scout.adapter.mongo.base import MongoAdapter
-from scout.constants import (
-    CASE_SEARCH_TERMS,
-    CASE_STATUSES,
-    DATE_DAY_FORMATTER,
-    ID_PROJECTION,
-    PHENOTYPE_GROUPS,
-)
+from scout.constants import CASE_STATUSES, DATE_DAY_FORMATTER, ID_PROJECTION, PHENOTYPE_GROUPS
 from scout.server.blueprints.variant.utils import predictions, update_representative_gene
 from scout.server.extensions import beacon, store
 from scout.server.utils import institute_and_case, user_institutes
@@ -435,20 +429,14 @@ def cases(store, request, institute_id):
     Returns:
         data(dict): includes the cases, how many there are and the limit.
     """
-    data = {"search_terms": CASE_SEARCH_TERMS}
+    data = {}
     institute_obj = institute_and_case(store, institute_id)
     data["institute"] = institute_obj
-    name_query = None
-    if request.args.get("search_term"):
-        name_query = "".join(
-            [
-                request.args.get("search_type"),
-                request.args["search_term"].strip(),
-            ]
-        )
-    data["name_query"] = name_query
+
+    name_query = request.form
     limit = int(request.args.get("search_limit")) if request.args.get("search_limit") else 100
-    data["form"] = populate_case_filter_form(request.args)
+
+    data["form"] = CaseFilterForm(request.form)
 
     ALL_CASES_PROJECTION = {
         "analysis_date": 1,
@@ -479,7 +467,6 @@ def cases(store, request, institute_id):
     # local function to add info to case obj
     def populate_case_obj(case_obj):
         analysis_types = set(ind["analysis_type"] for ind in case_obj["individuals"])
-        LOG.debug("Analysis types found in %s: %s", case_obj["_id"], ",".join(analysis_types))
         if len(analysis_types) > 1:
             LOG.debug("Set analysis types to {'mixed'}")
             analysis_types = set(["mixed"])
@@ -523,11 +510,11 @@ def cases(store, request, institute_id):
     all_cases = store.cases(
         collaborator=institute_id,
         name_query=name_query,
-        skip_assigned=request.args.get("skip_assigned"),
-        is_research=request.args.get("is_research"),
-        has_rna_data=request.args.get("has_rna"),
-        verification_pending=request.args.get("validation_ordered"),
-        has_clinvar_submission=request.args.get("clinvar_submitted"),
+        skip_assigned=request.form.get("skip_assigned"),
+        is_research=request.form.get("is_research"),
+        has_rna_data=request.form.get("has_rna"),
+        verification_pending=request.form.get("validation_ordered"),
+        has_clinvar_submission=request.form.get("clinvar_submitted"),
         projection=ALL_CASES_PROJECTION,
     )
     all_cases = _sort_cases(data, request, all_cases)
@@ -550,20 +537,6 @@ def cases(store, request, institute_id):
     return data
 
 
-def populate_case_filter_form(params):
-    """Populate filter form with params previosly submitted by user
-
-    Args:
-        params(werkzeug.datastructures.ImmutableMultiDict)
-
-    Returns:
-        form(scout.server.blueprints.cases.forms.CaseFilterForm)
-    """
-    form = CaseFilterForm(params)
-    form.search_type.default = params.get("search_type")
-    return form
-
-
 def _get_unevaluated_variants_for_case(
     case_obj: dict, var_ids_list: List[str], sanger_validated_by_user_by_case: Dict[str, List[str]]
 ) -> Tuple[Dict[str, list]]:

scout/server/blueprints/institutes/forms.py

@@ -157,11 +157,25 @@ class GeneVariantFiltersForm(FlaskForm):
 
 
 class CaseFilterForm(FlaskForm):
-    """Takes care of cases filtering in cases page"""
-
-    search_type = SelectField("Search by", [validators.Optional()], choices=CASE_SEARCH_KEY)
-    search_term = StringField("Search cases", default="")
+    """Takes care of cases filtering on cases page"""
+
+    case = StringField("Case or Individual name", [validators.Optional()])
+    exact_pheno = StringField("HPO terms, comma-separated", [validators.Optional()])
+    exact_dia = StringField("Disease terms, comma-separated", [validators.Optional()])
+    synopsis = StringField("Synopsis", [validators.Optional()])
+    panel = StringField("Gene panel name", [validators.Optional()])
+    status = StringField("Case status", [validators.Optional()])
+    tags = StringField("Case tag", [validators.Optional()])
+    track = StringField("Case track", [validators.Optional()])
+    pheno_group = StringField("Phenotype group", [validators.Optional()])
+    cohort = StringField("Cohort", [validators.Optional()])
+    similar_case = StringField("Similar case", [validators.Optional()])
+    similar_pheno = StringField("Similar phenotype", [validators.Optional()])
+    pinned = StringField("Pinned gene", [validators.Optional()])
+    causative = StringField("Causative gene", [validators.Optional()])
+    user = StringField("Assigned user", [validators.Optional()])
     search_limit = IntegerField("Limit", [validators.Optional()], default=100)
+    advanced_search = BooleanField("Advanced search options")
     skip_assigned = BooleanField("Hide assigned")
     is_research = BooleanField("Research only")
     clinvar_submitted = BooleanField("Has ClinVar submissions")

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

@@ -22,50 +22,133 @@
 
 
 {% macro search_form() %}
-<form action="{{ url_for('overview.cases', institute_id=institute._id) }}" method="GET" accept-charset="utf-8">
-    <div class="row d-flex align-items-end">
-      <div class="col-3">
-        {{ form.search_type.label(class="control-label") }}
-        {{ form.search_type(class="form-control") }}
-      </div>
-      <div class="col-3">
-          <label class="control-label" for="search_term">Search cases</label>
-          <input class="form-control" id="search_term" name="search_term" value="{{form.search_term.data if form.search_term.data}}" placeholder="example:18201" type="text" pattern="[^\\\<\>\?\!\=\/]*" title="Characters \<>?!=/ are not allowed">
-      </div>
-      <div class="col-1">
-        {{ form.search(class="btn btn-primary form-control") }}
-      </div>
-      <div class="col-1">
-        {{ form.search_limit.label(class="control-label") }}
-        {{ form.search_limit(class="form-control") }}
-      </div>
 
-      <div class="col-2">
-        <div class="form-check">
-          {{ form.skip_assigned(class="form-check-input") }}
-          {{ form.skip_assigned.label(class="form-check-label") }}
+<!-- Collect advanced search key/values -->
+{% set search = {} %}
+{% for field in form._fields %}
+  {% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
+    {% do search.update({field: form._fields[field].data}) %}
+  {% endif %}
+{% endfor %}
+
+<form action="{{ url_for('overview.cases', institute_id=institute._id) }}" method="POST" accept-charset="utf-8">
+    {{ form.hidden_tag() }}
+
+    <div class="row">
+        <div class="col-md-3 mb-3">
+            {{ form.case.label(class="form-label") }}
+            {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
         </div>
-        <div class="form-check">
-          {{ form.is_research(class="form-check-input") }}
-          {{ form.is_research.label(class="form-check-label") }}
+        <div class="col-md-1 mb-3">
+            {{ form.search_limit.label(class="form-label") }}
+            {{ form.search_limit(class="form-control") }}
         </div>
-        <div class="form-check">
-          {{ form.has_rna(class="form-check-input") }}
-          {{ form.has_rna.label(class="form-check-label") }}
+        <div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
+          {{ form.search(class="btn btn-lg btn-primary mt-4") }}
         </div>
-      </div>
-      <div class="col-2">
-        <div class="form-check">
-          {{ form.clinvar_submitted(class="form-check-input") }}
-          {{ form.clinvar_submitted.label(class="form-check-label") }}
+        <div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
+          <a href="{{ url_for('overview.cases', institute_id=institute._id) }}" class="btn btn-lg btn-secondary mt-4 text-white" role="button">Reset search</a>
         </div>
-        <div class="form-check">
-          {{ form.validation_ordered(class="form-check-input") }}
-          {{ form.validation_ordered.label(class="form-check-label") }}
+        <div class="col-md-3 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
+          {{ form.advanced_search(class="form-check-input") }}
+          {{ form.advanced_search.label(class="form-check-label") }}
         </div>
-      </div>
     </div>
+    <div class="row">
+        <div class="col-md-2 mb-3 form-check ms-3">
+            {{ form.skip_assigned(class="form-check-input") }}
+            {{ form.skip_assigned.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.is_research(class="form-check-input") }}
+            {{ form.is_research.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.clinvar_submitted(class="form-check-input") }}
+            {{ form.clinvar_submitted.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.has_rna(class="form-check-input") }}
+            {{ form.has_rna.label(class="form-check-label") }}
+        </div>
+        <div class="col-md-2 mb-3 form-check">
+            {{ form.validation_ordered(class="form-check-input") }}
+            {{ form.validation_ordered.label(class="form-check-label") }}
+        </div>
+    </div>
+    <!-- This div contains the advances search options -->
+    <div id="advancesSearchOptions">
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.exact_pheno.label(class="form-label") }}
+              {{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.exact_dia.label(class="form-label") }}
+              {{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.synopsis.label(class="form-label") }}
+              {{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.panel.label(class="form-label") }}
+              {{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.status.label(class="form-label") }}
+              {{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.tags.label(class="form-label") }}
+              {{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.track.label(class="form-label") }}
+              {{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.pheno_group.label(class="form-label") }}
+              {{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.cohort.label(class="form-label") }}
+              {{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.similar_case.label(class="form-label") }}
+              {{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.similar_pheno.label(class="form-label") }}
+              {{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+      <div class="row">
+          <div class="col-md-4 mb-3">
+              {{ form.pinned.label(class="form-label") }}
+              {{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.causative.label(class="form-label") }}
+              {{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+          <div class="col-md-4 mb-3">
+              {{ form.user.label(class="form-label") }}
+              {{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
+          </div>
+      </div>
+    </div> <!--End of advancedSearchOptions div -->
   </form>
+<div>
+  <span class="text-muted">The following search criteria were used: {{search}}</span>
+</div>
 {% endmacro %}
 
 {% macro cases_table(group_name, cases) %}
@@ -286,16 +369,24 @@
   {{ super() }}
   <script src="{{ url_for('overview.static', filename='form_scripts.js') }}"></script>
   <script>
-  var caseSearchTerms = {{ search_terms|safe }};
-  var searchTerm = document.getElementById('search_term'); // Case search term label
-  var sel = document.getElementById('search_type'); // Case search term select
-  document.getElementById("search_type").onchange = function() {
-    // Change case search term placeholder
-    selectedKey = sel.options[sel.selectedIndex].value.slice(0, -1);
-    searchTerm.placeholder=caseSearchTerms[selectedKey]["placeholder"];
-    // Reset search
-    searchTerm.value="";
-  };
+
+  // Show/hide advanced search options
+  let advSearchBlock = $('#advancesSearchOptions');
+
+  let advBlockCheckbox = $('#advanced_search');
+
+  window.onload = function(){
+    if(!advBlockCheckbox.is(':checked'))
+    advSearchBlock.hide();
+  }
+
+  advBlockCheckbox.on('click', function() {
+    if($(this).is(':checked')) {
+      advSearchBlock.show();
+    } else {
+      advSearchBlock.hide();
+    }
+  })
 
   var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'))
   var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {