scout-browser 4.96.0__py3-none-any.whl → 4.98.0__py3-none-any.whl

scout/server/blueprints/variant/templates/variant/components.html

@@ -1,3 +1,4 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
 {% from "variant/buttons.html" import variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button %}
 {% from "variants/utils.html" import compounds_table %}
 {% from "variant/variant_details.html" import severity_list %}
@@ -118,15 +119,7 @@
         {% endif %}
         </div>
       {% endfor %}
-      {% if config.chanjo_report %}
-        <div class="d-flex flex-wrap ms-1">
-          {% for gene in variant.genes %}
-            <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}">
-              Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
-            </a>
-          {% endfor %}
-        </div>
-      {% endif %}
+      {{ gene_coverage(institute, variant, case, config) }}
     </li>
     <li class="list-group-item">
       <div>
@@ -136,6 +129,30 @@
   </ul>
 {% endmacro %}
 
+{% macro gene_coverage(institute, variant, case, config) %}
+  {% if case.chanjo_coverage and config.chanjo_report %}
+    <div class="d-flex flex-wrap ms-1">
+      {% for gene in variant.genes %}
+        <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}" data-bs-toggle="tooltip" title="Chanjo coverage report">
+          Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
+        </a>
+      {% endfor %}
+    </div>
+  {% endif %}
+  {% if case.chanjo2_coverage %}
+    <div class="d-flex flex-wrap ms-1" data-bs-toggle="tooltip" title="Chanjo2 coverage reports">
+      {% for gene in variant.genes %}
+        {{ chanjo2_report_form(institute, case, gene.hgnc_symbol, 'overview', gene.hgnc_id, "Gene coverage " + (gene.common.hgnc_symbol if gene.common else gene.hgnc_id), "btn btn-sm btn-secondary text-white") }} <!--chanjo2 genes overview -->
+        {% if gene.common.hgnc_id in gene_has_full_coverage and gene.common.hgnc_id[gene.common.hgnc_id] %}
+          <span class="bg-success fa-solid fa-circle-check" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Chanjo2 coverage is at 100% completeness."></span>
+        {% else %}
+          <span class="bg-warning fa-solid fa-triangle-exclamation" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Note that Chanjo2 coverage is below 100% completeness."></span>
+        {% endif %}
+      {% endfor %}
+    </div>
+  {% endif %}
+{% endmacro %}
+
 {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
   <form action="{{ url_for('variant.variant_update', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
     <div class="d-flex justify-content-between">

scout/server/blueprints/variant/templates/variant/variant.html

@@ -339,6 +339,7 @@
         <thead class="thead table-light border-top">
           <tr class="active">
             <th>Gene</th>
+            <th data-bs-toggle="tooltip" title="Gene tolerance to a single copy of a truncating mutation (pLI) | Loss-of-function observed/expected upper bound fraction (LOEUF)">pLI score|LOEUF</th>
             <th>Region</th>
             <th>Consequence</th>
             {% if case.genome_build == "38" %}
@@ -349,11 +350,12 @@
         <tbody>
           {% for gene in variant.genes %}
             <tr>
-              <th>
+              <td>
                 <a href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">
                   {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
                 </a>
-              </th>
+              </td>
+              <td>{{gene.pli_score|round(2) if gene.pli_score else "n.a."}} | {{gene.loeuf|round(2) if gene.loeuf else "n.a."}}</td>
               <td>{{ gene.region_annotation }}</td>
               <td>{{ gene.functional_annotation|truncate(20, True) }}</td>
               {% if case.genome_build == "38" %} <!-- Display eventual functional annotations associated to MANE transcripts -->

scout/server/blueprints/variant/utils.py

@@ -282,6 +282,8 @@ def add_gene_info(
             )
 
             all_models.update(set(variant_gene["manual_inheritance"]))
+            variant_gene["pli_score"] = hgnc_gene.get("pli_score")
+            variant_gene["loeuf"] = hgnc_gene.get("constraint_lof_oe_ci_upper")
 
             update_inheritance_model(variant_gene, all_models, disease_terms)
 

scout/server/blueprints/variants/controllers.py

@@ -40,6 +40,7 @@ from scout.server.blueprints.variant.utils import (
     update_variant_case_panels,
 )
 from scout.server.blueprints.variants.forms import BetterDecimalField
+from scout.server.extensions import store
 from scout.server.links import add_gene_links, cosmic_links, str_source_link
 from scout.server.utils import (
     case_has_alignments,
@@ -83,6 +84,20 @@ def populate_force_show_unaffected_vars(institute_obj, form):
         form.show_unaffected.data = True
 
 
+def populate_persistent_filters_choices(
+    institute_id: str, category: str, form: ImmutableMultiDict
+) -> List[dict]:
+    """Populate the options present in the form.filters on variants page, directly setting on the form.
+    Also return a convenient list of filters for use in filter update macros.
+    """
+    available_filters = list(store.filters(institute_id, category))
+    form.filters.choices = [
+        (filter.get("_id"), filter.get("display_name"))
+        for filter in sorted(available_filters, key=lambda f: f.get("display_name", "").lower())
+    ]
+    return available_filters
+
+
 def populate_chrom_choices(form, case_obj):
     """Populate the option of the chromosome select according to the case genome build"""
     # Populate chromosome choices
@@ -90,6 +105,12 @@ def populate_chrom_choices(form, case_obj):
     form.chrom.choices = [(chrom, chrom) for chrom in chromosomes]
 
 
+def populate_institute_soft_filters(form, institute_obj):
+    """Populate the hidden field 'institute_soft_filters' with a string containing all institute's soft filters."""
+    if institute_obj.get("soft_filters"):
+        form.institute_soft_filters.data = ",".join(institute_obj["soft_filters"])
+
+
 def variants(
     store,
     institute_obj,
@@ -711,7 +732,7 @@ def _compound_follow_filter_clnsig(compound, compound_var_obj, query_form):
 
     There are some filter options that are rather unique, like the ClinVar one.
 
-    If clinsig_confident_always_returned is checked, variants are currently never dismissed on ClinSig alone.
+    If prioritise_clinvar is checked, variants are currently never dismissed on ClinSig alone.
 
     Args:
         compound(dict)
@@ -722,8 +743,7 @@ def _compound_follow_filter_clnsig(compound, compound_var_obj, query_form):
     query_rank = []
     query_str_rank = []
 
-    clinsig_always_returned = query_form.get("clinsig_confident_always_returned")
-    if clinsig_always_returned:
+    if query_form.get("prioritise_clinvar"):
         return False
 
     clinsig = query_form.get("clinsig")
@@ -2088,3 +2108,9 @@ def get_show_dismiss_block():
         session["show_dismiss_block"] = show_dismiss_block
 
     return show_dismiss_block
+
+
+def set_hpo_clinical_filter(case_obj: dict, request_form: dict):
+    """Set HPO clinical filter on case if requested through the form."""
+    if request_form.get("hpo_clinical_filter"):
+        case_obj["hpo_clinical_filter"] = True

scout/server/blueprints/variants/forms.py

@@ -113,6 +113,8 @@ class VariantFiltersForm(FlaskForm):
     compound_follow_filter = BooleanField("Compounds follow filter")
     cadd_inclusive = BooleanField("CADD inclusive")
     clinsig = NonValidatingSelectMultipleField("ClinVar CLINSIG", choices=CLINSIG_OPTIONS)
+    clinsig_exclude = BooleanField("Exclude")
+    prioritise_clinvar = BooleanField("Prioritise ClinVar")
 
     gnomad_frequency = BetterDecimalField("gnomadAF", validators=[validators.Optional()])
     local_obs_old = IntegerField("Local obs. (archive)", validators=[validators.Optional()])
@@ -151,11 +153,25 @@ class VariantFiltersForm(FlaskForm):
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 
+    size_selector = NonValidatingSelectField(
+        "Variant size in bp", choices=[("$gte", ">="), ("$lt", "<")]
+    )
+    size = IntegerField(
+        "",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="Number of bases must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+
     hide_dismissed = BooleanField("Hide dismissed", default=False)
     filter_variants = SubmitField(label="Filter variants")
     export = SubmitField(label="Filter and export")
 
-    show_unaffected = BooleanField("Show also variants present only in unaffected", default=False)
+    show_unaffected = BooleanField("Include variants present only in unaffected", default=True)
+    show_soft_filtered = BooleanField(f"Include soft-filtered variants", default=False)
+    institute_soft_filters = HiddenField()
 
 
 class FiltersForm(VariantFiltersForm):
@@ -163,11 +179,11 @@ class FiltersForm(VariantFiltersForm):
 
     symbol_file = FileField("Symbol File")
 
-    clinsig_confident_always_returned = BooleanField("CLINSIG Confident")
+    clinvar_trusted_revstat = BooleanField("CLINSIG Confident")
     spidex_human = SelectMultipleField("SPIDEX", choices=SPIDEX_CHOICES)
 
     clinical_filter = SubmitField(label="Clinical filter")
-    clinvar_tag = BooleanField("ClinVar hits")
+    clinvar_tag = BooleanField("ClinVar hits only")
 
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE
@@ -180,7 +196,7 @@ class CancerFiltersForm(VariantFiltersForm):
     alt_count = IntegerField("Min alt count", validators=[validators.Optional()])
     control_frequency = BetterDecimalField("Normal alt AF <", validators=[validators.Optional()])
     tumor_frequency = BetterDecimalField("Tumor alt AF >", validators=[validators.Optional()])
-    clinvar_tag = BooleanField("ClinVar hits")
+    clinvar_tag = BooleanField("ClinVar hits only")
     cosmic_tag = BooleanField("Cosmic hits")
     mvl_tag = BooleanField("Managed Variants hits")
     local_obs_cancer_somatic_old = IntegerField(
@@ -189,7 +205,6 @@ class CancerFiltersForm(VariantFiltersForm):
     local_obs_cancer_germline_old = IntegerField(
         "Local germline obs. (archive)", validators=[validators.Optional()]
     )
-
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE_CANCER
 
@@ -212,8 +227,6 @@ class StrFiltersForm(VariantFiltersForm):
 class SvFiltersForm(VariantFiltersForm):
     """Extends FiltersForm for structural variants"""
 
-    size = StringField("Length")
-    size_shorter = BooleanField("Length shorter than")
     svtype = SelectMultipleField("SVType", choices=SV_TYPE_CHOICES)
     decipher = BooleanField("Decipher")
     clingen_ngi = IntegerField("ClinGen NGI obs")
@@ -242,8 +255,6 @@ class CancerSvFiltersForm(SvFiltersForm):
 class FusionFiltersForm(VariantFiltersForm):
     """Extends FiltersForm for fusion variants"""
 
-    size = StringField("Length")
-    size_shorter = BooleanField("Length shorter than")
     decipher = BooleanField("Decipher")
     clinical_filter = SubmitField(label="Clinical filter")
     fusion_score = BetterDecimalField("Fusion score >=", validators=[validators.Optional()])
@@ -302,7 +313,23 @@ class OutlierFiltersForm(FlaskForm):
 
     clinical_filter_base = CLINICAL_FILTER_BASE_OUTLIER
 
-    show_unaffected = BooleanField("Show also variants present only in unaffected", default=False)
+    show_unaffected = BooleanField("Include variants present only in unaffected", default=False)
+
+    sort_by = NonValidatingSelectField(
+        choices=[
+            ("", "Sort by"),
+            ("p_value", "Sort by P-value"),
+            ("delta_psi", "Sort by Δψ"),
+            ("psi_value", "Sort by ψ value"),
+            ("zscore", "Sort by zscore"),
+            ("l2fc", "Sort by l2fc"),
+        ],
+        validators=[validators.Optional()],
+    )
+    sort_order = NonValidatingSelectField(
+        choices=[("", "Sort order"), ("asc", "asc"), ("desc", "desc")],
+        validators=[validators.Optional()],
+    )
 
 
 FILTERSFORMCLASS = {

scout/server/blueprints/variants/templates/variants/components.html

@@ -203,16 +203,18 @@
       {% endfor %}
 
       {% set panel_count = matching_panels|length %}
-      <a
-        class="badge bg-secondary text-white"
-        data-bs-toggle="popover"
-        data-bs-html="true"
-        data-bs-trigger="hover click"
-        title="Overlapping gene panels"
-        data-bs-content="{% for panel in matching_panels %}
-          {{ panel.panel_name|safe }}<br>
-        {% else %} No ovelapping gene panels {% endfor %}"
-      >{{ panel_count }}</a>
+      {% if panel_count %}
+        <a
+          class="badge bg-secondary text-white"
+          data-bs-toggle="popover"
+          data-bs-html="true"
+          data-bs-trigger="hover click"
+          title="Overlapping gene panels"
+          data-bs-content="{% for panel in matching_panels %}
+            {{ panel.panel_name|safe }}<br>
+          {% endfor %}"
+        >{{ panel_count }}</a>
+      {% endif %}
     {% endmacro %}
 
     {% if variant.category in ["cancer", "sv_cancer"] %}

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

@@ -36,12 +36,18 @@
       the_form.submit();
     }}
 
-    var show_unaffected =document.getElementById('show_unaffected');
+    var show_unaffected = document.getElementById('show_unaffected');
     if (show_unaffected) {
       show_unaffected.onchange = function() {
       the_form.submit();
     }}
 
+    var show_soft_filtered = document.getElementById('show_soft_filtered');
+    if (show_soft_filtered) {
+      show_soft_filtered.onchange = function() {
+      the_form.submit();
+    }}
+
     function resetPage(){
       document.getElementById('page').value = "1";
     }
@@ -102,6 +108,18 @@
         {{ form.hide_dismissed(class="form-check-input") }}
         {{ form.hide_dismissed.label(class="form-check-label ms-2") }}
       </div>
+      {% if institute.soft_filters %} <!-- Available only for institutes with soft filters in settings -->
+        <div class="form-check d-flex justify-content-start">
+          {{ form.show_soft_filtered(class="form-check-input") }}
+          {{ form.show_soft_filtered.label(
+              class="form-check-label ms-2",
+              data_bs_toggle="tooltip",
+              title="Filters are defined by an admin in the institute settings. Current filters are: " ~
+                form.institute_soft_filters.data|safe
+          ) }}
+          {{ form.institute_soft_filters() }}
+        </div>
+      {% endif %}
       <div class="form-check d-flex justify-content-start">
         {% if institute.check_show_all_vars %}
           <input type="checkbox" class="form-check-input" name="show_unaffected" id="show_unaffected" checked disabled>
@@ -275,6 +293,16 @@
 </div>
 {% endmacro %}
 
+{% macro variant_size_filter(form) %}
+<div class="col-2">
+  {{ form.size_selector.label(class="control-label") }}
+  <div class="input-group">
+    {{ form.size_selector(class="form-select") }}
+    {{ form.size(class="form-control") }}
+  </div>
+</div>
+{% endmacro %}
+
 {% macro snv_filters(form, institute, case, filters)%}
 <input type="hidden" name="variant_type" value="{{ form.variant_type.data }}">
   {{ variants_common_filters(form, "snv") }}
@@ -308,16 +336,28 @@
       {{ form.spidex_human(class="selectpicker", data_style="btn-secondary") }}
     </div>
     <div class="col-2">
-      {{ form.clinsig.label(class="control-label") }}
+      <span>{{ form.clinsig.label(class="control-label") }}</span>
+      <span style="float:right;">{{ form.clinsig_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Exclude variants with clinical significance among the selected categories.") }} {{form.clinsig_exclude}}</span>
       {{ form.clinsig(class="selectpicker", data_style="btn-secondary") }}
     </div>
-    <div class="col-1">
-      {{ form.clinsig_confident_always_returned.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Always show selected CLINSIG entries with trusted revision status levels.") }}
-      <div>{{ form.clinsig_confident_always_returned() }}</div>
-    </div>
-    <div class="col-1">
-      {{ form.clinvar_tag() }}
-      {{ form.clinvar_tag.label(class="ms-2") }}
+    <div class="col-2">
+      <div class="row">
+        <div class="class="form-check">
+          {{ form.clinvar_trusted_revstat(class="form-check-input") }}
+          {{ form.clinvar_trusted_revstat.label(class="form-check-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Limit search to variants with trusted ClinVar revision status levels: mult, multiple_submitters, single, single_submitter, exp, reviewed_by_expert_panel, guideline, practice_guideline.") }}
+        </div>
+      </div>
+      <div class="row">
+        <div class="class="form-check">
+        {{ form.clinvar_tag(class="form-check-input") }}
+        {{ form.clinvar_tag.label(class="form-check-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Return only variants with annotated ClinVar significance.") }}
+        </div>
+      </div>
+      <div class="row">
+        <div class="class="form-check">
+        {{ form.prioritise_clinvar(class="form-check-input") }}
+        {{ form.prioritise_clinvar.label(class="form-check-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Include variants matching the selected ClinVar conditions, in addition to those found using the other search criteria (broadens the search). Note that variants excluded using ClinVar tags will still be returned when found using the other search criteria.") }}
+      </div>
     </div>
   </div>
   <div class="row mb-2">
@@ -336,10 +376,10 @@
         </div>
       </div>
     </div>
-    <div class="col-2">
+    <div class="col-1">
       {{ wtf.form_field(form.start) }}
     </div>
-    <div class="col-2">
+    <div class="col-1">
       {{ wtf.form_field(form.end) }}
     </div>
     <div class="col-2">
@@ -348,6 +388,7 @@
     <div class="col-2">
       {{ wtf.form_field(form.cytoband_end) }}
     </div>
+     {{ variant_size_filter(form) }}
   </div>
   <div class="row">
     <div class="col-2">
@@ -577,16 +618,6 @@
         gene_panels=['hpo']) }}">HPO gene list</a>
     </div>
   </div>
-  <div class="col-2">
-    {{ form.size.label(class="control-label") }}
-    {{ form.size(class="form-control", type="number") }}
-  </div>
-  <div class="col-2 d-flex align-items-end">
-    <div class="mb-2 form-check">
-      {{ form.size_shorter.label(class="form-check-label") }}
-      {{ form.size_shorter(class="form-check-input",type="checkbox") }}
-    </div>
-  </div>
   <div class="col-1 d-flex align-items-end">
     <div class="mb-2 form-check">
       {{ form.decipher.label(class="form-check-label") }}
@@ -622,10 +653,10 @@
       </div>
     </div>
   </div>
-  <div class="col-2">
+  <div class="col-1">
     {{ wtf.form_field(form.start) }}
   </div>
-  <div class="col-2">
+  <div class="col-1">
     {{ wtf.form_field(form.end) }}
   </div>
   <div class="col-1">
@@ -634,6 +665,7 @@
   <div class="col-1">
     {{ wtf.form_field(form.cytoband_end) }}
   </div>
+  {{ variant_size_filter(form) }}
 </div>
 <div class="row mb-3">
   <div class="col-2">
@@ -694,7 +726,8 @@
         {{ form.genetic_models(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
-        {{ form.clinsig.label(class="control-label") }}
+        <span>{{ form.clinsig.label(class="control-label") }}</span>
+        <span style="float:right;">{{ form.clinsig_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Exclude variants with clinical significance among the selected categories.") }} {{form.clinsig_exclude}}</span>
         {{ form.clinsig(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
@@ -765,9 +798,9 @@
         <div class="col">
           {{ wtf.form_field(form.cytoband_end) }}
         </div>
+        {{ variant_size_filter(form) }}
       </div>
       <div class="row" style="margin-top:10px;">
-        <div class="col-2"></div>
         <div class="col-2">
           <a class="btn btn-secondary btn-sm form-control" data-bs-toggle="collapse" href="#stringcoords" aria-expanded="false" aria-controls="stringcoords">
             String coordinates
@@ -841,16 +874,6 @@
         {{ form.hgnc_symbols.label(class="control-label") }}
         {{ form.hgnc_symbols(class="form-control") }}
       </div>
-      <div class="col-2">
-        {{ form.size.label(class="control-label") }}
-        {{ form.size(class="form-control", type="number") }}
-      </div>
-      <div class="col-2 d-flex align-items-end">
-        <div class="form-check mb-2">
-          {{ form.size_shorter.label(class="form-check-label") }}
-          {{ form.size_shorter(class="form-check-input",type="checkbox") }}
-        </div>
-      </div>
       <div class="col-1">
       </div>
       <div class="col-1">
@@ -889,9 +912,9 @@
         <div class="col">
           {{ wtf.form_field(form.cytoband_end) }}
         </div>
+        {{ variant_size_filter(form) }}
       </div>
       <div class="row" style="margin-top:10px;">
-        <div class="col-2"></div>
         <div class="col-2">
           <a class="btn btn-secondary btn-sm form-control" data-bs-toggle="collapse" href="#stringcoords" aria-expanded="false" aria-controls="stringcoords">
             String coordinates