scout-browser 4.83__py3-none-any.whl → 4.85__py3-none-any.whl

scout/load/all.py

@@ -3,6 +3,7 @@ import logging
 
 from scout.constants import FILE_TYPE_MAP
 from scout.exceptions.config import ConfigError
+from scout.utils.sort import get_load_priority
 
 LOG = logging.getLogger(__name__)
 
@@ -62,7 +63,10 @@ def load_region(adapter, case_id, hgnc_id=None, chrom=None, start=None, end=None
                 (FILE_TYPE_MAP[file_type]["variant_type"], FILE_TYPE_MAP[file_type]["category"])
             )
 
-    for variant_type, category in case_file_types:
+    for variant_type, category in sorted(
+        case_file_types,
+        key=lambda tup: get_load_priority(variant_type=tup[0], category=tup[1]),
+    ):
         if variant_type == "research" and not case_obj["is_research"]:
             continue
 

scout/load/hgnc_gene.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import logging
+from typing import Dict
 
 from click import progressbar
 
@@ -16,6 +17,22 @@ from scout.utils.scout_requests import (
 LOG = logging.getLogger(__name__)
 
 
+def set_missing_gene_coordinates(gene_data: dict, cytoband_coords: Dict[str, dict]):
+    """Attempt at collecting gene coordinates from cytoband for genes missing Ensembl ID."""
+
+    if gene_data.get("ensembl_gene_id") not in [
+        "",
+        None,
+    ]:  # Coordinates are present, since they're collected from the Ensembl file
+        return
+    gene_data["ensembl_gene_id"] = None
+    cytoband_coord: dict = cytoband_coords.get(gene_data["location"])
+    if cytoband_coord:
+        gene_data["chromosome"]: str = cytoband_coord["chromosome"]
+        gene_data["start"]: int = cytoband_coord["start"]
+        gene_data["end"]: int = cytoband_coord["stop"]
+
+
 def load_hgnc_genes(
     adapter,
     genes=None,
@@ -36,7 +53,7 @@ def load_hgnc_genes(
     Args:
         adapter(scout.adapter.MongoAdapter)
         genes(dict): If genes are already parsed
-        ensembl_lines(iterable(str)): Lines formated with ensembl gene information
+        ensembl_lines(iterable(str)): Lines formatted with ensembl gene information
         hgnc_lines(iterable(str)): Lines with gene information from genenames.org
         exac_lines(iterable(str)): Lines with information pLi-scores from ExAC
         mim2gene(iterable(str)): Lines with map from omim id to gene symbol
@@ -78,20 +95,36 @@ def load_hgnc_genes(
             genemap_lines=genemap_lines,
         )
 
-    non_existing = 0
+    without_coords = 0
     nr_genes = len(genes)
     LOG.info(f"Building info for {nr_genes} genes")
+
+    cytoband_coords: Dict[str, dict] = adapter.cytoband_to_coordinates(build=build)
+
     with progressbar(genes.values(), label="Building genes", length=nr_genes) as bar:
         for gene_data in bar:
+            set_missing_gene_coordinates(gene_data=gene_data, cytoband_coords=cytoband_coords)
+
             if not gene_data.get("chromosome"):
-                non_existing += 1
+                without_coords += 1
                 continue
+            gene_obj = build_hgnc_gene(
+                gene_data,
+                build=build,
+            )
+
+            if gene_obj:
+                gene_objects.append(gene_obj)
+            else:
+                without_coords += 1
 
-            gene_obj = build_hgnc_gene(gene_data, build=build)
-            gene_objects.append(gene_obj)
+    LOG.info(
+        "Nr of genes without coordinates in build %s and therefore skipped: %s",
+        build,
+        without_coords,
+    )
+    LOG.info(f"Loading {len(gene_objects)} genes into the database")
 
-    LOG.info("Nr of genes without coordinates in build %s: %s", build, non_existing)
-    LOG.info(f"Loading {len(gene_objects)} genes to database")
     adapter.load_hgnc_bulk(gene_objects)
 
     LOG.info("Loading done. %s genes loaded", len(gene_objects))

scout/models/hgnc_map.py

@@ -2,6 +2,8 @@ from __future__ import unicode_literals
 
 from typing import List, Optional
 
+from pydantic import BaseModel, Field, field_validator, model_validator
+
 
 class Exon(dict):
     """Exon dictionary
@@ -66,90 +68,51 @@ class HgncTranscript(dict):
                 self["mane_plus_clinical"] = mane_plus_clinical
 
 
-class HgncGene(dict):
-    """HgncGene dictionary
-
-    'hgnc_id': int, # This is the hgnc id, required:
-    'hgnc_symbol': str, # The primary symbol, required
-    'ensembl_id': str, # required
-    'build': str, # '37' or '38', defaults to '37', required
-
-    'chromosome': str, # required
-    'start': int, # required
-    'end': int, # required
-
-    'description': str, # Gene description
-    'aliases': list(), # Gene symbol aliases, includes hgnc_symbol, str
-    'entrez_id': int,
-    'omim_id': int,
-    'pli_score': float,
-    'primary_transcripts': list(), # List of refseq transcripts (str)
-    'ucsc_id': str,
-    'uniprot_ids': list(), # List of str
-    'vega_id': str,
-
-    # Inheritance information
-    'inheritance_models': list(), # List of model names
-    'incomplete_penetrance': bool, # Acquired from HPO
-
-    # Phenotype information
-    'phenotypes': list(), # List of dictionaries with phenotype information
-    """
-
-    def __init__(
-        self,
-        hgnc_id,
-        hgnc_symbol,
-        ensembl_id,
-        chrom,
-        start,
-        end,
-        description=None,
-        aliases=None,
-        entrez_id=None,
-        omim_id=None,
-        pli_score=None,
-        primary_transcripts=None,
-        ucsc_id=None,
-        uniprot_ids=None,
-        vega_id=None,
-        inheritance_models=None,
-        incomplete_penetrance=False,
-        phenotypes=None,
-        build="37",
-    ):
-        super(HgncGene, self).__init__()
-        self["hgnc_id"] = int(hgnc_id)
-        self["hgnc_symbol"] = hgnc_symbol
-        self["ensembl_id"] = ensembl_id
-
-        self["chromosome"] = chrom
-        self["start"] = int(start)
-        self["end"] = int(end)
-        self["length"] = self["end"] - self["start"]
-
-        self["description"] = description
-        self["aliases"] = aliases
-        self["primary_transcripts"] = primary_transcripts
-        self["inheritance_models"] = inheritance_models
-        self["phenotypes"] = phenotypes
-
-        self["entrez_id"] = entrez_id
-        if entrez_id:
-            self["entrez_id"] = int(entrez_id)
-
-        self["omim_id"] = omim_id
-        if omim_id:
-            self["omim_id"] = int(omim_id)
-
-        self["ucsc_id"] = ucsc_id
-        self["uniprot_ids"] = uniprot_ids
-        self["vega_id"] = vega_id
-
-        self["pli_score"] = pli_score
-        if pli_score:
-            self["pli_score"] = float(pli_score)
-
-        self["incomplete_penetrance"] = incomplete_penetrance
-
-        self["build"] = build
+class HgncGene(BaseModel):
+    hgnc_id: int
+    hgnc_symbol: str
+    build: str
+    chromosome: str
+    start: int
+    end: int
+    length: int
+    description: Optional[str] = None
+    ensembl_id: Optional[str] = Field(None, alias="ensembl_gene_id")
+    aliases: Optional[List[str]] = Field(None, alias="previous_symbols")
+    entrez_id: Optional[int] = None
+    omim_id: Optional[int] = None
+    primary_transcripts: Optional[List[str]] = Field(None, alias="ref_seq")
+    ucsc_id: Optional[str] = None
+    uniprot_ids: Optional[List[str]] = None
+    vega_id: Optional[str] = None
+    inheritance_models: Optional[List[str]] = None
+    incomplete_penetrance: Optional[bool] = False
+    phenotypes: Optional[List[dict]] = None
+    pli_score: Optional[float] = None
+    constraint_lof_oe: Optional[float] = None
+    constraint_lof_oe_ci_lower: Optional[float] = None
+    constraint_lof_oe_ci_upper: Optional[float] = None
+    constraint_lof_z: Optional[float] = None
+    constraint_mis_oe: Optional[float] = None
+    constraint_mis_oe_ci_lower: Optional[float] = None
+    constraint_mis_oe_ci_upper: Optional[float] = None
+    constraint_mis_z: Optional[float] = None
+
+    @model_validator(mode="before")
+    def set_gene_length(cls, values) -> "HgncGene":
+        """Set gene length."""
+        if None in [values.get("end"), values.get("start")]:
+            values.update({"length": None})
+        else:
+            values.update({"length": values.get("end") - values.get("start")})
+        return values
+
+    @field_validator("phenotypes", mode="before")
+    @classmethod
+    def set_phenotypes_inheritance(cls, phenotypes) -> Optional[List[dict]]:
+        """Convert field 'inheritance' of each phenotype in phenotypes from set to list."""
+        for phenotype in phenotypes:
+            phenotype["inheritance_models"] = list(phenotype.get("inheritance", {}))
+            phenotype.pop("inheritance", None)
+
+        return phenotypes

scout/models/phenotype_term.py

@@ -14,9 +14,9 @@ class HpoTerm(BaseModel):
     """
 
     hpo_id: str  # id field in the hpo.obo file
-    hpo_number: Optional[
-        int
-    ] = None  # id field in the hpo.obo file, stripped of the 'HP:' part and the zeroes
+    hpo_number: Optional[int] = (
+        None  # id field in the hpo.obo file, stripped of the 'HP:' part and the zeroes
+    )
     description: str  # name field in the hpo.obo file
     ancestors: List = []
     all_ancestors: List = []

scout/parse/hgnc.py

@@ -24,6 +24,7 @@ def parse_hgnc_line(line, header):
     hgnc_gene["hgnc_symbol"] = hgnc_symbol
     hgnc_gene["hgnc_id"] = int(raw_info["hgnc_id"].split(":")[-1])
     hgnc_gene["description"] = raw_info["name"]
+    hgnc_gene["location"] = raw_info["location"]  # cytoband
 
     # We want to have the current symbol as an alias
     aliases = set([hgnc_symbol, hgnc_symbol.upper()])

scout/parse/orpha.py

@@ -1,4 +1,5 @@
 """Code for parsing ORPHA formatted files"""
+
 import logging
 from typing import Any, Dict, List
 from xml.etree.ElementTree import Element

scout/parse/variant/conservation.py

@@ -1,4 +1,5 @@
 """Code for parsing conservation"""
+
 import logging
 import numbers
 

scout/parse/variant/transcript.py

@@ -324,7 +324,7 @@ def set_variant_frequencies(transcript, entry):
                 continue
 
             value = entry[key]
-            if not value or value == ".":
+            if not value or value == "." or value.isalpha():
                 continue
 
             if key in THOUSAND_GENOMES_CSQ_KEYS:

scout/parse/variant/variant.py

@@ -231,10 +231,7 @@ def parse_variant(
         parsed_variant["revel_score"] = parsed_transcripts[0].get(
             "revel_rankscore"
         )  # This is actually the value of REVEL_rankscore
-
-        parsed_variant["revel"] = parsed_transcripts[0].get(
-            "revel_raw_score"
-        )  # This is actually the value of REVEL_score
+        parsed_variant["revel"] = get_highest_revel_score(parsed_transcripts)
 
     ###################### Add conservation ######################
     parsed_variant["conservation"] = parse_conservations(variant, parsed_transcripts)
@@ -261,6 +258,15 @@ def parse_variant(
     return parsed_variant
 
 
+def get_highest_revel_score(parsed_transcripts: List[dict]) -> Optional[float]:
+    """Retrieve the highest REVEL_score value from parsed variant transcripts."""
+    tx_revel_scores: List(float) = [
+        tx.get("revel_raw_score") for tx in parsed_transcripts if tx.get("revel_raw_score") != None
+    ]
+    if tx_revel_scores:
+        return max(tx_revel_scores)
+
+
 def get_genmod_key(case):
     """Gen genmod key
 

scout/server/blueprints/cases/controllers.py

@@ -64,6 +64,7 @@ JSON_HEADERS = {
 COVERAGE_REPORT_TIMEOUT = 20
 
 PANEL_PROJECTION = {"version": 1, "display_name": 1, "genes": 1}
+PANEL_HIDDEN_PROJECTION = {"version": 1, "display_name": 1, "hidden": 1}
 
 
 def phenomizer_diseases(hpo_ids, case_obj, p_value_treshold=1):
@@ -339,6 +340,8 @@ def case(
 
     case_obj["default_genes"] = _get_default_panel_genes(store, case_obj)
 
+    _set_panel_removed(store, case_obj)
+
     for hpo_term in itertools.chain(
         case_obj.get("phenotype_groups") or [], case_obj.get("phenotype_terms") or []
     ):
@@ -479,6 +482,18 @@ def _limit_genes_on_default_panels(default_genes: list, limit_genes: list) -> li
     return list(default_genes_set.intersection(limit_genes_set))
 
 
+def _set_panel_removed(store: MongoAdapter, case_obj: dict) -> list:
+    """Flag panel on list removed if the latest panel version is marked hidden."""
+
+    for panel_info in case_obj.get("panels", []):
+        latest_panel = store.gene_panel(
+            panel_info["panel_name"], projection=PANEL_HIDDEN_PROJECTION
+        )
+        panel_info["removed"] = (
+            latest_panel.get("hidden", False) if latest_panel is not None else False
+        )
+
+
 def _get_default_panel_genes(store: MongoAdapter, case_obj: dict) -> list:
     """Get unique genes on case default panels.
 
@@ -510,7 +525,6 @@ def _get_default_panel_genes(store: MongoAdapter, case_obj: dict) -> list:
             projection=PANEL_PROJECTION,
         )
         latest_panel = store.gene_panel(panel_name, projection=PANEL_PROJECTION)
-        panel_info["removed"] = False if latest_panel is None else latest_panel.get("hidden", False)
         if not panel_obj:
             panel_obj = latest_panel
             if not panel_obj:

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

@@ -65,7 +65,7 @@
                 <span class="badge rounded-pill bg-info text-body" data-bs-toggle="tooltip" data-bs-placement="left" title="Matching causatives and managed variants displayed on case page are NOT filtered by gene panel. Use caution to avoid incidental findings.">off</span>
               {% endif %}
             </div>
-        </div> <!--end of div class="row" -->
+        </div> <!--end of row -->
         <div class="row">
           <form id="case_status_form" method="POST" action="{{ url_for('cases.status', institute_id=institute._id, case_name=case.display_name) }}">
               <div class="btn-toolbar ms-2" role="toolbar">
@@ -105,7 +105,7 @@
                     {{ 'Inactive' if case.status == 'ignored' else 'Ignored' }}
                   </button>
                 </div>
-                <div class="btn-group ms-2 role="group">
+                <div class="btn-group ms-2" role="group">
                   <select name="tags" id="status_tags_case" multiple class="selectpicker" data-style="btn btn-secondary">
                     {% for tag, data in case_tag_options.items() %}
                       <option {% if 'tags' in case and tag~"" in case.tags %} selected {% endif %} value="{{ tag }}" title="{{ data.label }}">
@@ -119,103 +119,65 @@
         </div>
       </div>
 
+      {{ matching_variants() }}
+
       <div class="card panel-default" >
-        <div class="row mt-0">
-          <div class="col-sm-12 col-md-12 ms-3">
-           <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>{% if hide_matching == false %}
-               <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='True') }}" class="text-body"><span class="me-1 fa fa-caret-right"></span>Search for matching causatives and managed variants</a>
-             {% else %}
-               <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='False') }}" class="text-body"><span class="me-1 fa fa-caret-down"></span>Search for matching causatives and managed variants</a>
-             {% endif %}
-             </strong>
-           </div>
-          </div>
+        <div class="row">
+          <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
+          <div class="col">{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}</div>
+          <!-- end of data sharing panels -->
         </div>
-        {% if hide_matching == false %}
-        {% if other_causatives|length > 0 %}
-          <div class="row mt-0 ms-3">
-            <div class="col-xs-12 col-md-12 ms-3">{{ 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 ms-3">{{ 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 ms-3">{{ 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 ms-3">{{ 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 ms-3">No matching causatives or managed variants found</div>
-          </div>
-        {% endif %}
-      {% endif %}
-      <div class="row">
-        <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
-        <div class="col">{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}</div>
-        <!-- end of data sharing panels -->
-      </div>
 
-      <div class="row">
-        {% if case.track == 'cancer' %}
-          <div class="col-sm-12 col-md-12 mt-3">{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}</div>
-        {% else %}
-          <div class="mt-3 col-sm-8 col-md-{{"8" if case.madeline_info and case.individuals|length > 1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}</div>
-          {% if case.madeline_info and case.individuals|length > 1 %}
-            <div class="col-sm-4">
-              {{ pedigree_panel(case) }}
-            </div>
+        <div class="row">
+          {% if case.track == 'cancer' %}
+            <div class="col-sm-12 col-md-12 mt-3">{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}</div>
+          {% else %}
+            <div class="mt-3 col-sm-8 col-md-{{"8" if case.madeline_info and case.individuals|length > 1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}</div>
+            {% if case.madeline_info and case.individuals|length > 1 %}
+              <div class="col-sm-4">
+                {{ pedigree_panel(case) }}
+              </div>
+            {% endif %}
           {% endif %}
-        {% endif %}
-      </div>
-
-      <div class="row mt-3">
-        <div class="col-6">{{ synopsis_panel() }}</div>
-        <div class="col-6">{{ comments_panel(institute, case, current_user, comments) }}</div>
-      </div>
+        </div>
 
-      <div class="row">
-        <div class="col-sm-12">
-          {{ insert_multi_image_panel() }}
+        <div class="row mt-3">
+          <div class="col-6">{{ synopsis_panel() }}</div>
+          <div class="col-6">{{ comments_panel(institute, case, current_user, comments) }}</div>
         </div>
-      </div>
 
-      <div class="row">
-        <div class="col-sm-12">
-          {{ custom_image_panels() }}
+        <div class="row">
+          <div class="col-sm-12">
+            {{ insert_multi_image_panel() }}
+          </div>
         </div>
-      </div>
 
-      <!-- CASE DIAGNOSES AND PHENOTYPES -->
-      <div class="panel-default">
-        <div class="panel-heading"><span class="fa fa-user-md"></span>&nbsp;Phenotypes & diagnoses</div>
         <div class="row">
-          <div class="col-sm-6 ">
-            <div class="card h-100">
-              <div class="card-body">
-                {{ hpo_panel(case, institute, config) }}
+          <div class="col-sm-12">
+            {{ custom_image_panels() }}
+          </div>
+        </div>
+
+        <!-- CASE DIAGNOSES AND PHENOTYPES -->
+        <div class="panel-default">
+          <div class="panel-heading"><span class="fa fa-user-md"></span>&nbsp;Phenotypes & diagnoses</div>
+          <div class="row">
+            <div class="col-sm-6 ">
+              <div class="card h-100">
+                <div class="card-body">
+                  {{ hpo_panel(case, institute, config) }}
+                </div>
               </div>
             </div>
-          </div>
-          <div class="col-sm-6">
-            <div class="card h-100">
-              <div class="card-body">
-                {{ hpo_genelist_panel(case, institute, config) }}
+            <div class="col-sm-6">
+              <div class="card h-100">
+                <div class="card-body">
+                  {{ hpo_genelist_panel(case, institute, config) }}
+                </div>
               </div>
             </div>
-          </div>
-        </div> <!--end of <div class="row">-->
-        </div>
+          </div> <!--end of row>-->
+        </div> <!--end of card panel-default  -->
 
           <!-- diagnoses-related code-->
         {% if not case.track == 'cancer' %}
@@ -259,8 +221,8 @@
       {{ reanalysis_modal(institute, case) }}
       {{ beacon_modal(institute, case) }}
       {{ matchmaker_modal(institute, case, suspects, mme_nodes) }}
-  </div><!-- end of <div containter> -->
-</div><!-- end of <div col> -->
+  </div><!-- end of containter -->
+</div><!-- end of col -->
 {% endmacro %}
 
 {% macro variants_buttons() %}
@@ -390,7 +352,7 @@
                   <a href="{{ url_for('cases.case', institute_id=grouped_case.owner, case_name=grouped_case.display_name) }}">{{ grouped_case.display_name }}</a>
 
                   <a href="{{ url_for('cases.remove_case_group', institute_id=institute._id, case_name=grouped_case.display_name, case_group=group_id) }}" class="btn btn-link btn-sm">
-                      <span class="fa fa-remove text-dark"></span></a>
+                      <span class="fa fa-times text-dark"></span></a>
 
                 </div>
               {% endfor %}
@@ -398,7 +360,7 @@
           </div>
         {% endfor %}
       {% endif %}
-      </div> <!-- end of <div class="list-group" style="max-height:200px; overflow-y: scroll;" -->
+      </div> <!-- end of list-group -->
     </div>
   </div>
 {% endmacro %}
@@ -574,6 +536,51 @@
 </div>
 {% 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 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>
+        {% if hide_matching == false %}
+          <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='True') }}" class="text-body"><span class="me-1 fa fa-caret-down"></span>Search for matching causatives and managed variants</a>
+        {% else %}
+          <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='False') }}" class="text-body"><span class="me-1 fa fa-caret-right"></span>Search for matching causatives and managed variants</a>
+        {% endif %}
+        </strong>
+      </div>
+    </div>
+    {% 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>
+      {% 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>
+      {% 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>
+      {% 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>
+      {% 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>
+      {% endif %}
+    {% endif %}
+  </div>
+</div>
+{% endmacro %}
 
 {% block scripts %}
 {{ super() }}

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

@@ -247,7 +247,7 @@
             {% else %}
               <button type="submit" name="action" value="DELETE" class="btn btn-warning btn-xs form-control">
             {% endif %}
-                <span class="fa fa-remove"></span>
+                <span class="fa fa-times"></span>
                   {{ user.name }}
               </button>
         </form>