scout-browser 4.82.1__py3-none-any.whl → 4.83__py3-none-any.whl

scout/server/blueprints/cases/controllers.py

@@ -48,6 +48,7 @@ from scout.server.utils import (
     case_has_chanjo2_coverage,
     case_has_chanjo_coverage,
     case_has_mt_alignments,
+    case_has_mtdna_report,
     case_has_rna_tracks,
     institute_and_case,
 )
@@ -62,6 +63,8 @@ JSON_HEADERS = {
 
 COVERAGE_REPORT_TIMEOUT = 20
 
+PANEL_PROJECTION = {"version": 1, "display_name": 1, "genes": 1}
+
 
 def phenomizer_diseases(hpo_ids, case_obj, p_value_treshold=1):
     """Return the list of HGNC symbols that match annotated HPO terms on Phenomizer
@@ -278,22 +281,16 @@ def sma_case(store, institute_obj, case_obj):
     return data
 
 
-def case(store, institute_obj, case_obj):
+def case(
+    store: MongoAdapter, institute_obj: dict, case_obj: dict, hide_matching: bool = True
+) -> dict:
     """Preprocess a single case.
 
     Prepare the case to be displayed in the case view.
 
-    Args:
-        store(adapter.MongoAdapter)
-        institute_obj(models.Institute)
-        case_obj(models.Case)
-
-    Returns:
-        data(dict): includes the cases, how many there are and the limit.
-
+    The return data dict includes the cases, how many there are and the limit.
     """
     # Convert individual information to more readable format
-
     _populate_case_individuals(case_obj)
 
     case_obj["assignees"] = [
@@ -305,6 +302,7 @@ def case(store, institute_obj, case_obj):
     case_has_mt_alignments(case_obj)
     case_has_chanjo_coverage(case_obj)
     case_has_chanjo2_coverage(case_obj)
+    case_has_mtdna_report(case_obj)
 
     case_groups = {}
     case_group_label = {}
@@ -395,31 +393,40 @@ def case(store, institute_obj, case_obj):
             "case_images", case_obj["custom_images"].get("case", {})
         )
 
-    # Limit secondary findings according to institute settings
-    limit_genes = store.safe_genes_filter(institute_obj["_id"])
+    other_causatives = []
+    other_causatives_in_default_panels = []
+    default_managed_variants = []
+    managed_variants = []
 
-    limit_genes_default_panels = _limit_genes_on_default_panels(
-        case_obj["default_genes"], limit_genes
-    )
+    if hide_matching is False:
+        # Limit secondary findings according to institute settings
+        limit_genes = store.safe_genes_filter(institute_obj["_id"])
 
-    other_causatives, other_causatives_in_default_panels = _matching_causatives(
-        store, case_obj, limit_genes, limit_genes_default_panels
-    )
+        limit_genes_default_panels = _limit_genes_on_default_panels(
+            case_obj["default_genes"], limit_genes
+        )
 
-    data = {
-        "institute": institute_obj,
-        "case": case_obj,
-        "other_causatives": other_causatives,
-        "default_other_causatives": other_causatives_in_default_panels,
-        "managed_variants": [
+        other_causatives, other_causatives_in_default_panels = _matching_causatives(
+            store, case_obj, limit_genes, limit_genes_default_panels
+        )
+
+        managed_variants = [
             var for var in store.check_managed(case_obj=case_obj, limit_genes=limit_genes)
-        ],
-        "default_managed_variants": [
+        ]
+        default_managed_variants = [
             var
             for var in store.check_managed(
                 case_obj=case_obj, limit_genes=limit_genes_default_panels
             )
-        ],
+        ]
+
+    data = {
+        "institute": institute_obj,
+        "case": case_obj,
+        "other_causatives": other_causatives,
+        "default_other_causatives": other_causatives_in_default_panels,
+        "managed_variants": managed_variants,
+        "default_managed_variants": default_managed_variants,
         "comments": store.events(institute_obj, case=case_obj, comments=True),
         "hpo_groups": pheno_groups,
         "case_groups": case_groups,
@@ -441,6 +448,7 @@ def case(store, institute_obj, case_obj):
         "mme_nodes": matchmaker.connected_nodes,
         "gens_info": gens.connection_settings(case_obj.get("genome_build")),
         "display_rerunner": rerunner.connection_settings.get("display", False),
+        "hide_matching": hide_matching,
     }
 
     return data
@@ -496,8 +504,12 @@ def _get_default_panel_genes(store: MongoAdapter, case_obj: dict) -> list:
             continue
         panel_name = panel_info["panel_name"]
         panel_version = panel_info.get("version")
-        panel_obj = store.gene_panel(panel_name, version=panel_version)
-        latest_panel = store.gene_panel(panel_name)
+        panel_obj = store.gene_panel(
+            panel_name,
+            version=panel_version,
+            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
@@ -555,19 +567,17 @@ def check_outdated_gene_panel(panel_obj, latest_panel):
         missing_genes, extra_genes
     """
     # Create a list of minified gene object for the case panel {hgnc_id, gene_symbol}
-    case_panel_genes = [
-        {"hgnc_id": gene["hgnc_id"], "symbol": gene.get("symbol", gene["hgnc_id"])}
-        for gene in panel_obj["genes"]
-    ]
+    case_panel_genes = set([gene.get("symbol", gene["hgnc_id"]) for gene in panel_obj["genes"]])
     # And for the latest panel
-    latest_panel_genes = [
-        {"hgnc_id": gene["hgnc_id"], "symbol": gene.get("symbol", gene["hgnc_id"])}
-        for gene in latest_panel["genes"]
-    ]
+    latest_panel_genes = set(
+        [gene.get("symbol", gene["hgnc_id"]) for gene in latest_panel["genes"]]
+    )
     # Extract the genes unique to case panel
-    extra_genes = [gene["symbol"] for gene in case_panel_genes if gene not in latest_panel_genes]
+    extra_genes = case_panel_genes.difference(latest_panel_genes)
+
     # Extract the genes unique to latest panel
-    missing_genes = [gene["symbol"] for gene in latest_panel_genes if gene not in case_panel_genes]
+    missing_genes = latest_panel_genes.difference(case_panel_genes)
+
     return extra_genes, missing_genes
 
 
@@ -674,7 +684,7 @@ def case_report_content(store: MongoAdapter, institute_obj: dict, case_obj: dict
     return data
 
 
-def mt_coverage_stats(individuals, ref_chrom="14"):
+def mt_coverage_stats(individuals, ref_chrom="14") -> dict:
     """Send a request to chanjo report endpoint to retrieve MT vs autosome coverage stats
 
     Args:
@@ -732,10 +742,9 @@ def mt_excel_files(store, case_obj, temp_excel_dir):
     """
     today = datetime.datetime.now().strftime(DATE_DAY_FORMATTER)
     samples = case_obj.get("individuals")
-    file_header = MT_EXPORT_HEADER
     coverage_stats = None
     # if chanjo connection is established, include MT vs AUTOSOME coverage stats
-    if current_app.config.get("SQLALCHEMY_DATABASE_URI"):
+    if current_app.config.get("chanjo_report"):
         coverage_stats = mt_coverage_stats(samples)
 
     query = {"chrom": "MT"}
@@ -765,9 +774,8 @@ def mt_excel_files(store, case_obj, temp_excel_dir):
             for col, field in enumerate(line):  # each field in line becomes a cell
                 Report_Sheet.write(row, col, field)
 
-        if bool(
-            coverage_stats
-        ):  # it's None if app is not connected to Chanjo or {} if samples are not in Chanjo db
+        # coverage_stats is None if app is not connected to Chanjo or {} if samples are not in Chanjo db
+        if coverage_stats and sample_id in coverage_stats:
             # Write coverage stats header after introducing 2 empty lines
             for col, field in enumerate(MT_COV_STATS_HEADER):
                 Report_Sheet.write(row + 3, col, field)
@@ -805,27 +813,6 @@ def update_synopsis(store, institute_obj, case_obj, user_obj, new_synopsis):
         store.update_synopsis(institute_obj, case_obj, user_obj, link, content=new_synopsis)
 
 
-def _update_case(store, case_obj, user_obj, institute_obj, verb):
-    """Update case with new sample data, and create an associated event"""
-    store.update_case(case_obj, keep_date=True)
-
-    link = url_for(
-        "cases.case",
-        institute_id=institute_obj["_id"],
-        case_name=case_obj["display_name"],
-    )
-
-    store.create_event(
-        institute=institute_obj,
-        case=case_obj,
-        user=user_obj,
-        link=link,
-        category="case",
-        verb=verb,
-        subject=case_obj["display_name"],
-    )
-
-
 def update_individuals(store, institute_obj, case_obj, user_obj, ind, age, tissue):
     """Handle update of individual data (age and/or Tissue type) for a case"""
 
@@ -841,8 +828,13 @@ def update_individuals(store, institute_obj, case_obj, user_obj, ind, age, tissu
 
     case_obj["individuals"] = case_individuals
 
-    verb = "update_individual"
-    _update_case(store, case_obj, user_obj, institute_obj, verb)
+    link = url_for(
+        "cases.case",
+        institute_id=institute_obj["_id"],
+        case_name=case_obj["display_name"],
+    )
+
+    store.update_case_individual(case_obj, user_obj, institute_obj, link)
 
 
 def update_cancer_samples(
@@ -866,8 +858,13 @@ def update_cancer_samples(
 
     case_obj["individuals"] = case_samples
 
-    verb = "update_sample"
-    _update_case(store, case_obj, user_obj, institute_obj, verb)
+    link = url_for(
+        "cases.case",
+        institute_id=institute_obj["_id"],
+        case_name=case_obj["display_name"],
+    )
+
+    store.update_case_sample(case_obj, user_obj, institute_obj, link)
 
 
 def _all_hpo_gene_list_genes(
@@ -1431,13 +1428,13 @@ def _matching_causatives(
     other_causatives_in_default_panels = []
 
     for causative in matching_causatives:
-        hgnc_ids = [gene.get("hgnc_id") for gene in causative.get("genes", [])]
+        hgnc_ids = {gene.get("hgnc_id") for gene in causative.get("genes", [])}
         # Fetch all matching causatives if no causatives_filter defined
         # or only causatives matching the filter:
-        if not other_causatives_filter or (set(hgnc_ids) & set(other_causatives_filter)):
+        if not other_causatives_filter or (hgnc_ids & set(other_causatives_filter)):
             other_causatives.append(causative)
         # Only matching causatives in default gene panels:
-        if set(hgnc_ids) & set(other_causatives_in_default_panels_filter):
+        if hgnc_ids & set(other_causatives_in_default_panels_filter):
             other_causatives_in_default_panels.append(causative)
 
     return other_causatives, other_causatives_in_default_panels

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

@@ -120,30 +120,46 @@
       </div>
 
       <div class="card panel-default" >
-      {% if other_causatives|length > 0%}
         <div class="row mt-0">
-          <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">
-          <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">
-          <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">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
+          <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>
+        {% 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>
-
       <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>

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

@@ -1,5 +1,6 @@
 {% extends "cases/case_tabular_view.html" %}
 {% from "utils.html" import comments_panel, activity_panel %}
+{% from "cases/utils.html" import sex_table_cell_content %}
 
 {% block title %}
   {{ super() }}
@@ -96,18 +97,7 @@
                   {% if loop.index == 1 %}
                     <td> {{ ind.display_name }}</td>
                     <td style="font-weight: bold;">
-                    {% if ind.sex_human in ['female','male'] %}
-                      {% if ind.sex_human == 'female' %}
-                        F
-                      {% elif ind.sex_human == 'male' %}
-                        M
-                      {% else %}
-                        {{ind.sex_human}}
-                      {% endif %}
-                    {% endif %}
-                    {% if ind.confirmed_sex %}
-                      <i class="fa fa-check"></i>
-                    {% endif %}
+                      {{ sex_table_cell_content(ind) }}
                     </td>
                     <td>{{ ind.phenotype_human }}</td>
                   {% else %}
@@ -130,18 +120,7 @@
               <tr class="bg-secondary text-white">
                 <td> {{ ind.display_name }}</td>
                     <td style="font-weight: bold;">
-                    {% if ind.sex_human in ['female','male'] %}
-                      {% if ind.sex_human == 'female' %}
-                        F
-                      {% elif ind.sex_human == 'male' %}
-                        M
-                      {% else %}
-                        {{ind.sex_human}}
-                      {% endif %}
-                    {% endif %}
-                    {% if ind.confirmed_sex %}
-                      <i class="fa fa-check"></i>
-                    {% endif %}
+                      {{ sex_table_cell_content(ind) }}
                     </td>
                     <td>{{ ind.phenotype_human }}</td>
                   <td colspan="4">N/A</td>

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

@@ -124,9 +124,11 @@
                       {% else %}
                         n.a.
                       {% endif %}
-	                    {% if ind.confirmed_sex %}
-	                      <span class="badge rounded-pill py-1 bg-secondary">V</span>
-	                    {% endif %}
+                      {% if ind.confirmed_sex %}
+                        <span class="badge rounded-pill py-1 bg-secondary">V</span>
+                      {% else %}
+                        <span class="fa fa-exclamation-circle text-danger" data-bs-toggle='tooltip' title="Sex is not confirmed."></span>
+                      {% endif %}
 	                  </td>
 	                  <td>
 	                  {% if ind.phenotype==2 %} <!--for later use-->

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

@@ -1,6 +1,6 @@
 {% extends "cases/case_tabular_view.html" %}
 {% from "utils.html" import comments_panel, activity_panel %}
-{% from "cases/utils.html" import individuals_table %}
+{% from "cases/utils.html" import individuals_table, sex_table_cell_content %}
 
 {% block title %}
   {{ super() }}
@@ -100,18 +100,7 @@
                 {% endif %}>
               <td>{{ ind.display_name }}</td>
               <td style="font-weight: bold;">
-                {% if ind.sex_human in ['female','male'] %}
-                    {% if ind.sex_human == 'female' %}
-                      F
-                    {% elif ind.sex_human == 'male' %}
-                      M
-                    {% else %}
-                      {{ind.sex_human}}
-                    {% endif %}
-                  {% endif %}
-                {% if ind.confirmed_sex %}
-                  <i class="fa fa-check"></i>
-                {% endif %}
+                {{ sex_table_cell_content(ind) }}
               </td>
               <td>{{ ind.phenotype_human }}</td>
               <td>{{ ind.is_sma }}</td>

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

@@ -108,7 +108,7 @@
     {% endif %}
 
     <!-- Display mtDNA report for non-cancer cases -->
-    {% if case.track != "cancer" %}
+    {% if case.mtdna_report %}
     <div href="#" class="bg-dark list-group-item text-white">
       <div class="d-flex flex-row flex-fill bd-highlight">
         <div>

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

@@ -1,3 +1,4 @@
+{% from "cases/utils.html" import sex_table_cell_content %}
 
 {% macro cancer_individuals_table(case, institute, tissues, gens_info=None) %}
 <form method="POST" action="{{ url_for('cases.update_cancer_sample', institute_id=institute._id, case_name=case.display_name) }}">
@@ -138,18 +139,7 @@
                   <option {% if not ind.sex_human in ["female", "male"] %} selected= {% endif %} value="unknown">Unknown</option>
                 </select>
                 <div class="sex-display fw-bold">
-                  {% if ind.sex_human in ['female','male'] %}
-                    {% if ind.sex_human == 'female' %}
-                      F
-                    {% elif ind.sex_human == 'male' %}
-                      M
-                    {% else %}
-                      {{ind.sex_human}}
-                    {% endif %}
-                  {% endif %}
-                  {% if ind.confirmed_sex %}
-                    <i class="fa fa-check"></i>
-                  {% endif %}
+                  {{ sex_table_cell_content(ind) }}
                 </div>
               </td>
               <td><input name="age_{{ind.individual_id}}" type="number" step="0.1" min="0"

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

@@ -236,11 +236,13 @@
       <!-- Display and remove added HPO terms -->
       <div class="row mt-3">
         <div class="col-12 ms-3">
-          {% for hpo_term in case.phenotype_terms %}
-            {{ hpo_item(hpo_term, case) }}
-          {% else %}
-            <span class="text-mute">No phenotypes added yet</span>
-          {% endfor %}
+         {% if "phenotype_terms" in case and case.phenotype_terms|length > 0 %}
+           {% for hpo_term in case.phenotype_terms %}
+             {{ hpo_item(hpo_term, case) }}
+           {% endfor %}
+         {% else %}
+           <span class="text-mute">No phenotypes added yet</span>
+         {% endif %}
         </div>
       </div>
 
@@ -251,7 +253,7 @@
             <input class="ms-3" name="min_match" type="number" min="0" step="1" placeholder="Min matches" style="width:130px"/>
             {% if config.PHENOMIZER_USERNAME %}
               <button class="btn btn-secondary btn-sm" type="submit" name="action" value="PHENOMIZER"
-              {%if case.phenotype_terms|length == 0 %} disabled {%endif%}>Phenomizer</button>
+              {% if "phenotype_terms" not in case or case.phenotype_terms|length == 0 %} disabled {% endif %}>Phenomizer</button>
             {% endif %}
           </div>
           <div class="col-1">

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

@@ -633,8 +633,8 @@
 
 {% macro matching_causatives(other_causatives, institute, case, default=False) %}
     <div data-bs-toggle='tooltip' class="panel-heading" title="If there are any variants in this case
-      that have been marked as causative in another case for this insitute. {% if default %}Variants in default panels for the case only.{% endif %}">
-      <strong><a data-bs-toggle="collapse" href="#matchingCausatives{% if default %}Default{% endif %}" class="text-body">Matching causatives {% if default %}in case default panels{% endif %}({{other_causatives|length}})</a></strong>
+      matching a causative in another case for this institute. {% if default %}Variants in default panels for the case only.{% endif %}">
+      <strong><a data-bs-toggle="collapse" href="#matchingCausatives{% if default %}Default{% endif %}" class="text-body" aria-expanded="false"><span class="collapse-icon me-1"></span>Matching causatives {% if default %}in case default panels{% endif %}({{other_causatives|length}})</a></strong>
     </div>
     <ul class="list-group collapse" id="matchingCausatives{% if default %}Default{% endif %}">
       {% for variant in other_causatives %}
@@ -650,7 +650,7 @@
 {% macro matching_managed_variants(managed_variants, institute, case, default=False) %}
     <div data-bs-toggle='tooltip' class="panel-heading" title="Any variants in this case
       that have been marked as managed. {% if default %}Variants in default panels for the case only.{% endif %}">
-      <strong><a data-bs-toggle="collapse" class="text-body" href="#matchingManaged{% if default %}Default{% endif %}">Managed variants {% if default %}in case default panels{% endif %}({{managed_variants|length}})</a></strong>
+      <strong><a data-bs-toggle="collapse" class="text-body" href="#matchingManaged{% if default %}Default{% endif %}" aria-expanded="false"><span class="collapse-icon me-1"></span>Managed variants {% if default %}in case default panels{% endif %}({{managed_variants|length}})</a></strong>
     </div>
     <ul class="list-group">
       {% for variant in managed_variants %}
@@ -681,3 +681,20 @@
     </div>
   </form>
 {% endmacro %}
+
+{% macro sex_table_cell_content(ind) %}
+  {% if ind.sex_human in ['female','male'] %}
+    {% if ind.sex_human == 'female' %}
+      F
+    {% elif ind.sex_human == 'male' %}
+      M
+    {% else %}
+      {{ind.sex_human}}
+    {% endif %}
+  {% endif %}
+  {% if ind.confirmed_sex %}
+    <i class="fa fa-check"></i>
+  {% else %}
+    <span class="fa fa-exclamation-circle text-danger" data-bs-toggle='tooltip' title="Sex is not confirmed."></span>
+  {% endif %}
+{% endmacro %}

scout/server/blueprints/cases/views.py

@@ -4,6 +4,7 @@ import json
 import logging
 import os.path
 import shutil
+from ast import literal_eval
 from io import BytesIO
 from operator import itemgetter
 from typing import Generator, Optional, Union
@@ -86,7 +87,6 @@ def case(
     So do case_id, but we still call institute_and_case again to fetch institute
     and reuse its user access verification.
     """
-
     if case_id:
         case_obj = store.case(case_id=case_id, projection={"display_name": 1, "owner": 1})
 
@@ -102,7 +102,12 @@ def case(
         flash("Case {} does not exist in database!".format(case_name))
         return redirect(request.referrer)
 
-    data = controllers.case(store, institute_obj, case_obj)
+    hide_matching = (
+        literal_eval(request.args.get("hide_matching"))
+        if request.args.get("hide_matching")
+        else True
+    )
+    data = controllers.case(store, institute_obj, case_obj, hide_matching)
 
     return dict(
         **data,
@@ -271,10 +276,7 @@ def pdf_case_report(institute_id, case_name):
         store=store, institute_obj=institute_obj, case_obj=case_obj
     )
     # add coverage report on the bottom of this report
-    if (
-        current_app.config.get("SQLALCHEMY_DATABASE_URI")
-        and case_obj.get("track", "rare") != "cancer"
-    ):
+    if current_app.config.get("chanjo_report") and case_obj.get("track", "rare") != "cancer":
         data["coverage_report"] = controllers.coverage_report_contents(
             request.url_root, institute_obj, case_obj
         )

scout/server/blueprints/variant/controllers.py

@@ -28,7 +28,7 @@ from scout.server.blueprints.variant.utils import (
     update_variant_case_panels,
 )
 from scout.server.blueprints.variants.utils import update_case_panels
-from scout.server.extensions import LoqusDB, cloud_tracks, gens
+from scout.server.extensions import LoqusDB, config_igv_tracks, gens
 from scout.server.links import disease_link, get_variant_links
 from scout.server.utils import (
     case_has_alignments,
@@ -142,9 +142,9 @@ def get_igv_tracks(build: str = "37") -> set:
     # Collect hardcoded tracks, common for all Scout instances
     for track in IGV_TRACKS.get(build, []):
         igv_tracks.add(track.get("name"))
-    # Collect instance-specif cloud public tracks, if available
-    if hasattr(cloud_tracks, "public_tracks"):
-        for track in cloud_tracks.public_tracks.get(build, []):
+    # Collect instance-specific public tracks, if available
+    if hasattr(config_igv_tracks, "tracks"):
+        for track in config_igv_tracks.tracks.get(build, []):
             igv_tracks.add(track.get("name"))
     return igv_tracks
 
@@ -372,7 +372,7 @@ def variant(
         "ACMG_OPTIONS": ACMG_OPTIONS,
         "case_tag_options": CASE_TAGS,
         "inherit_palette": INHERITANCE_PALETTE,
-        "igv_tracks": get_igv_tracks(genome_build),
+        "igv_tracks": get_igv_tracks("38" if variant_obj["is_mitochondrial"] else genome_build),
         "has_rna_tracks": case_has_rna_tracks(case_obj),
         "gens_info": gens.connection_settings(genome_build),
         "evaluations": evaluations,