Fix #4862 - ORPHA inheritance patterns hidden

CHANGELOG.md

@@ -12,11 +12,12 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - `Mean MT coverage`, `Mean chrom 14 coverage` and `Estimated mtDNA copy number` on MT coverage file from chanjo2 if available
 ### Changed
 - Documentation for OMICS variants and updating a case
-- Include both creation and last modification dates in gene panels pages
+- Include both creation and deletion dates in gene panels pages
 - Moved code to collect MT copy number stats for the MT report to the chanjo extension
 - On the gene panelS page, show expanded gene panel version list in one column only
 - IGV.js WTS loci default to zoom to a region around a variant instead of whole gene
 - Refactored logging module
+- Case general report no longer shows ORPHA inheritance models. OMIM models are shown colored.
 ### Fixed
 - Broken heading anchors in the documentation (`admin-guide/login-system.md` and `admin-guide/setup-scout.md` files)
 - Avoid open login redirect attacks by always redirecting to cases page upon user login

scout/server/blueprints/cases/controllers.py

@@ -20,6 +20,7 @@
     CASE_TAGS,
     CUSTOM_CASE_REPORTS,
     DATE_DAY_FORMATTER,
+    INHERITANCE_PALETTE,
     MITODEL_HEADER,
     MT_COV_STATS_HEADER,
     MT_EXPORT_HEADER,
@@ -700,6 +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")

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 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
                 <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/variant/templates/variant/gene_disease_relations.html

@@ -50,7 +50,7 @@
               {% if gene.common and gene.disease_terms %}
                 {% for disease_term in gene.disease_terms %}
                   {% if disease_term.source == 'ORPHA' %}
-                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily the inheritance mode known for this gene.">
+                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily modes of inheritance known for this gene. ORPHA inheritance modes will not be shown on the general case report.">
                       <td>
                           <a href="http://omim.org/entry/{{ gene.common.omim_id }}" rel="noopener" target="_blank">
                             {{ gene.common.hgnc_symbol }}

scout/server/templates/report_base.html

@@ -6,6 +6,7 @@
 	{% block css %}
   <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
   <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+  <link rel="stylesheet" href="{{ url_for('static', filename='bs_styles.css') }}">
     <style>
 		tr.light-grey td{
 			background-color: LightGray;