scout-browser 4.90.1__py3-none-any.whl → 4.91__py3-none-any.whl

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

@@ -66,51 +66,70 @@
 {% endmacro %}
 
 {% macro alignments(institute, case, variant, current_user, config, igv_tracks, has_rna_tracks=False) %}
-   <ul class="list-group">
-        <li class="list-group-item d-flex justify-content-between">
-          {% if variant.chromosome in ["MT","M"] and case.mt_bams or case.bam_files %}
-            <span><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}" target="_blank">IGV viewer</a></span>
-          {% else %}
-            <span class="text-muted">BAM file(s) missing</span>
-          {% endif %}
-          {% if variant.category == "str" %}
-            <div class="ms-1">
-              {{ reviewer_button(case,variant,case_groups,institute._id) }}
-            </div>
-          {% endif %}
-          {% if has_rna_tracks %}
-            <div class="ms-1">
-              {{ splice_junctions_button(institute._id, case, variant._id) }}
-            </div>
-          {% endif %}
-          {% if variant.alamut_link %}
-            <div class="ms-1">
-              <a href="{{ variant.alamut_link }}" class="btn btn-sm btn-secondary" role="button" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with genome g. coordinate">Alamut g.</a>
-            </div>
-          {% endif %}
+  <ul class="list-group">
+    <li class="list-group-item d-flex justify-content-between">
+      {% if variant.is_mitochondrial and not case.mt_bams %}
+        <span data-bs-toggle="tooltip" title="Alignment file(s) missing">
+          <a href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}"
+             target="_blank"
+             class="btn btn-secondary btn-sm text-white disabled" aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV mtDNA
+          </a>
+        </span>
+      {% elif not case.bam_files and not variant.is_mitochondrial %}
+        <span data-bs-toggle="tooltip" title="Alignment file(s) missing">
+          <a href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}"
+            target="_blank"
+            class="btn btn-secondary btn-sm text-white disabled"
+            aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV gDNA
+          </a>
+        </span>
+      {% else %}
+        <span>
+          <a href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}"
+            target="_blank"
+            class="btn btn-secondary btn-sm text-white"><span class="fa fa-magnifying-glass fa-fw me-1"></span>
+            IGV {% if variant.is_mitochondrial %}mt{% else %}g{% endif %}DNA
+          </a>
+        </span>
+      {% endif %}
+      {% if variant.category == "str" %}
+        <div class="ms-1">
+          {{ reviewer_button(case,variant,case_groups,institute._id) }}
+        </div>
+      {% endif %}
+      {% if has_rna_tracks %}
+        <div class="ms-1">
+          {{ splice_junctions_button(institute._id, case, variant._id) }}
+        </div>
+      {% endif %}
+      {% if variant.alamut_link %}
+        <div class="ms-1">
+          <a href="{{ variant.alamut_link }}" class="btn btn-sm btn-secondary" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with genome g. coordinate">Alamut g.</a>
+        </div>
+      {% endif %}
+      {% for gene in variant.genes %}
+        <div class="d-flex flex-wrap ms-1">
+        {% if gene.alamut_link %}
+          <a href="{{ gene.alamut_link }}" class="btn btn-sm btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate">Alamut {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} c.</a>
+        {% endif %}
+        </div>
+      {% endfor %}
+      {% if config.chanjo_report %}
+        <div class="d-flex flex-wrap ms-1">
           {% for gene in variant.genes %}
-            <div class="d-flex flex-wrap ms-1">
-            {% if gene.alamut_link %}
-              <a href="{{ gene.alamut_link }}" class="btn btn-sm btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate">Alamut {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} c.</a>
-            {% endif %}
-            </div>
+            <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 %}
-          {% 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 %}
-        </li>
-        <li class="list-group-item">
-          <div>
-            {{ igv_track_selection(igv_tracks, current_user) }}
-          </div>
-        </li>
-      </ul>
+        </div>
+      {% endif %}
+    </li>
+    <li class="list-group-item">
+      <div>
+        {{ igv_track_selection(igv_tracks, current_user) }}
+      </div>
+    </li>
+  </ul>
 {% endmacro %}
 
 {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
@@ -224,7 +243,7 @@
       <div class="card-body mt-1 ms-3 mb-1" style="padding: 0;">
         Matching tiered:&nbsp;
         {% for tier, tiered_info in matching_tiered.items() %}
-          <a style="padding: 0;" class="btn btn-{{tiered_info.label}} btn-xs" data-bs-toggle="collapse" href="#collapse_{{tier}}" role="button" aria-expanded="false" aria-controls="collapseExample">
+          <a style="padding: 0;" class="btn btn-{{tiered_info.label}} btn-xs" data-bs-toggle="collapse" href="#collapse_{{tier}}" aria-expanded="false" aria-controls="collapseExample">
             {{tier}} ({{tiered_info.links|length}}x)
           </a>
           <div class="collapse" id="collapse_{{tier}}">

scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html

@@ -2,7 +2,7 @@
 {% from "utils.html" import comments_table, pedigree_panel %}
 {% from "variants/components.html" import frequency_cell_general %}
 {% from "variants/utils.html" import cell_rank, dismiss_variants_block, filter_form_footer, update_stash_filter_button_status, pagination_footer, pagination_hidden_div, str_filters %}
-{% from "variant/buttons.html" import igv_button, reviewer_button%}
+{% from "variant/buttons.html" import reviewer_button%}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - STR variants

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

@@ -92,7 +92,7 @@
 <div id="accordion">
   <div class="row">
     <div class="col-4 d-flex align-items-center">
-     <span><a data-bs-toggle="collapse" data-bs-parent="#accordion" href="#track_settings" class="text-secondary">Settings DNA <i class="fas fa-cogs text-secondary"></i></a></span>
+     <span><a data-bs-toggle="collapse" data-bs-parent="#accordion" href="#track_settings" class="text-secondary"><i class="fas fa-cogs text-secondary me-1"></i>Settings IGV DNA</a></span>
     </div>
     <div id="track_settings" class="col-8 collapse">
       <form action="{{url_for('variant.update_tracks_settings')}}" method="POST">
@@ -235,16 +235,24 @@
                   {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
                 </a>
               </td>
-              <td class="d-flex justify-content-around align-items-center">
-                <a target="_blank" href="{{ transcript.ensembl_link }}">
+              <td class="d-flex align-items-center">
+                <a target="_blank" class="float-start" href="{{ transcript.ensembl_link }}">
                   {{ transcript.transcript_id }}
                 </a>
+                {% if transcript.transcript_id in variant.mane_transcripts %}
+                  {% if variant.mane_transcripts[transcript.transcript_id].mane %}
+                    <a href="#" data-bs-toggle="tooltip" title="MANE Select - {{variant.mane_transcripts[transcript.transcript_id].mane}}"><span class="badge bg-success ms-3" title="MANE Select">M</span></a>
+                  {% endif %}
+                  {% if variant.mane_transcripts[transcript.transcript_id].mane_plus %}
+                    <a href="#" data-bs-toggle="tooltip" title="MANE Plus Clinical - {{variant.mane_transcripts[transcript.transcript_id].mane_plus}}"><span class="badge bg-success ms-3" title="MANE Plus Clinical">M+</span></a>
+                  {% endif %}
+                {% endif %}
                 {% if transcript.is_canonical %}
-                  <span class="badge bg-info">C</span>
+                  <span class="badge bg-info ms-3">C</span>
                 {% endif %}
               </td>
               <td>
-                {{ transcript.refseq_identifiers|join(',') }}
+                {{ transcript.refseq_identifiers|join(', ') }}
               </td>
               <td>{{ transcript.biotype or '' }}</td>
               <td data-bs-toggle="tooltip" data-bs-placement="right" title="{{ transcript.functional_annotations|join(', ') }}">
@@ -347,11 +355,31 @@
     {% endif %}
     </div>
     <div class="col-3">
-    {% if variant.is_mitochondrial and case.mt_bams or case.bam_files %}
-      <span><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], variant_id=variant['_id'], chrom=chrom, start=align_start, stop=align_end) }}" target="_blank">IGV viewer</a></span>
-    {% else %}
-      - BAM file(s) missing
-    {% endif %}
+      {% if variant.is_mitochondrial and not case.mt_bams %}
+        <span data-bs-toggle="tooltip" title="Alignment file(s) missing">
+          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], variant_id=variant['_id'], chrom=chrom, start=align_start, stop=align_end)}}"
+             target="_blank"
+              class="btn btn-secondary btn-sm text-white
+              disabled" title="Alignment file(s) missing" data-bs-toggle="tooltip" aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV mtDNA
+          </a>
+        </span>
+      {% elif not case.bam_files and not variant.is_mitochondrial%}
+        <span data-bs-toggle="tooltip" title="Alignment file(s) missing">
+          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], variant_id=variant['_id'], chrom=chrom, start=align_start, stop=align_end)}}"
+            target="_blank"
+            class="btn btn-secondary btn-sm text-white
+            disabled" title="Alignment file(s) missing" data-bs-toggle="tooltip" aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV gDNA
+          </a>
+        </span>
+      {% else %}
+        <span>
+          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], variant_id=variant['_id'], chrom=chrom, start=align_start, stop=align_end)}}"
+            target="_blank"
+            class="btn btn-secondary btn-sm text-white"><span class="fa fa-magnifying-glass fa-fw me-1"></span>
+            IGV {% if variant.is_mitochondrial %}mt{% else %}g{% endif %}DNA
+          </a>
+        </span>
+      {% endif %}
     </div>
     <div class="col-1">
       <!--Define build variable to be used in the UCSC link-->

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

@@ -21,7 +21,7 @@
 
 {% block top_nav %}
   {{ super() }}
-   <li class="nav-item">
+  <li class="nav-item">
     <a class="nav-link" href="{{ url_for('cases.index') }}">Institutes</a>
   </li>
   <li class="nav-item">

scout/server/blueprints/variants/controllers.py

@@ -969,8 +969,6 @@ def get_str_mc(variant_obj: dict) -> Optional[int]:
         alt_mc = int(alt_num.group())
         return alt_mc
 
-    return None
-
 
 def download_str_variants(case_obj, variant_objs):
     """Download filtered STR variants for a case to a CSV file
@@ -1004,11 +1002,11 @@ def download_str_variants(case_obj, variant_objs):
     for variant in variant_objs.limit(EXPORTED_VARIANTS_LIMIT):
         variant_line = []
         variant_line.append(str(variant.get("variant_rank", "")))  # index
-        variant_line.append(variant.get("str_repid"))  # Repeat locus
+        variant_line.append(variant.get("str_repid", variant.get("str_trid", "")))  # Repeat locus
         variant_line.append(
             variant.get("str_display_ru", variant.get("str_ru", ""))
         )  # Reference repeat unit
-        variant_line.append(get_str_mc(variant) or ".")  # Estimated size
+        variant_line.append(str(get_str_mc(variant) or "."))  # Estimated size
         variant_line.append(str(variant.get("str_ref", "")))  # Reference size
         variant_line.append(str(variant.get("str_status", "")))  # Status
         gt_cell = ""
@@ -1078,6 +1076,13 @@ def variant_export_lines_common(store: MongoAdapter, variant: dict, case_obj: di
     position = variant["position"]
     change = variant["reference"] + ">" + variant["alternative"]
     variant_line.append(variant.get("rank_score", "N/A"))
+    cat = (
+        variant.get("sub_category")
+        if variant["category"] in ["sv", "cancer_sv"]
+        else variant.get("category")
+    )
+    variant_line.append(cat.upper() if cat else "")
+    variant_line.append("  ".join([f"{name}:{caller}" for name, caller in callers(variant)]))
     variant_line.append(variant["chromosome"])
     variant_line.append(position)
     variant_line.append(change)

scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/utils.html" import cancer_sv_filters,cell_rank, pagination_footer, pagination_hidden_div, filter_form_footer, filter_script_main, update_stash_filter_button_status, dismiss_variants_block %}
+{% from "variants/utils.html" import cancer_sv_filters,cell_rank, pagination_footer, pagination_hidden_div, filter_form_footer, filter_script_main, update_stash_filter_button_status, dismiss_variants_block, callers_cell %}
 {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
@@ -38,7 +38,7 @@
 {% endblock %}
 
 {% block content_main %}
-<form method="POST" id="filters_form" action="{{url_for('variants.cancer_sv_variants', institute_id=institute._id, case_name=case.display_name)}}" >
+<form method="POST" id="filters_form" action="{{url_for('variants.cancer_sv_variants', institute_id=institute._id, case_name=case.display_name)}}" enctype="multipart/form-data" onsubmit="return validateForm()">
   <div class="container-float">
     {{ pagination_hidden_div(page) }}
     <div class="card panel-default" id="accordion">
@@ -57,8 +57,9 @@
         <thead class="thead table-light">
           <tr>
             <th style="width:2%"></th>
-            <th style="width:9%">Index</th>
+            <th style="width:3%">Index</th>
             <th>Type</th>
+            <th style="width:9%">Callers</th>
             <th style="width:5%">Chr</th>
             <th>Start</th>
             <th>End</th>
@@ -103,8 +104,11 @@
     <td>
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
-    <td><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
-      {{ variant.sub_category|upper }}</span>
+    <td>
+      {{ variant.sub_category|upper }}
+    </td>
+    <td>
+      {{ callers_cell(variant) }}
     </td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
     <td class="col-2"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>

scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -1,7 +1,7 @@
 {% extends "layout.html" %}
 
-{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general %}
-{% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
+{% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
 {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
 
 {% block title %}
@@ -56,14 +56,14 @@
               <th title="Gene">Gene</th>
               <th title="Variant" style="width:12%">HGVS[c/p]</th>
               <th title="Assessments including variant tier" style="width:8%">Assessment</th>
-              <th title="Quality markers" style="width:6%">Qual</th>
               <th title="Rank scores" style="width:4%">Rank</th>
               <th title="CADD scores" style="width:4%">CADD</th>
               <th title="Genomic coordinate" style="width:8%">Chr pos</th>
               <th title="Population frequency">Pop Freq</th>
               <th title="Observed" style="width:7%">Observed</th>
               <th title="Variant type">Type</th>
-              <th title="Functional consequence annotation" style="width:18%">Consequence</th>
+              <th title="Callers" style="width:8%">Callers</th>
+              <th title="Functional consequence annotation" style="width:10%">Consequence</th>
               <th data-bs-toggle="tooltip" data-bs-placement="top" title="Tumor alt. AF. &#013; Alt. allele count | Ref. allele count">Tumor</th>
               <th data-bs-toggle="tooltip" data-bs-placement="top" title="Normal alt. AF. &#013; Alt. allele count | Ref. allele count">Normal</th>
             </tr>
@@ -110,18 +110,14 @@
               {{ causative_badge(variant, case) }}
               {{ other_tiered_variants(variant) }}
             </td>
-            <td>{{ quality_cell(variant) }}</td>
             <td>{{ rank_cell(variant) }}</td>
             <td>{{ cadd_cell(variant) }}</td>
             <td>{{ position_cell(variant) }}</td>
             <td class="text-end">{{ frequency_cell_general(variant) }}</td>
             <td>{{ observed_cell_general(variant) }}</td>
             <td>{{ variant.sub_category }}</td>
-            <td>
-              {% for annotation in variant.functional_annotations %}
-                <div>{{ annotation }}</div>
-              {% endfor %}
-            </td>
+            <td>{{ callers_cell(variant) }}</td>
+            <td>{{ variant_funct_anno_cell(variant) }}</td>
             <td>{{ allele_cell(variant.tumor or {}) }}</td>
             <td>{{ allele_cell(variant.normal or {}) }}</td>
           </tr>
@@ -177,13 +173,6 @@
   {% endif %}
 {% endmacro %}
 
-{% macro quality_cell(variant) %}
-  {% for filter in variant.filters %}
-    <div data-bs-toggle="tooltip" data-bs-placement="top" title="{{ filter.description }}" class="badge bg-{{ filter.label_class }}">{{ filter.label }}</div>
-  {% endfor %}
-{% endmacro %}
-
-
 {% macro position_cell(variant) %}
   {{ variant.chromosome }}<span class="text-muted">:{{ variant.position }}</span>
 {% endmacro %}

scout/server/blueprints/variants/templates/variants/str-variants.html

@@ -108,9 +108,9 @@
               {{ variant.position|human_longint|safe }}</span>
               {{ reviewer_button(case,variant,case_groups,institute._id) }}
               {% if case.bam_files %}
-                <a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}" rel="noopener" target="_blank">IGV viewer</a>
+                <span><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=institute['_id'], case_name=case['display_name'], variant_id=variant['_id'])}}" rel="noopener" target="_blank"><i class="fa fa-magnifying-glass fa-fw me-1"></i>IGV gDNA</a></span>
               {% else %}
-                <button title="BAM file(s) missing" class="btn btn-secondary btn-sm" disabled>IGV viewer</button>
+                <span data-bs-toggle="tooltip" title="BAM file(s) missing"><button class="btn btn-secondary btn-sm" disabled><i class="fa fa-times-circle fa-fw me-1"></i>IGV gDNA</button></span>
               {% endif %}
 
             </td>

scout/server/blueprints/variants/templates/variants/sv-variants.html

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %}
+{% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
 {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
@@ -60,6 +60,7 @@ onsubmit="return validateForm()">
             <th>Rank</th>
             <th>Score</th>
             <th>Type</th>
+            <th>Callers</th>
             <th>Chr</th>
             <th>Start</th>
             <th>End</th>
@@ -102,6 +103,12 @@ onsubmit="return validateForm()">
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
     <td class="text-end">{{ variant.rank_score|int }}</td>
+    <td>
+      {{ variant.sub_category|upper }}
+    </td>
+    <td>
+      {{ callers_cell(variant) }}
+    </td>
     <td><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
       {{ variant.sub_category|upper }}</span></td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>

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

@@ -48,6 +48,20 @@
   </script>
 {% endmacro %}
 
+
+{% macro callers_cell(variant) %}
+   {% for filter in variant.filters %} <!-- collect info from variant's filters (PASS) -->
+      <span class="badge bg-{{ filter.label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="{{ filter.description }}">
+        {{ filter.label }}
+      </span>
+    {% endfor %}
+  {% for name, caller in variant.callers %} <!-- Collect info for specific callers -->
+      <span class="badge {% if caller == 'Pass' %}bg-success{% elif caller == 'Filtered' %}bg-secondary{% else %}bg-black{% endif %}" data-bs-toggle="tooltip" data-bs-html="true" title="{{caller}}">
+        {{ name }}
+      </span>
+  {% endfor %}
+{% endmacro %}
+
 {% macro mark_heteroplasmic_mt(individuals, samples) %}
   {% for ind in individuals if ind.phenotype == 2 %}
     {% for gt in samples|selectattr("sample_id", "equalto", ind.individual_id) %}

scout/server/extensions/__init__.py

@@ -18,6 +18,7 @@ from .ldap_extension import LdapManager
 from .loqus_extension import LoqusDB
 from .matchmaker_extension import MatchMaker
 from .mongo_extension import MongoDB
+from .panelapp_extension import PanelAppClient
 from .phenopacket_extension import PhenopacketAPI
 from .rerunner_extension import RerunnerError, RerunnerService
 
@@ -39,3 +40,4 @@ config_igv_tracks = AlignTrackHandler()
 bionano_access = BioNanoAccessAPI()
 chanjo_report = ChanjoReport()
 chanjo2 = Chanjo2Client()
+panelapp = PanelAppClient()

scout/server/extensions/panelapp_extension.py

@@ -0,0 +1,75 @@
+import logging
+from typing import Optional
+
+import requests
+
+API_PANELS_URL = "https://panelapp.genomicsengland.co.uk/api/v1/panels/"
+
+LOG = logging.getLogger(__name__)
+
+
+class PanelAppClient:
+    """Class that retrieves PanelAll green genes using the NHS-NGS/panelapp library."""
+
+    def __init__(self):
+        self.panels_page = 1
+        self.panel_types = set()
+        self.panel_ids = []
+
+    def get_panel_types(self) -> list:
+        """Returns available panel types, collected from processed panels"""
+        return sorted(list(self.panel_types))
+
+    def get_panels(self, page: int, signed_off: bool = False) -> Optional[dict]:
+        """Return a dictionary {panel_id: Panelapp.Panel} with all panels, signed off or not."""
+
+        panels_url = f"{API_PANELS_URL}?page={page}"
+        if signed_off:
+            panels_url = f"{API_PANELS_URL}signedoff/?page={page}"
+
+        resp = requests.get(panels_url, headers={"Content-Type": "application/json"})
+        if not resp.ok:
+            resp.raise_for_status()
+            return
+
+        return resp.json()
+
+    def set_panel_types(self, json_panels: dict):
+        """Collect available panel types from a page of panels and add them to the self.panel_types variable."""
+
+        for panel in json_panels.get("results", []):
+            for type in panel.get("types", []):
+                self.panel_types.add(type["slug"])
+
+    def get_panel_ids(self, signed_off: bool) -> list[int]:
+        """Returns a list of panel ids contained in a json document with gene panels data."""
+
+        def get_ids(json_panels):
+            LOG.info(f"Retrieving IDs from API page {self.panels_page}")
+            for panel in json_panels.get("results", []):
+                self.panel_ids.append(panel["id"])
+            self.panels_page += 1
+
+        json_panels: dict = self.get_panels(
+            signed_off=signed_off, page=self.panels_page
+        )  # first page of results
+        get_ids(json_panels=json_panels)
+        self.set_panel_types(json_panels=json_panels)
+
+        # Iterate over remaining pages of results
+        while json_panels["next"] is not None:
+            json_panels = self.get_panels(signed_off=signed_off, page=self.panels_page)
+            get_ids(json_panels=json_panels)
+            self.set_panel_types(json_panels=json_panels)
+
+        return self.panel_ids
+
+    def get_panel(self, panel_id: str) -> Optional[dict]:
+        """Retrieve a gene_panel. Apply filters on panel type, if available."""
+        panel_url = f"{API_PANELS_URL}{panel_id}"
+        resp = requests.get(panel_url, headers={"Content-Type": "application/json"})
+        if not resp.ok:
+            resp.raise_for_status()
+            return
+
+        return resp.json()

scout/server/links.py

@@ -355,7 +355,7 @@ def add_tx_links(tx_obj, build=37, hgnc_symbol=None):
     return tx_obj
 
 
-##  Transcript links
+# Transcript links
 def refseq(refseq_id):
     link = "http://www.ncbi.nlm.nih.gov/nuccore/{}"
     if not refseq_id:
@@ -480,6 +480,7 @@ def get_variant_links(institute_obj: dict, variant_obj: dict, build: int = None)
         swegen_link=swegen_link(variant_obj),
         cosmic_links=cosmic_links(variant_obj),
         beacon_link=beacon_link(variant_obj, build),
+        franklin_link=franklin_link(variant_obj, build),
         ucsc_link=ucsc_link(variant_obj, build),
         decipher_link=decipher_link(variant_obj, build),
         ensembl_link=ensembl_link(variant_obj, build),
@@ -633,6 +634,23 @@ def swegen_link(variant_obj):
     return url_template.format(this=variant_obj)
 
 
+def franklin_link(variant_obj: dict, build: int = 37):
+    """Compose link to Franklin Variant Frequency Database."""
+    if variant_obj["category"] in ["cancer", "cancer_sv"]:
+        url_template = (
+            "https://franklin.genoox.com/clinical-db/variant/snpTumor/chr{this[chromosome]}-"
+            "{this[position]}-{this[reference]}-{this[alternative]}"
+        )
+    else:
+        url_template = (
+            "https://franklin.genoox.com/clinical-db/variant/snp/chr{this[chromosome]}-"
+            "{this[position]}-{this[reference]}-{this[alternative]}"
+        )
+    if build == 38:
+        url_template += "-hg38"
+    return url_template.format(this=variant_obj)
+
+
 def cosmic_links(variant_obj):
     """Compose link to COSMIC Database.
 

scout/server/utils.py

@@ -297,51 +297,43 @@ def _check_path_name(ind: Dict, path_name: str) -> bool:
     return False
 
 
-def case_append_alignments(case_obj):
+def case_append_alignments(case_obj: dict):
     """Deconvolute information about files to case_obj.
 
-    This function prepares the bam/cram files in a certain way so that they are easily accessed in
-    the templates.
-
-    Loops over the the individuals and gather bam/cram files, indexes and sample display names in
-    lists
-
-    Args:
-        case_obj(scout.models.Case)
+    This function prepares bam/cram files and their indexes for easy access in templates.
     """
     unwrap_settings = [
         {"path": "bam_file", "append_to": "bam_files", "index": "bai_files"},
         {"path": "mt_bam", "append_to": "mt_bams", "index": "mt_bais"},
-        {"path": "rhocall_bed", "append_to": "rhocall_beds", "index": "no_index"},
-        {"path": "rhocall_wig", "append_to": "rhocall_wigs", "index": "no_index"},
-        {
-            "path": "upd_regions_bed",
-            "append_to": "upd_regions_beds",
-            "index": "no_index",
-        },
-        {"path": "upd_sites_bed", "append_to": "upd_sites_beds", "index": "no_index"},
-        {
-            "path": "tiddit_coverage_wig",
-            "append_to": "tiddit_coverage_wigs",
-            "index": "no_index",
-        },
+        {"path": "rhocall_bed", "append_to": "rhocall_beds", "index": None},
+        {"path": "rhocall_wig", "append_to": "rhocall_wigs", "index": None},
+        {"path": "upd_regions_bed", "append_to": "upd_regions_beds", "index": None},
+        {"path": "upd_sites_bed", "append_to": "upd_sites_beds", "index": None},
+        {"path": "tiddit_coverage_wig", "append_to": "tiddit_coverage_wigs", "index": None},
     ]
 
-    for individual in case_obj["individuals"]:
+    def process_file(case_obj, individual, setting):
+        """Process a single file and its optional index."""
+        file_path = individual.get(setting["path"])
         append_safe(
             case_obj,
-            "sample_names",
-            case_obj.get("display_name", "") + " - " + individual.get("display_name", ""),
+            setting["append_to"],
+            file_path if file_path and os.path.exists(file_path) else "missing",
         )
+        if setting["index"]:
+            index_path = (
+                find_index(file_path) if file_path and os.path.exists(file_path) else "missing"
+            )
+            append_safe(case_obj, setting["index"], index_path)
+
+    for individual in case_obj["individuals"]:
+        # Add sample name
+        sample_name = f"{case_obj.get('display_name', '')} - {individual.get('display_name', '')}"
+        append_safe(case_obj, "sample_names", sample_name)
+
+        # Process all file settings
         for setting in unwrap_settings:
-            file_path = individual.get(setting["path"])
-            if not (file_path and os.path.exists(file_path)):
-                continue
-            append_safe(case_obj, setting["append_to"], file_path)
-            if not setting["index"] == "no_index":
-                append_safe(
-                    case_obj, setting["index"], find_index(file_path)
-                )  # either bai_files or mt_bais
+            process_file(case_obj, individual, setting)
 
 
 def append_safe(obj, obj_index, elem):