scout-browser 4.98.0__py3-none-any.whl → 4.100.0__py3-none-any.whl

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

@@ -1,5 +1,6 @@
 {% import "bootstrap/wtf.html" as wtf %}
 {% from "utils.html" import comments_table %}
+{% from "cases/utils.html" import pretty_link_variant %}
 {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, research_assessments_badge %}
 
 {% macro filter_script_main(cytobands) %}
@@ -192,9 +193,9 @@
         {% endif %}
           <td>
               {% if compound.not_loaded %}
-                {{ compound.display_name }} <small>(not loaded)</small>
+                {{ compound.display_name|truncate(20, True) }} <small>(not loaded)</small>
               {% elif is_popover %}
-                {{ compound.display_name }}
+                {{ compound.display_name|truncate(20, True) }}
               {% else %}
                 <a href='{{ url_for("variant.variant",
                 institute_id=institute._id,
@@ -217,7 +218,7 @@
           <td>
             {% for annotation in compound.functional_annotations %}
               {{ annotation }}<br>
-            {% endfor %}
+            {% endfor %}x
           </td>
         </tr>
       {% endfor %}
@@ -225,30 +226,25 @@
   </table>
 {% endmacro %}
 
-{% macro svs_table(institute, case, overlapping) %}
+{% macro overlapping_tooltip_table(institute, case, overlapping) %}
   <table class='table table-bordered table-hover table-condensed'>
     <thead>
       <tr>
-        <th>Region</th>
+        <th>Pos</th>
         <th>Type</th>
         <th>Length</th>
         <th>Rank score</th>
       </tr>
     </thead>
     <tbody>
-      {% for sv in overlapping %}
+      {% for variant in overlapping %}
         <tr>
           <td>
-              <a href='{{ url_for("variant.sv_variant",
-                                 institute_id=institute._id,
-                                 case_name=case.display_name,
-                                 variant_id=sv._id) }}'>
-                {{ sv.chromosome }}{{ sv.cytoband_start }}
-              </a>
+            {{ pretty_link_variant(variant, case) }}
           </td>
-          <td class='text-end'>{{ sv.sub_category }}</td>
-          <td class='text-end'>{{ sv.length if sv.length < 100000000000 else "-" }}</td>
-          <td class='text-end'>{{ sv.rank_score }}</td>
+          <td class='text-end'>{{ variant.sub_category }}</td>
+          <td class='text-end'>{{ variant.length if variant.length and variant.length < 100000000000 else '-' }}</td>
+          <td class='text-end'>{{ variant.rank_score }}</td>
         </tr>
       {% endfor %}
     </tbody>
@@ -336,7 +332,7 @@
       {{ form.spidex_human(class="selectpicker", data_style="btn-secondary") }}
     </div>
     <div class="col-2">
-      <span>{{ form.clinsig.label(class="control-label") }}</span>
+      <span>{{ form.clinsig.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Germline classification criteria.") }}</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>
@@ -625,7 +621,7 @@
     </div>
   </div>
   <div class="col-2">
-    {{ form.clinsig.label(class="control-label") }}
+    {{ form.clinsig.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Germline classification criteria.") }}
     {{ form.clinsig(class="selectpicker", data_style="btn-secondary") }}
   </div>
   <div class="col-1">
@@ -726,26 +722,17 @@
         {{ form.genetic_models(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
-        <span>{{ form.clinsig.label(class="control-label") }}</span>
+        <span>{{ form.clinsig.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Germline classification criteria.") }}</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">
-        <div class="form-check d-flex justify-content-start">
-          {{ form.mvl_tag(class="form-check-input",type="checkbox") }}
-          {{ form.mvl_tag.label(class="ms-2 form-check-label") }}
-        </div>
-        <div class="form-check d-flex justify-content-start">
-          {{ form.clinvar_tag(class="form-check-input",type="checkbox") }}
-          {{ form.clinvar_tag.label(class="ms-2 form-check-label") }}
-        </div>
-        <div class="form-check d-flex justify-content-start">
-          {{ form.cosmic_tag(class="form-check-input",type="checkbox") }}
-          {{ form.cosmic_tag.label(class="ms-2 form-check-label") }}
-        </div>
+        <span>{{ form.clinsig_onc.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="ClinVar oncogenicity criteria will be applied alongside the other search criteria, not as an alternative. Oncogenicity annotations are still sparse in ClinVar, so relying solely on them could be too restrictive.") }}</span>
+        <span style="float:right;">{{ form.clinsig_onc_exclude.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Exclude variants with oncogenicity among the selected categories.") }} {{form.clinsig_onc_exclude}}</span>
+        {{ form.clinsig_onc(class="selectpicker", data_style="btn-secondary") }}
       </div>
     </div>
-    <div class="row">
+    <div class="row mt-2">
       <div class="col-4">
         {{ form.hgnc_symbols.label(class="control-label") }}
         {{ form.hgnc_symbols(class="form-control") }}
@@ -766,14 +753,28 @@
         {{ form.alt_count.label(class="control-label") }}
         {{ form.alt_count(class="form-control") }}
       </div>
-      <div class="col-2">
+      <div class="col-1">
         {{ form.tumor_frequency.label(class="control-label") }}
         {{ form.tumor_frequency(class="form-control", min="0", max=1) }}
       </div>
-      <div class="col-2">
+      <div class="col-1">
         {{ form.control_frequency.label(class="control-label") }}
         {{ form.control_frequency(class="form-control", min="0", max=1) }}
       </div>
+      <div class="col-2">
+        <div class="form-check d-flex justify-content-start">
+          {{ form.mvl_tag(class="form-check-input",type="checkbox") }}
+          {{ form.mvl_tag.label(class="ms-2 form-check-label") }}
+        </div>
+        <div class="form-check d-flex justify-content-start">
+          {{ form.clinvar_tag(class="form-check-input",type="checkbox") }}
+          {{ form.clinvar_tag.label(class="ms-2 form-check-label") }}
+        </div>
+        <div class="form-check d-flex justify-content-start">
+          {{ form.cosmic_tag(class="form-check-input",type="checkbox") }}
+          {{ form.cosmic_tag.label(class="ms-2 form-check-label") }}
+        </div>
+      </div>
     </div>
     <div class="form" id="chromosome_search">
       <div class="row" style="margin-top:20px;">
@@ -865,7 +866,7 @@
         {{ form.genetic_models(class="selectpicker", data_style="btn-secondary") }}
       </div>
       <div class="col-2">
-        {{ form.clinsig.label(class="control-label") }}
+        {{ form.clinsig.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="left", title="Germline classification criteria.") }}
         {{ form.clinsig(class="selectpicker", data_style="btn-secondary") }}
       </div>
     </div>

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

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
-{% from "variants/utils.html" import compounds_table, svs_table, snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, gene_cell, observed_cell_general  %}
+{% from "variants/utils.html" import snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, gene_cell, observed_cell_general, overlapping_cell  %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ form.variant_type.data|capitalize }} variants
@@ -59,7 +59,7 @@
               <th style="width:5%" title="Rank score">Score</th>
               <th style="width:4%" title="Chromosome">Chr.</th>
               <th style="width:12%" title="HGNC symbols">Gene</th>
-              <th style="width:6%" title="Pop Freq">Pop Freq</th>
+              <th style="width:6%" title="Population Frequency">Pop Freq</th>
               <th style="width:10%" title="Observed database matches">Observed</th>
               <th style="width:5%" title="CADD score">CADD</th>
               <th style="width:18%" title="Functional annotation">Function</th>
@@ -93,7 +93,7 @@
                   {{ functional_annotation_cell(variant) }}
                 </td>
                 <td>{{ cell_models(variant) }}</td>
-                <td>{{ overlapping_cell(variant) }}</td>
+                <td>{{ overlapping_cell(variant, institute, case) }}</td>
               </tr>
             {% else %}
               <tr>
@@ -159,27 +159,6 @@
   {% endif %}
 {% endmacro %}
 
-{% macro overlapping_cell(variant) %}
-
-  {% if variant.compounds %}
-    {% set ns=namespace(show_compounds=false) %}
-    {% for compound in variant.compounds if not compound.is_dismissed %}
-      {% set ns.show_compounds = true %}
-    {% endfor %}
-    {% if ns.show_compounds %}
-      <a href="#" class="badge bg-primary text-white" data-bs-toggle="popover" data-bs-placement="left"
-        data-bs-html="true" data-bs-trigger="hover click"
-        data-bs-content="{{ compounds_table(institute, case, variant.compounds[:20], is_popover=true) }}">Compounds</a>
-    {% endif %}
-  {% endif %}
-
-  {% if variant.overlapping %}
-  <a href="#" class="badge bg-warning" data-bs-toggle="popover" data-bs-placement="left"
-    data-bs-html="true" data-bs-trigger="hover click"
-    data-bs-content="{{ svs_table(institute, case, variant.overlapping[:20]) }}">Overlapping SVs</a>
-  {% endif %}
-{% endmacro %}
-
 {% block scripts %}
   {{ super() }}
   {{ external_scripts() }}

scout/server/config.py

@@ -38,6 +38,14 @@ ACCREDITATION_BADGE = "swedac-1926-iso17025.png"
 #    discovery_url="https://accounts.google.com/.well-known/openid-configuration",
 # )
 
+# Parameters required for login with Keycloak
+# KEYCLOAK = dict(
+#    client_id="<name_of_client>",
+#    client_secret="secret",
+#    discovery_url="http://localhost:8080/realms/<name_of_realm>/.well-known/openid-configuration",
+#    logout_url="http://localhost:8080/realms/<name_of_realm>/protocol/openid-connect/logout",
+# )
+
 # Chanjo database connection string - used by chanjo report to create coverage reports
 # SQLALCHEMY_DATABASE_URI = "mysql+pymysql://test_user:test_passwordw@127.0.0.1:3306/chanjo"
 

scout/server/extensions/bionano_extension.py

@@ -7,7 +7,6 @@ For further development, the server has a Swagger-like demo interface at https:/
 which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
 """
 
-import json
 import logging
 from typing import Dict, Iterable, List, Optional, Tuple
 

scout/server/extensions/chanjo2_extension.py

@@ -1,11 +1,13 @@
 import logging
-from typing import Dict, List
+from typing import Dict
 
 import requests
-from flask import current_app
+from flask import Flask, current_app
+
+from scout.server.utils import get_case_mito_chromosome
+from scout.utils.scout_requests import get_request_json, post_request_json
 
 REF_CHROM = "14"
-MT_CHROM = "MT"
 LOG = logging.getLogger(__name__)
 
 CHANJO_BUILD_37 = "GRCh37"
@@ -15,14 +17,33 @@ CHANJO_BUILD_38 = "GRCh38"
 class Chanjo2Client:
     """Runs requests to chanjo2 and returns results in the expected format."""
 
-    def mt_coverage_stats(self, individuals: dict) -> Dict[str, dict]:
+    def init_app(self, app: Flask):
+        """The chanjo2 client has nothing to init, just check chanjo2 heartbeat."""
+        self.get_status(app)
+
+    def get_status(self, app: Flask) -> dict:
+        """Check Chanjo2 heartbeat, LOG status and return status."""
+        chanjo2_heartbeat_url: str = app.config.get("CHANJO2_URL")
+        json_resp = get_request_json(chanjo2_heartbeat_url)
+
+        if not json_resp:
+            LOG.warning(
+                f"Chanjo2 is configured at {chanjo2_heartbeat_url} but does not return heartbeat."
+            )
+            return json_resp
+
+        LOG.info(f"{json_resp.get('content',{}).get('message')}")
+        return json_resp
+
+    def mt_coverage_stats(self, case_obj: dict) -> Dict[str, dict]:
         """Sends a POST requests to the chanjo2 coverage/d4/interval to collect stats for the MT case report."""
 
         chanjo2_chrom_cov_url: str = "/".join(
             [current_app.config.get("CHANJO2_URL"), "coverage/d4/interval/"]
         )
         coverage_stats = {}
-        for ind in individuals:
+        case_mt_chrom = get_case_mito_chromosome(case_obj)
+        for ind in case_obj.get("individuals", []):
 
             if not ind.get("d4_file"):
                 continue
@@ -30,14 +51,21 @@ class Chanjo2Client:
 
             # Get mean coverage over chr14
             chrom_cov_query["chromosome"] = REF_CHROM
-            resp = requests.post(chanjo2_chrom_cov_url, json=chrom_cov_query)
-            autosome_cov = resp.json().get("mean_coverage")
 
-            # Get mean coverage over chrMT
-            chrom_cov_query["chromosome"] = MT_CHROM
-            resp = requests.post(chanjo2_chrom_cov_url, json=chrom_cov_query)
+            autosome_cov_json = post_request_json(chanjo2_chrom_cov_url, chrom_cov_query)
+            if autosome_cov_json.get("status_code") != 200:
+                raise ValueError(
+                    f"Chanjo2 get autosome coverage failed: {autosome_cov_json.get('message')}"
+                )
+
+            autosome_cov = autosome_cov_json.get("content", {}).get("mean_coverage")
 
-            mt_cov = resp.json().get("mean_coverage")
+            # Get mean coverage over chrMT
+            chrom_cov_query["chromosome"] = case_mt_chrom
+            mt_cov_json = post_request_json(chanjo2_chrom_cov_url, chrom_cov_query)
+            if mt_cov_json.get("status_code") != 200:
+                raise ValueError(f"Chanjo2 get MT coverage failed: {mt_cov_json.get('message')}")
+            mt_cov = mt_cov_json.get("content", {}).get("mean_coverage")
 
             coverage_info = dict(
                 mt_coverage=mt_cov,
@@ -66,6 +94,8 @@ class Chanjo2Client:
             "interval_type": "genes",
             "samples": [],
         }
+        analysis_types = []
+
         for ind in individuals:
             if not ind.get("d4_file"):
                 continue
@@ -73,10 +103,21 @@ class Chanjo2Client:
             gene_cov_query["samples"].append(
                 {"coverage_file_path": ind["d4_file"], "name": ind["individual_id"]}
             )
+            analysis_types.append(ind.get("analysis_type"))
 
-        resp = requests.post(chanjo2_gene_cov_url, json=gene_cov_query)
-        gene_cov = resp.json()
+        if "wes" in analysis_types:
+            gene_cov_query["interval_type"] = "exons"
+        elif "wts" in analysis_types:
+            gene_cov_query["interval_type"] = "transcripts"
+
+        gene_cov_json = post_request_json(chanjo2_gene_cov_url, gene_cov_query)
+
+        if gene_cov_json.get("status_code") != 200:
+            raise ValueError(
+                f"Chanjo2 get complete coverage failed: {gene_cov_json.get('message')}"
+            )
 
+        gene_cov = gene_cov_json.get("content")
         full_coverage = bool(gene_cov)
         for sample in gene_cov.keys():
             if gene_cov[sample]["coverage_completeness_percent"] < 100:

scout/server/links.py

@@ -54,6 +54,7 @@ def add_gene_links(
     gene_obj["string_link"] = string(ensembl_id)
     gene_obj["reactome_link"] = reactome(ensembl_id)
     gene_obj["clingen_link"] = clingen(hgnc_id)
+    gene_obj["cspec_link"] = clingen_cspec(hgnc_id)
     gene_obj["gencc_link"] = gencc(hgnc_id)
     gene_obj["expression_atlas_link"] = expression_atlas(ensembl_id)
     gene_obj["exac_link"] = exac(ensembl_id)
@@ -80,6 +81,7 @@ def add_gene_links(
     gene_obj["gnomad_str_link"] = gnomad_str_gene(hgnc_symbol)
     gene_obj["panelapp_link"] = panelapp_gene(hgnc_symbol)
     gene_obj["decipher_link"] = decipher_gene(hgnc_symbol)
+    gene_obj["cancer_hotspots_link"] = cancer_hotspots_gene(hgnc_symbol)
     if institute:
         gene_obj["alamut_link"] = alamut_gene_link(institute, gene_obj, build)
 
@@ -90,6 +92,12 @@ def decipher_gene(hgnc_symbol: str) -> Optional[str]:
         return f"https://www.deciphergenomics.org/gene/{hgnc_symbol}/overview/clinical-info"
 
 
+def cancer_hotspots_gene(hgnc_symbol: str) -> Optional[str]:
+    """Create link to Decipher gene."""
+    if hgnc_symbol:
+        return f"https://www.cancerhotspots.org/#/home?search={hgnc_symbol}"
+
+
 def panelapp_gene(hgnc_symbol):
     link = "https://panelapp.genomicsengland.co.uk/panels/entities/{}"
 
@@ -250,6 +258,13 @@ def clingen(hgnc_id):
     return link.format(hgnc_id)
 
 
+def clingen_cspec(hgnc_id):
+    link = "https://cspec.genome.network/cspec/ui/svi/?search=HGNC:{}"
+    if not hgnc_id:
+        return None
+    return link.format(hgnc_id)
+
+
 def gencc(hgnc_id):
     link = "https://search.thegencc.org/genes/HGNC:{}"
     if not hgnc_id:

scout/server/static/bs_styles.css

@@ -371,6 +371,23 @@ body {
 }
 /* end of sidebar-related stuff */
 
+/* A collapse icon for button use */
+.btn[aria-expanded="false"] .collapse-button-icon::before {
+  content: " \f0da";
+  font-family: "Font Awesome 5 Free", ui-monospace;
+  font-weight: 900;
+  display: inline;
+  text-align: left;
+}
+
+.btn[aria-expanded="true"] .collapse-button-icon::before {
+  content: " \f0d7";
+  font-family: "Font Awesome 5 Free", ui-monospace;
+  font-weight: 900;
+  display: inline;
+  text-align: left;
+
+
 option {
   width: 100%;
 }
@@ -386,9 +403,20 @@ option {
 }
 
 .str-variants-reviewer-container {
-   padding: 20px 5px;
- }
- .str-variants-reviewer-container svg {
-   width: 100%;
-   height: auto;
- }
+	padding: 20px 5px;
+}
+
+.str-variants-reviewer-container svg {
+	width: 100%;
+	height: auto;
+}
+
+.blink_me {
+	animation: blinker 2s linear infinite;
+}
+
+@keyframes blinker {
+	 50% {
+    opacity: 0;
+  }
+}

scout/server/templates/utils.html

@@ -234,16 +234,15 @@
 {% endmacro %}
 
 {% macro db_table_external_stylesheets() %}
-  <link rel="stylesheet" href="https://cdn.datatables.net/1.12.0/css/dataTables.bootstrap5.min.css" integrity="sha512-r9doM4NDlA2Cr0R56ielwMfkzL8miUuqbwNV4G1detiqlX58aTINapm2g2CoASFYedwgn3ulX6xmcDmRS0bmzw==" crossorigin="anonymous">
-  <link rel="stylesheet" href="https://cdn.datatables.net/buttons/2.2.3/css/buttons.dataTables.min.css" integrity="sha512-tnmsL7vm/5wo8jsDSW4033D6dW3xn8qyIDZTIssv/3YKyLU3pMg5IZB0k88RGmZPlyyUoK7EEghuaoXZIinDXA==" crossorigin="anonymous">
-  <link rel="stylesheet" href="https://cdn.datatables.net/buttons/2.2.3/css/buttons.bootstrap5.min.css" integrity="sha512-VX0h3jcn1Oc0lFy0aRxuq6U/tTk/6Ryurar5O3Az2DHLA1mpURv2Zgzl5MJJ5weChE7rdlsiB/ka5rUstkTN8g==" crossorigin="anonymous">
-  {% endmacro %}
+  <link rel="stylesheet" href="https://cdn.datatables.net/2.2.2/css/dataTables.bootstrap5.min.css" integrity="sha512-pVSTZJo4Kj/eLMUG1w+itkGx+scwF00G5dMb02FjgU9WwF7F/cpZvu1Bf1ojA3iAf8y94cltGnuPV9vwv3CgZw==" referrerpolicy="no-referrer" crossorigin="anonymous">
+  <link rel="stylesheet" href="https://cdn.datatables.net/buttons/3.2.2/css/buttons.bootstrap5.min.css" integrity="sha512-9Mi4C/wtfinscXIdOGZvqv0ZYvhBUOQCrwqmTZyiYuEgJQHWnXenkYQOC44I3kyh7uaOmz9eNxeMkC8xGBLOWg==" referrerpolicy="no-referrer" crossorigin="anonymous">
+{% endmacro %}
 
 {% macro db_table_external_scripts() %}
-  <script src="https://cdn.datatables.net/1.12.0/js/jquery.dataTables.min.js" integrity="sha512-fu0WiDG5xqtX2iWk7cp17Q9so54SC+5lk/z/glzwlKFdEOwGG6piUseP2Sik9hlvlmyOJ0lKXRSuv1ltdVk9Jg==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
-  <script src="https://cdn.datatables.net/1.12.0/js/dataTables.bootstrap5.min.js" integrity="sha512-nfoMMJ2SPcUdaoGdaRVA1XZpBVyDGhKQ/DCedW2k93MTRphPVXgaDoYV1M/AJQLCiw/cl2Nbf9pbISGqIEQRmQ==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
-  <script src="https://cdn.datatables.net/buttons/2.2.3/js/dataTables.buttons.min.js" integrity="sha512-QT3oEXamRhx0x+SRDcgisygyWze0UicgNLFM9Dj5QfJuu2TVyw7xRQfmB0g7Z5/TgCdYKNW15QumLBGWoPefYg==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
-  <script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.2.0/jszip.min.js" integrity="sha512-0zVs73boVJk7Mlo/06K7cX+GWqW4xv0waiKkfXPGEhQ3Ww3UznkFlywBKIx4XetI/StJwac4bUNoeBGJY3Yugw==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
-  <script src="https://cdn.datatables.net/buttons/2.2.3/js/buttons.html5.js" integrity="sha512-BSdPiqLbAJOVF1Q+rleIJJIio/8Ihf1zXxfYMinSHMpKdRWX634Mi4Rt8LRYfn0k5nbSlFO7Y7klzNCG8tokFQ==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
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+  <script src="https://cdn.datatables.net/2.2.2/js/dataTables.min.js" integrity="sha512-iwuEh+XTZQNzwdjYrqsxyWJXyReKVclGX4D2uGYBGNIR6o0VBwIfeYQv+lQjxmye87K6C6mc7qrqJlCcaeZJhA==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
+  <script src="https://cdn.datatables.net/2.2.2/js/dataTables.bootstrap5.min.js" integrity="sha512-Cwi0jz7fz7mrX990DlJ1+rmiH/D9/rjfOoEex8C9qrPRDDqwMPdWV7pJFKzhM10gAAPlufZcWhfMuPN699Ej0w==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
+  <script src="https://cdn.datatables.net/buttons/3.2.2/js/dataTables.buttons.min.js" integrity="sha512-T/4qQRgBJ8Ev6Lk8M943pMIbCpgqtVf5XI77hxe3nQn0f9a0gn/WKXWMbuGv6cpjp9NM8Mc+3/3GnpW+3+TckA==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
+  <script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.10.1/jszip.min.js" integrity="sha512-XMVd28F1oH/O71fzwBnV7HucLxVwtxf26XV8P4wPk26EDxuGZ91N8bsOttmnomcCD3CS5ZMRL50H0GgOHvegtg==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
+  <script src="https://cdn.datatables.net/buttons/3.2.2/js/buttons.html5.min.js" integrity="sha512-I86DAquH004N60kPVNHp+9QkC5y61C5ODHj6ewhddXnewOJ31wyOJHNlNEr8NUR3xqtGozfMb557So1pR0uDCA==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
+  <script src="https://cdn.datatables.net/buttons/3.2.2/js/buttons.bootstrap5.min.js" integrity="sha512-rVAaUqNTbX7lADp767RxnIMvbROobK+gn7SpbbPc+qMUPotgAkSsRhCKF5ziUEquBsdGcv3eOaZK1fIbGwh5CA==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
 {% endmacro %}

scout/server/utils.py

@@ -206,6 +206,19 @@ def user_institutes(store, login_user):
     return institutes
 
 
+def get_case_genome_build(case_obj: dict) -> str:
+    """returns the genome build of a case, as a string."""
+    return "38" if "38" in case_obj.get("genome_build", "37") else "37"
+
+
+def get_case_mito_chromosome(case_obj: dict) -> str:
+    """Returns MT or M, according to the genome build of a case."""
+    case_build = get_case_genome_build(case_obj)
+    if case_build == "38":
+        return "M"
+    return "MT"
+
+
 def case_has_mtdna_report(case_obj: dict):
     """Display mtDNA report on the case sidebar only for some specific cases."""
     if case_obj.get("track", "rare") == "cancer":
@@ -244,15 +257,23 @@ def case_has_chanjo2_coverage(case_obj: dict):
 def case_has_alignments(case_obj: dict):
     """Add info on bam/cram files availability to a case dictionary
 
+    This sets the availability of alignments for autosomal chromosomes.
+    If paraphase or de novo assembly alignments, this is also sufficient to set
+    alignment availability.
     Args:
         case_obj(scout.models.Case)
     """
-    case_obj["bam_files"] = False  # Availability of alignments for autosomal chromosomes
+    case_obj["bam_files"] = False
     for ind in case_obj.get("individuals"):
-        bam_path = ind.get("bam_file")
-        if bam_path and os.path.exists(bam_path):
-            case_obj["bam_files"] = True
-            return
+        for alignment_path_key in [
+            "bam_file",
+            "assembly_alignment_path",
+            "paraphase_alignment_path",
+        ]:
+            bam_path = ind.get(alignment_path_key)
+            if bam_path and os.path.exists(bam_path):
+                case_obj["bam_files"] = True
+                return
 
 
 def case_has_mt_alignments(case_obj: dict):
@@ -301,14 +322,28 @@ def case_append_alignments(case_obj: dict):
     """Deconvolute information about files to case_obj.
 
     This function prepares bam/cram files and their indexes for easy access in templates.
+
+    index is set only if it is expected as a separate key on the indiviudal: an
+    attempt at discovery is still made for files with index: None.
     """
     unwrap_settings = [
         {"path": "bam_file", "append_to": "bam_files", "index": "bai_files"},
+        {"path": "assembly_alignment_path", "append_to": "assembly_alignments", "index": None},
         {"path": "mt_bam", "append_to": "mt_bams", "index": "mt_bais"},
+        {
+            "path": "paraphase_alignment_path",
+            "append_to": "paraphase_alignments",
+            "index": None,
+        },
         {"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": "minor_allele_frequency_wig",
+            "append_to": "minor_allele_frequency_wigs",
+            "index": None,
+        },
         {"path": "tiddit_coverage_wig", "append_to": "tiddit_coverage_wigs", "index": None},
     ]
 

scout/utils/acmg.py

@@ -173,7 +173,7 @@ def get_acmg_criteria(acmg_terms: set) -> tuple:
         finally, check remaining prefixes if no suffix match or stand-alone criteria match
 
     Return a tuple with
-        pvs: This variable indicates if Pathogenicity Very Strong exists
+        pvs_terms: This variable indicates if Pathogenicity Very Strong exists
         ps_terms: Collection of terms with Pathogenicity Strong
         pm_terms: Collection of terms with Pathogenicity moderate
         pp_terms: Collection of terms with Pathogenicity supporting
@@ -182,25 +182,29 @@ def get_acmg_criteria(acmg_terms: set) -> tuple:
         bp_terms: Collection of terms with supporting Benign evidence
     """
 
-    pvs = False
+    pvs_terms = []
     ps_terms = []
     pm_terms = []
     pp_terms = []
 
-    ba = False
+    ba_terms = []
     bs_terms = []
     bp_terms = []
 
     suffix_map = {
+        "_Stand-alone": {"B": ba_terms},
+        "_Very Strong": {"P": pvs_terms},
         "_Strong": {"P": ps_terms, "B": bs_terms},
         "_Moderate": {"P": pm_terms},
         "_Supporting": {"P": pp_terms, "B": bp_terms},
     }
 
     prefix_map = {
+        "PVS": pvs_terms,
         "PS": ps_terms,
         "PM": pm_terms,
         "PP": pp_terms,
+        "BA": ba_terms,
         "BS": bs_terms,
         "BP": bp_terms,
     }
@@ -216,17 +220,12 @@ def get_acmg_criteria(acmg_terms: set) -> tuple:
                     continue
                 break
         else:
-            if term.startswith("PVS"):
-                pvs = True
-            elif term.startswith("BA"):
-                ba = True
-            else:
-                for prefix, term_list in prefix_map.items():
-                    if term.startswith(prefix):
-                        term_list.append(term)
-                        break
+            for prefix, term_list in prefix_map.items():
+                if term.startswith(prefix):
+                    term_list.append(term)
+                    break
 
-    return (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms)
+    return (pvs_terms, ps_terms, pm_terms, pp_terms, ba_terms, bs_terms, bp_terms)
 
 
 def get_acmg(acmg_terms: set) -> Optional[str]:
@@ -316,19 +315,19 @@ def get_acmg_temperature(acmg_terms: set) -> Optional[dict]:
     if not acmg_terms:
         return {}
 
-    (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms) = get_acmg_criteria(acmg_terms)
-
-    if ba:
-        points = -8
-    else:
-        points = (
-            8 * pvs
-            + 4 * len(ps_terms)
-            + 2 * len(pm_terms)
-            + len(pp_terms)
-            - 4 * len(bs_terms)
-            - len(bp_terms)
-        )
+    (pvs_terms, ps_terms, pm_terms, pp_terms, ba_terms, bs_terms, bp_terms) = get_acmg_criteria(
+        acmg_terms
+    )
+
+    points = (
+        8 * len(pvs_terms)
+        + 4 * len(ps_terms)
+        + 2 * len(pm_terms)
+        + len(pp_terms)
+        - 8 * len(ba_terms)
+        - 4 * len(bs_terms)
+        - len(bp_terms)
+    )
 
     if points <= -7:
         point_classification = "benign"