scout-browser 4.79.1__py3-none-any.whl → 4.81__py3-none-any.whl

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

@@ -145,7 +145,7 @@
   <div class="card panel-default">
     <div class="panel-heading d-flex justify-content-between">
       <a href="https://github.com/moonso/loqusdb" target="_blank">Local observations</a>
-      <span data-bs-toggle="tooltip" title="Nr of observations is the total number of occurrences in the loqusdb instance. Missing links on greyed out case names for shared local case variants might be caused by variants not loaded after a rerun or inexact SV matching. Only names of collaborator cases are shown.">?</span>
+      <span data-bs-toggle="tooltip" title="Nr of observations is the total number of cases where the variant occurs in the loqusdb instance. Names of collaborator cases are shown.">?</span>
     </div>
     <div class="card-body">
       <table class="table">
@@ -165,27 +165,39 @@
                <td>{{ obs.homozygote|default('N/A') }}</td>
                <td>{{ obs.total|default('N/A') }}</td>
              </tr>
-           {% if obs.cases %}
-             <tr>
-               <td colspan="4">
-                     {% for data in obs.cases %}
-                       {% if data.variant and data.variant.category == "snv"%}
-                         <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
-                       {% elif data.variant and data.variant.category == "sv"%}
-                         <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
-                       {% else %}
+            {% if obs.cases or obs.observations == 1 %}
+              <tr>
+                <td colspan="4">
+                  {% if obs.observations == 1 %}
+                  {% if obs.case_match == True %}
+                     Observed only in this case
+                     <span id="case_match_tooltip"  data-bs-toggle='tooltip' title="Subsequent analysis of the same individual or multiple occurrences within the same family will usually not result in an increased observation count, even if performed by different institutes.">
+                       <i class="mx-1 fas fa-info-circle"></i>
+                     </span>
+                  {% elif obs.case_match == False %}
+                     Observed in one other case
+                     <span id="case_mismatch_tooltip"  data-bs-toggle='tooltip' title="Low sequencing quality for the variant or previous loqusdb upload of data from the same individuals may prevent the current case from occurring in loqusdb">
+                       <i class="mx-1 fas fa-info-circle"></i>
+                     </span>
+                  {% endif %}
+                  {% endif %}
+                  {% for data in obs.cases %}
+                     {% if data.variant and data.variant.category == "snv"%}
+                       <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
+                     {% elif data.variant and data.variant.category == "sv"%}
+                       <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
+                     {% else %}
+                       <span data-bs-toggle="tooltip" title="Missing link, this might be caused by variants not loaded after a rerun or inexact SV matching.">
                          <span class="ml-3 badge rounded-pill bg-light text-dark">{{ data.case.display_name }}</span>
-                       {% endif %}
-                     {% endfor %}
-                     {% if obs.cases|length > 10 %}
-                       + more
+                       </span>
                      {% endif %}
-                     {% if obs.observations == 1 %}
-                       Observed only in this case
-                     {% endif %}
-               </td>
-             </tr>
-           {% endif %}
+                  {% endfor %}
+                  {% if obs.cases|length > 10 %}
+                     + more
+                  {% endif %}
+                </td>
+              </tr>
+            {% endif %}
           {% endfor %}
         </tbody>
       </table>

scout/server/blueprints/variants/controllers.py

@@ -1,7 +1,7 @@
 import decimal
 import logging
 import re
-from typing import Any, Dict
+from typing import Any, Dict, List, Optional
 
 import bson
 from flask import Response, flash, session, url_for
@@ -16,20 +16,22 @@ from scout.adapter import MongoAdapter
 from scout.constants import (
     ACMG_COMPLETE_MAP,
     ACMG_MAP,
+    CANCER_EXPORT_HEADER,
     CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
     CANCER_TIER_OPTIONS,
     CHROMOSOMES,
     CHROMOSOMES_38,
     CLINSIG_MAP,
     DISMISS_VARIANT_OPTIONS,
+    EXPORT_HEADER,
     EXPORTED_VARIANTS_LIMIT,
+    FUSION_EXPORT_HEADER,
     MANUAL_RANK_OPTIONS,
     MOSAICISM_OPTIONS,
     SPIDEX_HUMAN,
     VARIANT_FILTERS,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
-from scout.constants.variants_export import CANCER_EXPORT_HEADER, EXPORT_HEADER
 from scout.server.blueprints.variant.utils import (
     callers,
     clinsig_human,
@@ -331,17 +333,17 @@ def fusion_variants(
         if clinical_var_obj is not None:
             variant_obj["clinical_assessments"] = get_manual_assessments(clinical_var_obj)
 
-        variants.append(
-            parse_variant(
-                store,
-                institute_obj,
-                case_obj,
-                variant_obj,
-                genome_build=genome_build,
-                case_dismissed_vars=case_dismissed_vars,
-            )
+        parsed_variant = parse_variant(
+            store,
+            institute_obj,
+            case_obj,
+            variant_obj,
+            genome_build=genome_build,
+            case_dismissed_vars=case_dismissed_vars,
         )
 
+        variants.append(parsed_variant)
+
     return {"variants": variants, "more_variants": more_variants}
 
 
@@ -958,7 +960,7 @@ def parse_variant(
 
 
 def download_str_variants(case_obj, variant_objs):
-    """Download filtered STR variants for a case to an excel file
+    """Download filtered STR variants for a case to a CSV file
 
     Args:
         case_obj(dict)
@@ -1024,21 +1026,17 @@ def download_str_variants(case_obj, variant_objs):
     )
 
 
-def download_variants(store, case_obj, variant_objs):
-    """Download filtered variants for a case to an excel file
-
-    Args:
-        store(adapter.MongoAdapter)
-        case_obj(dict)
-        variant_objs(PyMongo cursor)
+def download_variants(
+    store: MongoAdapter, case_obj: dict, variant_objs: CursorType, category: Optional[str] = None
+) -> Response:
+    """Download filtered variants for a case to a CSV file
 
     Returns:
         an HTTP response containing a csv file
     """
-    document_header = variants_export_header(case_obj)
-    export_lines = []
+    document_header = variants_export_header(case_obj, category)
     export_lines = variant_export_lines(
-        store, case_obj, variant_objs.limit(EXPORTED_VARIANTS_LIMIT)
+        store, case_obj, variant_objs.limit(EXPORTED_VARIANTS_LIMIT), category
     )
 
     def generate(header, lines):
@@ -1060,85 +1058,168 @@ def download_variants(store, case_obj, variant_objs):
     )
 
 
-def variant_export_lines(store, case_obj, variants_query):
+def variant_export_lines_common(store: MongoAdapter, variant: dict, case_obj: dict) -> list:
+    """
+    Get common variant info to be exported. Returns a list to be merged into a string
+    in suitable export format.
+    """
+    variant_line = []
+    position = variant["position"]
+    change = variant["reference"] + ">" + variant["alternative"]
+    variant_line.append(variant.get("rank_score", "N/A"))
+    variant_line.append(variant["chromosome"])
+    variant_line.append(position)
+    variant_line.append(change)
+    variant_line.append("_".join([str(position), change]))
+
+    gene_list: List[dict] = variant.get("genes", [])
+
+    if gene_list:
+        gene_info = variant_export_genes_info(store, gene_list, case_obj.get("genome_build"))
+        variant_line += gene_info
+    else:
+        empty_col = 0
+        while empty_col < 5:
+            variant_line.append(
+                "-"
+            )  # empty HGNC id, empty gene name, two empty transcripts columns, and consequence
+            empty_col += 1
+
+    if variant.get("cadd_score"):
+        variant_line.append(round(variant["cadd_score"], 2))
+    else:
+        variant_line.append("N/A")
+
+    if variant.get("gnomad_frequency"):
+        variant_line.append(round(variant["gnomad_frequency"], 5))
+    else:
+        variant_line.append("N/A")
+
+    return variant_line
+
+
+def get_fusion_variant_field(variant: dict, field: str) -> str:
+    """Get fusion variant fields that could be from multiple fusion partners.
+    Split if comma separated, and join with 'or' sign, so as not to interfere with csv file generation.
+    Avoid empty values and use "N/A" instead.
+    """
+    value = variant.get(field, "N/A")
+    if "," in value:
+        value = value.split(",")
+    if isinstance(value, list):
+        value = " | ".join(value)
+    if value is None or value == []:
+        value = "N/A"
+    return value
+
+
+def get_fusion_exons(variant: dict) -> str:
+    """Get RNAfusion specific variant exons for all genes/transcripts listed. Join with pipe 'or' character."""
+    exon = ""
+    for gene in variant.get("genes", []):
+        for transcript in gene.get("transcripts", []):
+            if bool(transcript.get("exon")):
+                if exon:
+                    exon = exon + " | "
+                exon = exon + transcript["exon"]
+
+    return exon
+
+
+def variant_export_lines_fusion(variant: dict, case_obj: dict) -> list:
+    """Get RNAfusion specific variant info to be exported. Returns a list to be merged into a string
+    in suitable export format.
+    """
+    variant_line = []
+
+    for field in ["fusion_genes", "orientation", "frame_status", "found_db"]:
+        variant_line.append(get_fusion_variant_field(variant, field))
+
+    variant_line.append(get_fusion_exons(variant))
+
+    variant_gts = variant["samples"]  # list of coverage and gt calls for case samples
+    for individual in case_obj["individuals"]:
+        for variant_gt in variant_gts:
+            if individual["individual_id"] != variant_gt["sample_id"]:
+                continue
+            variant_line.append(variant_gt.get("read_depth", "N/A"))
+            variant_line.append(variant_gt.get("split_read", "N/A"))
+            variant_line.append(variant_gt.get("ffpm", "N/A"))
+
+    return variant_line
+
+
+def variant_export_lines_cancer(variant: dict) -> list:
+    """
+    Get cancer specific variant info to be exported. Returns a list to be merged into a string
+    in suitable export format.
+    """
+    variant_line = []
+
+    # Add cancer and normal VAFs
+    for sample in ["tumor", "normal"]:
+        allele = variant.get(sample)
+        if not allele:
+            variant_line.append("-")
+            continue
+        alt_freq = round(allele.get("alt_freq", 0), 4)
+        alt_depth = allele.get("alt_depth")
+        ref_depth = allele.get("ref_depth")
+
+        vaf_sample = f"{alt_freq} ({alt_depth}|{ref_depth})"
+        variant_line.append(vaf_sample)
+
+    # ADD eventual COSMIC ID
+    cosmic_ids = variant.get("cosmic_ids") or ["-"]
+    variant_line.append(" | ".join(cosmic_ids))
+
+    return variant_line
+
+
+def variant_export_lines_rare(variant: dict, case_obj: dict) -> list:
+    """
+    Get generic rare disease variant info to be exported. Returns a list to be merged into a string
+    in suitable export format.
+    """
+    variant_line = []
+
+    variant_gts = variant["samples"]  # list of coverage and gt calls for case samples
+    for individual in case_obj["individuals"]:
+        for variant_gt in variant_gts:
+            if individual["individual_id"] != variant_gt["sample_id"]:
+                continue
+
+            variant_line.append(variant_gt["genotype_call"])
+            # gather coverage info
+            variant_line.append(variant_gt["allele_depths"][0])  # AD reference
+            variant_line.append(variant_gt["allele_depths"][1])  # AD alternate
+            # gather genotype quality info
+            variant_line.append(variant_gt["genotype_quality"])
+
+    return variant_line
+
+
+def variant_export_lines(
+    store: MongoAdapter, case_obj: dict, variants_query: CursorType, category: Optional[str] = None
+) -> List[str]:
     """Get variants info to be exported to file, one list (line) per variant.
-    Args:
-        store(scout.adapter.MongoAdapter)
-        case_obj(scout.models.Case)
-        variants_query: a list of variant objects, each one is a dictionary
+
     Returns:
         export_variants: a list of strings. Each string  of the list corresponding to the fields
-                         of a variant to be exported to file, separated by comma
+                         of a variant to be exported to file, separated by comma.
     """
 
     export_variants = []
 
     for variant in variants_query:
-        variant_line = []
-        position = variant["position"]
-        change = variant["reference"] + ">" + variant["alternative"]
-        variant_line.append(variant.get("rank_score", "N/A"))
-        variant_line.append(variant["chromosome"])
-        variant_line.append(position)
-        variant_line.append(change)
-        variant_line.append("_".join([str(position), change]))
-
-        # gather gene info:
-        gene_list = variant.get("genes")  # this is a list of gene objects
-
-        # if variant is in genes
-        if gene_list:
-            gene_info = variant_export_genes_info(store, gene_list, case_obj.get("genome_build"))
-            variant_line += gene_info
-        else:
-            empty_col = 0
-            while empty_col < 4:
-                variant_line.append(
-                    "-"
-                )  # empty HGNC id, empty gene name and empty transcripts columns
-                empty_col += 1
-
-        if variant.get("cadd_score"):
-            variant_line.append(round(variant["cadd_score"], 2))
-        else:
-            variant_line.append("N/A")
-
-        if variant.get("gnomad_frequency"):
-            variant_line.append(round(variant["gnomad_frequency"], 5))
-        else:
-            variant_line.append("N/A")
-
-        if case_obj.get("track") == "cancer":
-            # Add cancer and normal VAFs
-            for sample in ["tumor", "normal"]:
-                allele = variant.get(sample)
-                if not allele:
-                    variant_line.append("-")
-                    continue
-                alt_freq = round(allele.get("alt_freq", 0), 4)
-                alt_depth = allele.get("alt_depth")
-                ref_depth = allele.get("ref_depth")
-
-                vaf_sample = f"{alt_freq} ({alt_depth}|{ref_depth})"
-                variant_line.append(vaf_sample)
-
-            # ADD eventual COSMIC ID
-            cosmic_ids = variant.get("cosmic_ids") or ["-"]
-            variant_line.append(" | ".join(cosmic_ids))
+        variant_line = variant_export_lines_common(store, variant, case_obj)
 
+        if category == "fusion":
+            variant_line.extend(variant_export_lines_fusion(variant, case_obj))
+        elif case_obj.get("track") == "cancer":
+            variant_line.extend(variant_export_lines_cancer(variant))
         else:
-            variant_gts = variant["samples"]  # list of coverage and gt calls for case samples
-            for individual in case_obj["individuals"]:
-                for variant_gt in variant_gts:
-                    if individual["individual_id"] != variant_gt["sample_id"]:
-                        continue
-
-                    variant_line.append(variant_gt["genotype_call"])
-                    # gather coverage info
-                    variant_line.append(variant_gt["allele_depths"][0])  # AD reference
-                    variant_line.append(variant_gt["allele_depths"][1])  # AD alternate
-                    # gather genotype quality info
-                    variant_line.append(variant_gt["genotype_quality"])
+            variant_line.extend(variant_export_lines_rare(variant, case_obj))
 
         variant_line = [str(i) for i in variant_line]
         export_variants.append(",".join(variant_line))
@@ -1224,16 +1305,20 @@ def variant_export_genes_info(store, gene_list, genome_build="37"):
     return gene_info
 
 
-def variants_export_header(case_obj):
+def variants_export_header(case_obj: dict, category: str = "snv") -> List[str]:
     """Returns a header for the CSV file with the filtered variants to be exported.
     Args:
         case_obj(scout.models.Case)
+        category: Variant category to prepare export for e.g. "fusion"
     Returns:
         header: includes the fields defined in scout.constants.variants_export EXPORT_HEADER
                 + AD_reference, AD_alternate, GT_quality for each sample analysed for a case
     """
+
     header = []
-    if case_obj.get("track") == "cancer":
+    if category == "fusion":
+        header = header + FUSION_EXPORT_HEADER
+    elif case_obj.get("track") == "cancer":
         header = header + CANCER_EXPORT_HEADER
     else:
         header = header + EXPORT_HEADER
@@ -1244,6 +1329,7 @@ def variants_export_header(case_obj):
             header.append("AD_reference_" + display_name)  # Add AD reference field for a sample
             header.append("AD_alternate_" + display_name)  # Add AD alternate field for a sample
             header.append("GT_quality_" + display_name)  # Add Genotype quality field for a sample
+
     return header
 
 

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

@@ -34,11 +34,12 @@
         href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">{{ gene.hgnc_symbol or gene.hgnc_id }}
         </a> <br>
     {% endfor %}
-  {% else %}
-    {% for symbol in variant.fusion_genes %}
-      {{ symbol }} <br>
-    {% endfor %}
   {% endif %}
+  {% for symbol in variant.fusion_genes %}
+    {% if symbol not in variant.hgnc_symbols %}
+      {{ symbol }} <br>
+    {% endif %}
+  {% endfor %}
 </div>
 {% endmacro %}
 

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

@@ -127,7 +127,7 @@ onsubmit="return validateForm()">
       {% if variant.genes %}
         {% for gene in variant.genes %}
           {% for transcript in gene.transcripts %}
-            <div>{{ transcript.exon|int }} </div>
+            <div>{% if "exon" in transcript %}{{ transcript.exon|int }}{% endif %} </div>
           {% endfor %}
         {% endfor %}
       {% endif %}

scout/server/blueprints/variants/views.py

@@ -1,4 +1,5 @@
 """Views for the variants"""
+
 import io
 import logging
 
@@ -122,7 +123,6 @@ def variants(institute_id, case_name):
             return redirect(request.referrer)
 
         hgnc_symbols_set = set(form.hgnc_symbols.data)
-        LOG.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
         new_hgnc_symbols = controllers.upload_panel(store, institute_id, case_name, stream)
         hgnc_symbols_set.update(new_hgnc_symbols)
         form.hgnc_symbols.data = hgnc_symbols_set
@@ -131,9 +131,12 @@ def variants(institute_id, case_name):
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    cytobands = store.cytoband_by_chrom(case_obj.get("genome_build"))
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    cytobands = store.cytoband_by_chrom(genome_build)
 
-    variants_query = store.variants(case_obj["_id"], query=form.data, category=category)
+    variants_query = store.variants(
+        case_obj["_id"], query=form.data, category=category, build=genome_build
+    )
     result_size = store.count_variants(case_obj["_id"], form.data, None, category)
 
     if request.form.get("export"):
@@ -217,12 +220,15 @@ def str_variants(institute_id, case_name):
 
     controllers.activate_case(store, institute_obj, case_obj, current_user)
 
-    cytobands = store.cytoband_by_chrom(case_obj.get("genome_build"))
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    cytobands = store.cytoband_by_chrom(genome_build)
 
     query = form.data
     query["variant_type"] = variant_type
 
-    variants_query = store.variants(case_obj["_id"], category=category, query=query).sort(
+    variants_query = store.variants(
+        case_obj["_id"], category=category, query=query, build=genome_build
+    ).sort(
         [
             ("str_repid", pymongo.ASCENDING),
             ("chromosome", pymongo.ASCENDING),
@@ -297,12 +303,14 @@ def sv_variants(institute_id, case_name):
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build")) else "37"
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    variants_query = store.variants(case_obj["_id"], category=category, query=form.data)
+    variants_query = store.variants(
+        case_obj["_id"], category=category, query=form.data, build=genome_build
+    )
 
     result_size = store.count_variants(case_obj["_id"], form.data, None, category)
 
@@ -389,12 +397,14 @@ def mei_variants(institute_id, case_name):
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build")) else "37"
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    variants_query = store.variants(case_obj["_id"], category=category, query=form.data)
+    variants_query = store.variants(
+        case_obj["_id"], category=category, query=form.data, build=genome_build
+    )
 
     result_size = store.count_variants(case_obj["_id"], form.data, None, category)
 
@@ -496,7 +506,8 @@ def cancer_variants(institute_id, case_name):
     controllers.populate_chrom_choices(form, case_obj)
 
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
-    genome_build = "38" if "38" in str(case_obj.get("genome_build")) else "37"
+
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
@@ -576,12 +587,14 @@ def cancer_sv_variants(institute_id, case_name):
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build")) else "37"
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    variants_query = store.variants(case_obj["_id"], category=category, query=form.data)
+    variants_query = store.variants(
+        case_obj["_id"], category=category, query=form.data, build=genome_build
+    )
 
     result_size = store.count_variants(case_obj["_id"], form.data, None, category)
 
@@ -659,18 +672,20 @@ def fusion_variants(institute_id, case_name):
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
-    genome_build = "38"
+    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    variants_query = store.variants(case_obj["_id"], category=category, query=form.data)
+    variants_query = store.variants(
+        case_obj["_id"], category=category, query=form.data, build=genome_build
+    )
 
     result_size = store.count_variants(case_obj["_id"], form.data, None, category)
 
     # if variants should be exported
     if request.form.get("export"):
-        return controllers.download_variants(store, case_obj, variants_query)
+        return controllers.download_variants(store, case_obj, variants_query, category=category)
 
     data = controllers.fusion_variants(
         store, institute_obj, case_obj, variants_query, result_size, page

scout/server/config.py

@@ -41,6 +41,9 @@ ACCREDITATION_BADGE = "swedac-1926-iso17025.png"
 # 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"
 
+# URL to an instance of Chanjo2, for generating coverage report
+# CHANJO2_URL = "http://chanjo2-stage.scilifelab.se"
+
 # Configure gens service
 # GENS_HOST = "127.0.0.1"
 # GENS_PORT = 5000

scout/server/templates/report_base.html

@@ -4,7 +4,7 @@
 	<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
 
 	{% block css %}
-	<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.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" />
     <style>
 		tr.light-grey td{
@@ -22,8 +22,8 @@
 	{% endblock %}
 
 	{% block scripts %}
-	<script src="https://code.jquery.com/jquery-3.1.1.min.js"></script>
-	<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"></script>
+  <script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
+	<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.min.js" integrity="sha384-QJHtvGhmr9XOIpI6YVutG+2QOK9T+ZnN4kzFN1RtK3zEFEIsxhlmWl5/YESvpZ13" crossorigin="anonymous"></script>
 	{% endblock %}
 </body>
 </html>