scout-browser 4.100.2__py3-none-any.whl → 4.102.0__py3-none-any.whl

scout/server/blueprints/institutes/controllers.py

@@ -25,7 +25,11 @@ from scout.server.blueprints.variant.utils import (
     update_representative_gene,
 )
 from scout.server.extensions import beacon, store
-from scout.server.utils import institute_and_case, user_institutes
+from scout.server.utils import (
+    get_case_genome_build,
+    institute_and_case,
+    user_institutes,
+)
 
 from .forms import BeaconDatasetForm, CaseFilterForm
 
@@ -47,6 +51,28 @@ VAR_SPECIFIC_EVENTS = [
     "cancel_sanger",
 ]
 
+# Projection for fetching cases
+ALL_CASES_PROJECTION = {
+    "analysis_date": 1,
+    "assignees": 1,
+    "beacon": 1,
+    "case_id": 1,
+    "display_name": 1,
+    "genome_build": 1,
+    "individuals": 1,
+    "is_rerun": 1,
+    "is_research": 1,
+    "mme_submission": 1,
+    "owner": 1,
+    "panels": 1,
+    "phenotype_terms": 1,
+    "rank_model_version": 1,
+    "status": 1,
+    "sv_rank_model_version": 1,
+    "track": 1,
+    "vcf_files": 1,
+}
+
 
 def get_timeline_data(limit):
     """Retrieve chronologially ordered events from the database to display them in the timeline page
@@ -519,92 +545,106 @@ def export_case_samples(institute_id, filtered_cases) -> Response:
     )
 
 
-def cases(store: MongoAdapter, request: request, institute_id: str) -> dict:
-    """Preprocess case objects for the 'cases' view."""
-    data = {}
+def get_cases_by_query(
+    store: MongoAdapter,
+    request: request,
+    institute_id: str,
+) -> list:
+    """Fetch additional cases based on filters given in request query form.
 
-    # Initialize data (institute info, filters, and case counts)
-    institute_obj = institute_and_case(store, institute_id)
-    data["institute"] = institute_obj
-    data["form"] = CaseFilterForm(request.form)
-    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
-    data["nr_cases"] = sum(data["status_ncases"].values())
+    Sets metadata in data, e.g. sort order.
+    """
 
-    # Fetch Sanger unevaluated and validated cases
-    sanger_ordered_not_validated = get_sanger_unevaluated(store, institute_id, current_user.email)
-    data["sanger_unevaluated"], data["sanger_validated_by_others"] = sanger_ordered_not_validated
+    name_query = request.form
+    all_cases = store.cases(
+        collaborator=institute_id,
+        name_query=name_query,
+        skip_assigned=request.form.get("skip_assigned"),
+        is_research=request.form.get("is_research"),
+        has_rna_data=request.form.get("has_rna"),
+        verification_pending=request.form.get("validation_ordered"),
+        has_clinvar_submission=request.form.get("clinvar_submitted"),
+        projection=ALL_CASES_PROJECTION,
+    )
+    return all_cases
 
-    # Projection for fetching cases
-    ALL_CASES_PROJECTION = {
-        "analysis_date": 1,
-        "assignees": 1,
-        "beacon": 1,
-        "case_id": 1,
-        "display_name": 1,
-        "genome_build": 1,
-        "individuals": 1,
-        "is_rerun": 1,
-        "is_research": 1,
-        "mme_submission": 1,
-        "owner": 1,
-        "panels": 1,
-        "phenotype_terms": 1,
-        "rank_model_version": 1,
-        "status": 1,
-        "sv_rank_model_version": 1,
-        "track": 1,
-        "vcf_files": 1,
-    }
+
+def get_and_set_cases_by_status(
+    store: MongoAdapter,
+    request: request,
+    institute_obj: dict,
+    previous_query_result_cases: list,
+    data: dict,
+) -> dict:
+    """Process cases for statuses that require all cases to be shown.
+    Group cases by status, process additional cases for the remaining statuses
+    and ensure that we don't dim cases that already appeared in query search results.
+    """
+
+    status_show_all_cases = institute_obj.get("show_all_cases_status", ["prioritized"])
+    nr_cases_showall_statuses = 0
 
     # Group cases by status
     case_groups = {status: [] for status in CASE_STATUSES}
-    nr_cases_showall_statuses = 0
-    status_show_all_cases = institute_obj.get("show_all_cases_status") or ["prioritized"]
 
-    # Process cases for statuses that require all cases to be shown
     for status in status_show_all_cases:
         cases_in_status = store.cases_by_status(
-            institute_id=institute_id, status=status, projection=ALL_CASES_PROJECTION
+            institute_id=institute_obj["_id"], status=status, projection=ALL_CASES_PROJECTION
         )
         cases_in_status = _sort_cases(data, request, cases_in_status)
         for case_obj in cases_in_status:
             populate_case_obj(case_obj, store)
+            case_obj["dimmed_in_search"] = True
             case_groups[status].append(case_obj)
             nr_cases_showall_statuses += 1
 
-    # Fetch additional cases based on filters
-    name_query = request.form
-    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
-    all_cases = store.cases(
-        collaborator=institute_id,
-        name_query=name_query,
-        skip_assigned=request.form.get("skip_assigned"),
-        is_research=request.form.get("is_research"),
-        has_rna_data=request.form.get("has_rna"),
-        verification_pending=request.form.get("validation_ordered"),
-        has_clinvar_submission=request.form.get("clinvar_submitted"),
-        projection=ALL_CASES_PROJECTION,
-    )
+    nr_name_query_matching_displayed_cases = 0
+    limit = int(request.form.get("search_limit", 100))
+    for case_obj in previous_query_result_cases:
+        if case_obj["status"] in status_show_all_cases:
+            for group_case in case_groups[status]:
+                if group_case["_id"] == case_obj["_id"]:
+                    group_case["dimmed_in_search"] = False
+        elif nr_name_query_matching_displayed_cases == limit:
+            break
+        else:
+            populate_case_obj(case_obj, store)
+            case_groups[case_obj["status"]].append(case_obj)
+            nr_name_query_matching_displayed_cases += 1
+
+    data["found_cases"] = nr_name_query_matching_displayed_cases + nr_cases_showall_statuses
+    data["limit"] = limit
+    return case_groups
+
+
+def cases(store: MongoAdapter, request: request, institute_id: str):
+    """Preprocess case objects for the 'cases' view.
+
+    Returns data dict for view display, or response in case of file export.
+    """
+    data = {}
+
+    # Initialize data (institute info, filters, and case counts)
+    institute_obj = institute_and_case(store, institute_id)
+    data["institute"] = institute_obj
+    data["form"] = CaseFilterForm(request.form)
+    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
+    data["nr_cases"] = sum(data["status_ncases"].values())
+
+    # Fetch Sanger unevaluated and validated cases
+    sanger_ordered_not_validated = get_sanger_unevaluated(store, institute_id, current_user.email)
+    data["sanger_unevaluated"], data["sanger_validated_by_others"] = sanger_ordered_not_validated
+
+    all_cases = get_cases_by_query(store, request, institute_id)
     all_cases = _sort_cases(data, request, all_cases)
 
     if request.form.get("export"):
         return export_case_samples(institute_id, all_cases)
 
-    # Process additional cases for the remaining statuses
-    nr_cases = 0
-    for case_obj in all_cases:
-        if case_obj["status"] not in status_show_all_cases:
-            if nr_cases == limit:
-                break
-            populate_case_obj(case_obj, store)
-            case_groups[case_obj["status"]].append(case_obj)
-            nr_cases += 1
+    case_groups = get_and_set_cases_by_status(store, request, institute_obj, all_cases, data)
 
     # Compile the final data
     data["cases"] = [(status, case_groups[status]) for status in CASE_STATUSES]
-    data["found_cases"] = nr_cases + nr_cases_showall_statuses
-    data["limit"] = limit
-
     return data
 
 
@@ -615,7 +655,9 @@ def populate_case_obj(case_obj: dict, store: MongoAdapter):
         analysis_types = set(["mixed"])
     case_obj["analysis_types"] = list(analysis_types)
 
-    case_obj["assignees"] = [store.user(user_email) for user_email in case_obj.get("assignees", [])]
+    case_obj["assignees"] = [
+        store.user(user_id=user_id) for user_id in case_obj.get("assignees", [])
+    ]
 
     last_analysis_date = case_obj.get("analysis_date", datetime.datetime.now())
     all_analyses_dates = {
@@ -821,7 +863,7 @@ def gene_variants(store, pymongo_cursor, variant_count, page=1, per_page=50):
         case_display_name = variant_case_obj.get("display_name")
         variant_obj["case_display_name"] = case_display_name
 
-        genome_build = get_genome_build(variant_case_obj)
+        genome_build = get_case_genome_build(variant_case_obj)
         update_variant_genes(store, variant_obj, genome_build)
         variants.append(variant_obj)
 
@@ -885,14 +927,6 @@ def update_variant_genes(store, variant_obj, genome_build):
     variant_obj["functional_annotations"] = get_annotations(gene_symbols, functional_annotations)
 
 
-def get_genome_build(variant_case_obj):
-    """Find genom build in `variant_case_obj`. If not found use build #37"""
-    build = str(variant_case_obj.get("genome_build"))
-    if build in ["37", "38"]:
-        return build
-    return "37"
-
-
 def get_hgvs(gene_obj: Dict) -> Tuple[str, str, str]:
     """Analyse gene object for hgvs info
     Return:

scout/server/blueprints/institutes/templates/overview/cases.html

@@ -63,7 +63,7 @@
 
 
 {% macro case_row(case) %}
-  <tr class="{% if case.status == 'solved' %}causative{% endif %}">
+  <tr class="{% if case.status == 'solved' %}causative{% elif case.dimmed_in_search %}dismiss{% endif %}">
     <td>
       <a class="me-2"
          {% if case.individuals|length == 1 %} data-bs-toggle="tooltip" title="{{case.individuals[0].display_name}}" {% endif %}
@@ -94,13 +94,14 @@
         <span class="badge bg-primary">migrated</span>
       {% endif %}
     </td>
-    <td class="d-flex justify-content-between align-items-center">
-      {{ case.analysis_date.date() }}
-      {% if case.rerun_requested %}
+    <td>
+      <div class="d-flex align-items-center justify-content-between">{{ case.analysis_date.date() }}
+        {% if case.rerun_requested %}
           <span class="badge bg-secondary">rerun pending</span>
-      {% elif case.is_rerun %}
-        <span class="badge bg-secondary">rerun</span>
-      {% endif %}
+        {% elif case.is_rerun %}
+          <span class="badge bg-secondary">rerun</span>
+        {% endif %}
+      </div>
     </td>
     <td>
       {% if case.is_research %}

scout/server/blueprints/login/controllers.py

@@ -98,7 +98,7 @@ def google_login() -> Optional[Response]:
 
     redirect_uri: str = url_for("login.authorized", _external=True)
     try:
-        return oauth_client.google.authorize_redirect(redirect_uri)
+        return oauth_client.google.authorize_redirect(redirect_uri, prompt="select_account")
     except Exception:
         flash("An error has occurred while logging in user using Google OAuth", "warning")
         return None
@@ -151,6 +151,7 @@ def perform_flask_login(user_dict: "LoginUser") -> Response:
 
 def logout_oidc_user(session, provider: str):
     """Log out a user from an OIDC login provider-"""
+
     logout_url = current_app.config[provider].get("logout_url")
     if not logout_url or not session.get("token_response"):
         return

scout/server/blueprints/login/views.py

@@ -13,7 +13,7 @@ from flask import (
     session,
     url_for,
 )
-from flask_login import login_user, logout_user
+from flask_login import logout_user
 
 from scout.server.extensions import login_manager, oauth_client, store
 from scout.server.utils import public_endpoint
@@ -102,11 +102,14 @@ def authorized():
 
 @login_bp.route("/logout")
 def logout():
+    session.pop("email", None)
+    session.pop("name", None)
+    session.pop("locale", None)
+    session.pop("consent_given", None)
     logout_user()  # logs out user from scout
     for provider in ["GOOGLE", "KEYCLOAK"]:
         if current_app.config.get(provider):
             controllers.logout_oidc_user(session, provider)
-    session.clear()
     flash("you logged out", "success")
     return redirect(url_for("public.index"))
 

scout/server/blueprints/omics_variants/views.py

@@ -17,7 +17,7 @@ from scout.server.blueprints.variants.controllers import (
 )
 from scout.server.blueprints.variants.forms import OutlierFiltersForm
 from scout.server.extensions import store
-from scout.server.utils import institute_and_case, templated
+from scout.server.utils import get_case_genome_build, institute_and_case, templated
 
 from . import controllers
 
@@ -71,7 +71,7 @@ def outliers(institute_id, case_name):
     # Populate chromosome select choices
     populate_chrom_choices(form, case_obj)
 
-    genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
+    genome_build = get_case_genome_build(case_obj)
     cytobands = store.cytoband_by_chrom(genome_build)
 
     update_form_hgnc_symbols(store, case_obj, form)

scout/server/blueprints/panels/views.py

@@ -3,7 +3,16 @@ import datetime
 import json
 import logging
 
-from flask import Blueprint, Response, flash, redirect, render_template, request, send_file, url_for
+from flask import (
+    Blueprint,
+    Response,
+    flash,
+    redirect,
+    render_template,
+    request,
+    send_file,
+    url_for,
+)
 from flask_login import current_user
 from markupsafe import escape
 
@@ -96,7 +105,7 @@ def panels():
 
         panel_groups.append((institute_obj, institute_panels))
     return dict(
-        panel_groups=panel_groups,
+        panel_groups=sorted(panel_groups, key=lambda x: x[0]["_id"]),
         panel_names=panel_names,
         panel_versions=panel_versions,
         institutes=institutes,

scout/server/blueprints/phenotypes/controllers.py

@@ -1,7 +1,17 @@
 # -*- coding: utf-8 -*-
 
+from typing import Optional
 
-def hpo_terms(store, query=None, limit=None, page=None):
+from scout.adapter import MongoAdapter
+from scout.constants import HPO_LINK_URL
+
+
+def hpo_terms(
+    store: MongoAdapter,
+    query: Optional[str] = None,
+    limit: Optional[str] = None,
+    page: Optional[str] = None,
+) -> dict:
     """Retrieves a list of HPO terms from scout database
 
     Args:
@@ -29,4 +39,7 @@ def hpo_terms(store, query=None, limit=None, page=None):
         hpo_phenotypes["phenotypes"] = list(store.hpo_terms(query=query, limit=limit, skip=skip))
     else:
         hpo_phenotypes["phenotypes"] = list(store.hpo_terms(limit=limit, skip=skip))
-    return hpo_phenotypes
+
+    data = hpo_phenotypes
+    data["hpo_link_url"] = HPO_LINK_URL
+    return data

scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html

@@ -34,7 +34,7 @@
                 </thead>
                 {% for pheno in phenotypes %}
                 <tr>
-                  <td><a href="http://hpo.jax.org/app/browse/term/{{pheno.hpo_id}}" referrerpolicy="no-referrer" target="_blank">{{ pheno.hpo_id }}</a></td>
+                  <td><a href="{{hpo_link_url}}{{pheno.hpo_id}}" referrerpolicy="no-referrer" target="_blank">{{ pheno.hpo_id }}</a></td>
                   <td><span class="text-body">{{ pheno.description }}</span></td>
                   <td><span class="text-body">{{pheno.genes|length}}</span></td>
                 </tr>

scout/server/blueprints/variant/controllers.py

@@ -28,6 +28,7 @@ from scout.constants import (
     VERBS_MAP,
 )
 from scout.server.blueprints.variant.utils import (
+    get_str_mc,
     update_representative_gene,
     update_variant_case_panels,
 )
@@ -40,6 +41,7 @@ from scout.server.utils import (
     case_has_chanjo_coverage,
     case_has_mt_alignments,
     case_has_rna_tracks,
+    get_case_genome_build,
     user_institutes,
     variant_institute_and_case,
 )
@@ -232,9 +234,7 @@ def variant(
 
     variant_id = variant_obj["variant_id"]
 
-    genome_build = str(case_obj.get("genome_build", "37"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "37"
+    genome_build = get_case_genome_build(case_obj)
 
     # is variant located on the mitochondria
     variant_obj["is_mitochondrial"] = any(
@@ -314,6 +314,9 @@ def variant(
 
     variant_obj["end_position"] = end_position(variant_obj)
 
+    # common motif count for STR variants
+    variant_obj["str_mc"] = get_str_mc(variant_obj)
+
     # Add general variant links
     variant_obj.update(get_variant_links(institute_obj, variant_obj, int(genome_build)))
     variant_obj["frequencies"] = frequencies(variant_obj)
@@ -425,9 +428,7 @@ def get_gene_has_full_coverage(institute_obj, case_obj, variant_obj) -> Dict[int
     if not case_obj.get("chanjo2_coverage"):
         return {}
 
-    genome_build = str(case_obj.get("genome_build", "37"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "37"
+    genome_build = get_case_genome_build(case_obj)
 
     gene_has_full_coverage: dict = {
         hgnc_id: chanjo2.get_gene_complete_coverage(
@@ -436,7 +437,7 @@ def get_gene_has_full_coverage(institute_obj, case_obj, variant_obj) -> Dict[int
             individuals=case_obj.get("individuals"),
             build=genome_build,
         )
-        for hgnc_id in [gene.get("hgnc_id") for gene in variant_obj.get("genes")]
+        for hgnc_id in [gene.get("hgnc_id") for gene in variant_obj.get("genes", [])]
     }
     return gene_has_full_coverage
 
@@ -555,7 +556,7 @@ def observations(store: MongoAdapter, loqusdb: LoqusDB, variant_obj: dict) -> Di
                 f"Could not find a Loqus instance with id:{loqus_id}",
                 "warning",
             )
-            obs_data[loqus_id]["observations"] = "N/A"
+            obs_data[loqus_id] = {"observations": "N/A"}
             continue
 
         if obs_data[loqus_id] == {}:  # Variant was not found
@@ -656,9 +657,7 @@ def variant_acmg(store: MongoAdapter, institute_id: str, case_name: str, variant
         store, variant_obj, institute_id, case_name
     )
 
-    genome_build = str(case_obj.get("genome_build", "37"))
-    if genome_build not in ["37", "38"]:
-        genome_build = "37"
+    genome_build = get_case_genome_build(case_obj)
 
     add_gene_info(store, variant_obj, genome_build=genome_build)
 

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

@@ -396,7 +396,7 @@
     <div class="col-1">
       <!--Define build variable to be used in the UCSC link-->
       {% set build = "hg19" %}
-      {% if case.genome_build == 38 or variant.chromosome == "MT" %}
+      {% if case.genome_build == "38" or variant.chromosome == "MT" %}
         {% set build = "hg38" %}
       {% endif %}
 

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

@@ -164,38 +164,42 @@
   </div>
 {% endmacro %}
 
+{% macro frequencies_table(variant) %}
+<table class="table table-sm align-middle mb-1" style="font-size: 0.875rem;">
+  <thead class="table-light">
+    <tr>
+      <th scope="col" class="py-1 px-2">Source</th>
+      <th scope="col" class="py-1 px-2">Frequency</th>
+    </tr>
+  </thead>
+  <tbody>
+    {% for freq_name, value, link in variant.frequencies %}
+      <tr>
+        <td class="py-1 px-2">
+          {% if link %}
+            <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
+          {% else %}
+            {{ freq_name }}
+          {% endif %}
+        </td>
+        <td class="py-1 px-2">
+          {% if value %}
+            <span class="badge bg-secondary" style="font-size: 0.75rem;">{{ value|human_decimal }}</span>
+          {% else %}
+            -
+          {% endif %}
+        </td>
+      </tr>
+    {% endfor %}
+  </tbody>
+</table>
+{% endmacro %}
+
 {% macro frequencies(variant) %}
   <div class="card panel-default">
     <div class="panel-heading">Frequencies</div>
     <div class="card-body">
-      <table class="table">
-          <thead class="thead table-light">
-            <tr>
-              <th scope="col">Source</th>
-              <th scope="col">Frequency</th>
-            </tr>
-          </thead>
-          <tbody>
-            {% for freq_name, value, link in variant.frequencies %}
-              <tr>
-                <td>
-                  {% if link %}
-                    <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
-                  {% else %}
-                    {{ freq_name }}
-                  {% endif %}
-                </td>
-                <td>
-                  {% if value %}
-                    <span class="badge bg-secondary">{{ value|human_decimal }}</span>
-                  {% else %}
-                    -
-                  {% endif %}
-                </td>
-              </tr>
-            {% endfor %}
-          </tbody>
-      </table>
+      {{ frequencies_table(variant) }}
     </div>
   </div>
 {% endmacro %}
@@ -282,6 +286,41 @@
   </div>
 {% endmacro %}
 
+{% macro old_observations_table(variant) %}
+<table class="table">
+  <thead class="thead table-light">
+    <tr>
+      <th scope="col">Local archive</th>
+      <th scope="col">Nr obs.</th>
+      <th scope="col">Nr homo.</th>
+      <th scope="col">Frequency</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>RD</td>
+      <td>{{ variant.local_obs_old|default('N/A') }}</td>
+      <td>{{ variant.local_obs_hom_old|default('N/A') }}</td>
+      <td>{% if variant.local_obs_old_freq %} {{variant.local_obs_old_freq|round(6)}} {% elif variant.local_obs_old_nr_cases and variant.local_obs_old %} {{ (variant.local_obs_old/variant.local_obs_old_nr_cases)|round(5) }} {% elif variant.local_obs_old_nr_cases %} 0 / {{variant.local_obs_old_nr_cases}} {% else %} N/A {% endif %}</td>
+    </tr>
+    {% if variant.category in ['cancer', 'cancer_sv'] %}
+      <tr>
+        <td>Cancer Germline</td>
+        <td>{{ variant.local_obs_cancer_germline_old|default('N/A') }}</td>
+        <td>{{ variant.local_obs_cancer_germline_hom_old|default('N/A') }}</td>
+        <td>{% if variant.local_obs_cancer_germline_old_freq %} {{variant.local_obs_cancer_germline_old_freq|round(6)}} {% elif variant.local_obs_cancer_germline_old_nr_cases and variant.local_obs_cancer_germline_old %} {{ (variant.local_obs_cancer_germline_old/variant.local_obs_cancer_germline_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_germline_old_nr_cases %} 0 / {{variant.local_obs_cancer_germline_old_nr_cases}} {% else %} N/A {% endif %}</td>
+      </tr>
+      <tr>
+        <td>Cancer Somatic</td>
+        <td>{{ variant.local_obs_cancer_somatic_old|default('N/A') }}</td>
+        <td>{{ variant.local_obs_cancer_somatic_hom_old|default('N/A') }}</td>
+        <td>{% if variant.local_obs_cancer_somatic_old_freq %} {{variant.local_obs_cancer_somatic_old_freq|round(6)}} {% elif variant.local_obs_cancer_somatic_old_nr_cases and variant.local_obs_cancer_somatic_old %} {{ (variant.local_obs_cancer_somatic_old/variant.local_obs_cancer_somatic_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_somatic_old_nr_cases %} 0 / {{variant.local_obs_cancer_somatic_old_nr_cases}} {% else %} N/A {% endif %}</td>
+      </tr>
+    {% endif %}
+  </tbody>
+</table>
+{% endmacro %}
+
 {% macro old_observations(variant, obs_date) %}
 {% if "SHOW_OBSERVED_VARIANT_ARCHIVE" in config and config["SHOW_OBSERVED_VARIANT_ARCHIVE"] == true %}
   <div class="card panel-default">
@@ -289,38 +328,7 @@
       <a href="https://github.com/moonso/loqusdb" target="_blank" data-bs-toggle="tooltip" title="Local observations annotated from an archive copy of the loqusdb local frequency database. Only variants above a quality threshold are included, and each case is included only once. {% if variant.local_obs_old_desc %} {{variant.local_obs_old_desc}} {% endif %}">Local observations (archive {{ obs_date or variant.local_obs_old_date or "version"}})</a>
     </div>
     <div class="card-body">
-      <table class="table">
-        <thead class="thead table-light">
-          <tr>
-            <th scope="col">Archive</th>
-            <th scope="col">Nr obs.</th>
-            <th scope="col">Nr homo.</th>
-            <th scope="col">Frequency</th>
-          </tr>
-        </thead>
-        <tbody>
-          <tr>
-            <td>RD</td>
-            <td>{{ variant.local_obs_old|default('N/A') }}</td>
-            <td>{{ variant.local_obs_hom_old|default('N/A') }}</td>
-            <td>{% if variant.local_obs_old_freq %} {{variant.local_obs_old_freq|round(6)}} {% elif variant.local_obs_old_nr_cases and variant.local_obs_old %} {{ (variant.local_obs_old/variant.local_obs_old_nr_cases)|round(5) }} {% elif variant.local_obs_old_nr_cases %} 0 / {{variant.local_obs_old_nr_cases}} {% else %} N/A {% endif %}</td>
-          </tr>
-          {% if variant.category in ['cancer', 'cancer_sv'] %}
-            <tr>
-              <td>Cancer Germline</td>
-              <td>{{ variant.local_obs_cancer_germline_old|default('N/A') }}</td>
-              <td>{{ variant.local_obs_cancer_germline_hom_old|default('N/A') }}</td>
-              <td>{% if variant.local_obs_cancer_germline_old_freq %} {{variant.local_obs_cancer_germline_old_freq|round(6)}} {% elif variant.local_obs_cancer_germline_old_nr_cases and variant.local_obs_cancer_germline_old %} {{ (variant.local_obs_cancer_germline_old/variant.local_obs_cancer_germline_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_germline_old_nr_cases %} 0 / {{variant.local_obs_cancer_germline_old_nr_cases}} {% else %} N/A {% endif %}</td>
-            </tr>
-            <tr>
-              <td>Cancer Somatic</td>
-              <td>{{ variant.local_obs_cancer_somatic_old|default('N/A') }}</td>
-              <td>{{ variant.local_obs_cancer_somatic_hom_old|default('N/A') }}</td>
-              <td>{% if variant.local_obs_cancer_somatic_old_freq %} {{variant.local_obs_cancer_somatic_old_freq|round(6)}} {% elif variant.local_obs_cancer_somatic_old_nr_cases and variant.local_obs_cancer_somatic_old %} {{ (variant.local_obs_cancer_somatic_old/variant.local_obs_cancer_somatic_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_somatic_old_nr_cases %} 0 / {{variant.local_obs_cancer_somatic_old_nr_cases}} {% else %} N/A {% endif %}</td>
-            </tr>
-          {% endif %}
-        </tbody>
-      </table>
+      {{ old_observations_table(variant) }}
     </div>
   </div>
 {% endif %}