scout-browser 4.82.2__py3-none-any.whl → 4.84__py3-none-any.whl

scout/server/blueprints/cases/templates/cases/case.html

@@ -65,7 +65,7 @@
                 <span class="badge rounded-pill bg-info text-body" data-bs-toggle="tooltip" data-bs-placement="left" title="Matching causatives and managed variants displayed on case page are NOT filtered by gene panel. Use caution to avoid incidental findings.">off</span>
               {% endif %}
             </div>
-        </div> <!--end of div class="row" -->
+        </div> <!--end of row -->
         <div class="row">
           <form id="case_status_form" method="POST" action="{{ url_for('cases.status', institute_id=institute._id, case_name=case.display_name) }}">
               <div class="btn-toolbar ms-2" role="toolbar">
@@ -105,7 +105,7 @@
                     {{ 'Inactive' if case.status == 'ignored' else 'Ignored' }}
                   </button>
                 </div>
-                <div class="btn-group ms-2 role="group">
+                <div class="btn-group ms-2" role="group">
                   <select name="tags" id="status_tags_case" multiple class="selectpicker" data-style="btn btn-secondary">
                     {% for tag, data in case_tag_options.items() %}
                       <option {% if 'tags' in case and tag~"" in case.tags %} selected {% endif %} value="{{ tag }}" title="{{ data.label }}">
@@ -119,87 +119,65 @@
         </div>
       </div>
 
+      {{ matching_variants() }}
+
       <div class="card panel-default" >
-      {% if other_causatives|length > 0%}
-        <div class="row mt-0">
-          <div class="col-xs-12 col-md-12">{{ matching_causatives(other_causatives, institute, case) }}</div>
-        </div>
-      {% endif %}
-      {% if default_other_causatives|length > 0%}
-        <div class="row mt-0">
-          <div class="col-xs-12 col-md-12">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
+        <div class="row">
+          <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
+          <div class="col">{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}</div>
+          <!-- end of data sharing panels -->
         </div>
-      {% endif %}
 
-      {% if managed_variants|length > 0%}
-        <div class="row mt-0">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
+        <div class="row">
+          {% if case.track == 'cancer' %}
+            <div class="col-sm-12 col-md-12 mt-3">{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}</div>
+          {% else %}
+            <div class="mt-3 col-sm-8 col-md-{{"8" if case.madeline_info and case.individuals|length > 1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}</div>
+            {% if case.madeline_info and case.individuals|length > 1 %}
+              <div class="col-sm-4">
+                {{ pedigree_panel(case) }}
+              </div>
+            {% endif %}
+          {% endif %}
         </div>
-      {% endif %}
 
-      {% if default_managed_variants|length > 0%}
-        <div class="row mt-0">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
+        <div class="row mt-3">
+          <div class="col-6">{{ synopsis_panel() }}</div>
+          <div class="col-6">{{ comments_panel(institute, case, current_user, comments) }}</div>
         </div>
-      {% endif %}
-      </div>
-
-      <div class="row">
-        <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
-        <div class="col">{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}</div>
-        <!-- end of data sharing panels -->
-      </div>
-
-      <div class="row">
-        {% if case.track == 'cancer' %}
-          <div class="col-sm-12 col-md-12 mt-3">{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}</div>
-        {% else %}
-          <div class="mt-3 col-sm-8 col-md-{{"8" if case.madeline_info and case.individuals|length > 1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}</div>
-          {% if case.madeline_info and case.individuals|length > 1 %}
-            <div class="col-sm-4">
-              {{ pedigree_panel(case) }}
-            </div>
-          {% endif %}
-        {% endif %}
-      </div>
 
-      <div class="row mt-3">
-        <div class="col-6">{{ synopsis_panel() }}</div>
-        <div class="col-6">{{ comments_panel(institute, case, current_user, comments) }}</div>
-      </div>
-
-      <div class="row">
-        <div class="col-sm-12">
-          {{ insert_multi_image_panel() }}
+        <div class="row">
+          <div class="col-sm-12">
+            {{ insert_multi_image_panel() }}
+          </div>
         </div>
-      </div>
 
-      <div class="row">
-        <div class="col-sm-12">
-          {{ custom_image_panels() }}
+        <div class="row">
+          <div class="col-sm-12">
+            {{ custom_image_panels() }}
+          </div>
         </div>
-      </div>
 
-      <!-- CASE DIAGNOSES AND PHENOTYPES -->
-      <div class="panel-default">
-        <div class="panel-heading"><span class="fa fa-user-md"></span>&nbsp;Phenotypes & diagnoses</div>
-        <div class="row">
-          <div class="col-sm-6 ">
-            <div class="card h-100">
-              <div class="card-body">
-                {{ hpo_panel(case, institute, config) }}
+        <!-- CASE DIAGNOSES AND PHENOTYPES -->
+        <div class="panel-default">
+          <div class="panel-heading"><span class="fa fa-user-md"></span>&nbsp;Phenotypes & diagnoses</div>
+          <div class="row">
+            <div class="col-sm-6 ">
+              <div class="card h-100">
+                <div class="card-body">
+                  {{ hpo_panel(case, institute, config) }}
+                </div>
               </div>
             </div>
-          </div>
-          <div class="col-sm-6">
-            <div class="card h-100">
-              <div class="card-body">
-                {{ hpo_genelist_panel(case, institute, config) }}
+            <div class="col-sm-6">
+              <div class="card h-100">
+                <div class="card-body">
+                  {{ hpo_genelist_panel(case, institute, config) }}
+                </div>
               </div>
             </div>
-          </div>
-        </div> <!--end of <div class="row">-->
-        </div>
+          </div> <!--end of row>-->
+        </div> <!--end of card panel-default  -->
 
           <!-- diagnoses-related code-->
         {% if not case.track == 'cancer' %}
@@ -243,8 +221,8 @@
       {{ reanalysis_modal(institute, case) }}
       {{ beacon_modal(institute, case) }}
       {{ matchmaker_modal(institute, case, suspects, mme_nodes) }}
-  </div><!-- end of <div containter> -->
-</div><!-- end of <div col> -->
+  </div><!-- end of containter -->
+</div><!-- end of col -->
 {% endmacro %}
 
 {% macro variants_buttons() %}
@@ -382,7 +360,7 @@
           </div>
         {% endfor %}
       {% endif %}
-      </div> <!-- end of <div class="list-group" style="max-height:200px; overflow-y: scroll;" -->
+      </div> <!-- end of list-group -->
     </div>
   </div>
 {% endmacro %}
@@ -558,6 +536,51 @@
 </div>
 {% endmacro %}
 
+{% macro matching_variants() %}
+<div class="card mt-3">
+  <div class="row mt-0 ms-3">
+    <div class="col-sm-12 col-md-12">
+      <div data-bs-toggle='tooltip' class="panel-heading" title="Check if there are any variants in this case
+        marked as causative in another case for this institute, or are on the managed variants list.">
+        <strong>
+        {% if hide_matching == false %}
+          <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='True') }}" class="text-body"><span class="me-1 fa fa-caret-down"></span>Search for matching causatives and managed variants</a>
+        {% else %}
+          <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='False') }}" class="text-body"><span class="me-1 fa fa-caret-right"></span>Search for matching causatives and managed variants</a>
+        {% endif %}
+        </strong>
+      </div>
+    </div>
+    {% if hide_matching == false %}
+      {% if other_causatives|length > 0 %}
+        <div class="row mt-0 ms-3">
+          <div class="col-xs-12 col-md-12">{{ matching_causatives(other_causatives, institute, case) }}</div>
+        </div>
+      {% endif %}
+      {% if default_other_causatives|length > 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-xs-12 col-md-12">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
+        </div>
+      {% endif %}
+      {% if managed_variants|length > 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
+        </div>
+      {% endif %}
+      {% if default_managed_variants|length > 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
+        </div>
+      {% endif %}
+      {% if other_causatives|length == 0 and default_other_causatives|length == 0 and managed_variants|length == 0 and default_managed_variants|length == 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-sm-12 col-md-12">No matching causatives or managed variants found</div>
+        </div>
+      {% endif %}
+    {% endif %}
+  </div>
+</div>
+{% endmacro %}
 
 {% block scripts %}
 {{ super() }}

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -108,7 +108,7 @@
     {% endif %}
 
     <!-- Display mtDNA report for non-cancer cases -->
-    {% if case.track != "cancer" %}
+    {% if case.mtdna_report %}
     <div href="#" class="bg-dark list-group-item text-white">
       <div class="d-flex flex-row flex-fill bd-highlight">
         <div>

scout/server/blueprints/cases/templates/cases/phenotype.html

@@ -236,11 +236,13 @@
       <!-- Display and remove added HPO terms -->
       <div class="row mt-3">
         <div class="col-12 ms-3">
-          {% for hpo_term in case.phenotype_terms %}
-            {{ hpo_item(hpo_term, case) }}
-          {% else %}
-            <span class="text-mute">No phenotypes added yet</span>
-          {% endfor %}
+         {% if "phenotype_terms" in case and case.phenotype_terms|length > 0 %}
+           {% for hpo_term in case.phenotype_terms %}
+             {{ hpo_item(hpo_term, case) }}
+           {% endfor %}
+         {% else %}
+           <span class="text-mute">No phenotypes added yet</span>
+         {% endif %}
         </div>
       </div>
 
@@ -251,7 +253,7 @@
             <input class="ms-3" name="min_match" type="number" min="0" step="1" placeholder="Min matches" style="width:130px"/>
             {% if config.PHENOMIZER_USERNAME %}
               <button class="btn btn-secondary btn-sm" type="submit" name="action" value="PHENOMIZER"
-              {%if case.phenotype_terms|length == 0 %} disabled {%endif%}>Phenomizer</button>
+              {% if "phenotype_terms" not in case or case.phenotype_terms|length == 0 %} disabled {% endif %}>Phenomizer</button>
             {% endif %}
           </div>
           <div class="col-1">

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

@@ -633,8 +633,8 @@
 
 {% macro matching_causatives(other_causatives, institute, case, default=False) %}
     <div data-bs-toggle='tooltip' class="panel-heading" title="If there are any variants in this case
-      that have been marked as causative in another case for this insitute. {% if default %}Variants in default panels for the case only.{% endif %}">
-      <strong><a data-bs-toggle="collapse" href="#matchingCausatives{% if default %}Default{% endif %}" class="text-body">Matching causatives {% if default %}in case default panels{% endif %}({{other_causatives|length}})</a></strong>
+      matching a causative in another case for this institute. {% if default %}Variants in default panels for the case only.{% endif %}">
+      <strong><a data-bs-toggle="collapse" href="#matchingCausatives{% if default %}Default{% endif %}" class="text-body" aria-expanded="false"><span class="collapse-icon me-1"></span>Matching causatives {% if default %}in case default panels{% endif %}({{other_causatives|length}})</a></strong>
     </div>
     <ul class="list-group collapse" id="matchingCausatives{% if default %}Default{% endif %}">
       {% for variant in other_causatives %}
@@ -650,7 +650,7 @@
 {% macro matching_managed_variants(managed_variants, institute, case, default=False) %}
     <div data-bs-toggle='tooltip' class="panel-heading" title="Any variants in this case
       that have been marked as managed. {% if default %}Variants in default panels for the case only.{% endif %}">
-      <strong><a data-bs-toggle="collapse" class="text-body" href="#matchingManaged{% if default %}Default{% endif %}">Managed variants {% if default %}in case default panels{% endif %}({{managed_variants|length}})</a></strong>
+      <strong><a data-bs-toggle="collapse" class="text-body" href="#matchingManaged{% if default %}Default{% endif %}" aria-expanded="false"><span class="collapse-icon me-1"></span>Managed variants {% if default %}in case default panels{% endif %}({{managed_variants|length}})</a></strong>
     </div>
     <ul class="list-group">
       {% for variant in managed_variants %}

scout/server/blueprints/cases/views.py

@@ -4,6 +4,7 @@ import json
 import logging
 import os.path
 import shutil
+from ast import literal_eval
 from io import BytesIO
 from operator import itemgetter
 from typing import Generator, Optional, Union
@@ -86,7 +87,6 @@ def case(
     So do case_id, but we still call institute_and_case again to fetch institute
     and reuse its user access verification.
     """
-
     if case_id:
         case_obj = store.case(case_id=case_id, projection={"display_name": 1, "owner": 1})
 
@@ -102,7 +102,12 @@ def case(
         flash("Case {} does not exist in database!".format(case_name))
         return redirect(request.referrer)
 
-    data = controllers.case(store, institute_obj, case_obj)
+    hide_matching = (
+        literal_eval(request.args.get("hide_matching"))
+        if request.args.get("hide_matching")
+        else True
+    )
+    data = controllers.case(store, institute_obj, case_obj, hide_matching)
 
     return dict(
         **data,
@@ -271,10 +276,7 @@ def pdf_case_report(institute_id, case_name):
         store=store, institute_obj=institute_obj, case_obj=case_obj
     )
     # add coverage report on the bottom of this report
-    if (
-        current_app.config.get("SQLALCHEMY_DATABASE_URI")
-        and case_obj.get("track", "rare") != "cancer"
-    ):
+    if current_app.config.get("chanjo_report") and case_obj.get("track", "rare") != "cancer":
         data["coverage_report"] = controllers.coverage_report_contents(
             request.url_root, institute_obj, case_obj
         )

scout/server/blueprints/panels/forms.py

@@ -1,4 +1,5 @@
 """Code for panel gene form"""
+
 from flask_wtf import FlaskForm
 from wtforms import BooleanField, SelectMultipleField, StringField
 

scout/server/blueprints/variant/controllers.py

@@ -28,7 +28,7 @@ from scout.server.blueprints.variant.utils import (
     update_variant_case_panels,
 )
 from scout.server.blueprints.variants.utils import update_case_panels
-from scout.server.extensions import LoqusDB, cloud_tracks, gens
+from scout.server.extensions import LoqusDB, config_igv_tracks, gens
 from scout.server.links import disease_link, get_variant_links
 from scout.server.utils import (
     case_has_alignments,
@@ -142,9 +142,9 @@ def get_igv_tracks(build: str = "37") -> set:
     # Collect hardcoded tracks, common for all Scout instances
     for track in IGV_TRACKS.get(build, []):
         igv_tracks.add(track.get("name"))
-    # Collect instance-specif cloud public tracks, if available
-    if hasattr(cloud_tracks, "public_tracks"):
-        for track in cloud_tracks.public_tracks.get(build, []):
+    # Collect instance-specific public tracks, if available
+    if hasattr(config_igv_tracks, "tracks"):
+        for track in config_igv_tracks.tracks.get(build, []):
             igv_tracks.add(track.get("name"))
     return igv_tracks
 
@@ -372,7 +372,7 @@ def variant(
         "ACMG_OPTIONS": ACMG_OPTIONS,
         "case_tag_options": CASE_TAGS,
         "inherit_palette": INHERITANCE_PALETTE,
-        "igv_tracks": get_igv_tracks(genome_build),
+        "igv_tracks": get_igv_tracks("38" if variant_obj["is_mitochondrial"] else genome_build),
         "has_rna_tracks": case_has_rna_tracks(case_obj),
         "gens_info": gens.connection_settings(genome_build),
         "evaluations": evaluations,
@@ -486,26 +486,21 @@ def observations(store: MongoAdapter, loqusdb: LoqusDB, variant_obj: dict) -> Di
     loqus_query = loqusdb.get_loqus_query(variant_obj, category)
 
     for loqus_id in inst_loqus_ids:  # Loop over all loqusdb instances of an institute
-        obs_data[loqus_id] = {}
-        loqus_settings = loqusdb.loqusdb_settings.get(loqus_id)
+        # collect observation on that loqusdb instance
+        obs_data[loqus_id] = loqusdb.get_variant(loqus_query, loqusdb_id=loqus_id)
 
-        if loqus_settings is None:  # An instance might have been renamed or removed
+        if obs_data[loqus_id] is None:
             flash(
-                f"Could not connect to the preselected loqusdb '{loqus_id}' instance",
+                f"Could not find a Loqus instance with id:{loqus_id}",
                 "warning",
             )
-            obs_data[loqus_id]["total"] = "N/A"
+            obs_data[loqus_id]["observations"] = "N/A"
             continue
-        obs_data[loqus_id] = loqusdb.get_variant(
-            loqus_query, loqusdb_id=loqus_id
-        )  # collect observation on that loqus instance
-
-        if not obs_data[loqus_id]:  # data is an empty dictionary
-            # Collect count of variants in variant's case
-            obs_data[loqus_id] = loqusdb.get_variant(loqus_query, loqusdb_id=loqus_id)
-            if obs_data[loqus_id].get("total"):
-                obs_data[loqus_id]["observations"] = 0
+
+        if obs_data[loqus_id] == {}:  # Variant was not found
+            obs_data[loqus_id]["observations"] = 0
             continue
+
         # Check if the current case is represented in the loqusdb instance
         obs_data[loqus_id]["case_match"] = variant_obj["case_id"] in obs_data[loqus_id].get(
             "families", []

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

@@ -29,22 +29,27 @@
     <form action="{{ url_for('variant.variant_acmg', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
       <div class="card panel-default mt-3">
         <div class="card-body">
-          {% if not evaluation %}
-              <div class="mt-3 fixed-bottom bg-light border">
-                <div class="text-center">
-                  {% for option in ACMG_OPTIONS %}
-                    <a id="acmg-{{ option.code }}" class="btn acmg-preview">{{ option.label }}</a>
-                  {% endfor %}
-                </div>
-              </div>
-            <button class="btn btn-primary form-control">Submit</button>
-          {% else %}
-            <h4>
+          {% if evaluation %}
+             <h4>
               {{ evaluation.classification.label }}
               <span class="badge bg-info">{{ evaluation.classification.short }}</span>
             </h4>
             By {{ evaluation.user_name }} on {{ evaluation.created_at.date() }}
+            {% if edit %}
+              <br><br>
+              <button class="btn btn-primary form-control" data-bs-toggle="tooltip" title="Editing this classification will result in a new classification">Reclassify</button>
+            {% endif %}
+          {% elif not evaluation %}
+            <button class="btn btn-primary form-control">Submit</button>
           {% endif %}
+          <!-- classification preview in the footer-->
+          <div class="mt-3 fixed-bottom bg-light border">
+              <div class="text-center">
+                {% for option in ACMG_OPTIONS %}
+                  <a id="acmg-{{ option.code }}" class="btn acmg-preview">{{ option.label }}</a>
+                {% endfor %}
+              </div>
+          </div>
         </div>
       </div>
 
@@ -72,14 +77,14 @@
                         {{ criterion.short }}
                       </div>
                       <div class="form-check form-switch">
-                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.criteria }} {{ 'disabled' if evaluation }}>
+                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.criteria }} {{ 'disabled' if evaluation and edit is false}}>
                         <label class="form-check-label" for="checkbox-{{ criterion_code }}"></label>
                       </div>
                     </div>
                     <div id="comment-{{ criterion_code }}" class="{{ 'collapse' if not (comment or link or modifier) }} mt-2">
                       {% if criterion.documentation %}<div class="row"><span class="me-1 fw-light text-wrap">{{ criterion.documentation | safe}}</span></div>{% endif %}
                       <div class="row">
-                        <select {{ 'disabled' if evaluation }} id="modifier-{{ criterion_code }}" name="modifier-{{ criterion_code }}" class="form-control form-select">
+                        <select {{ 'disabled' if evaluation and edit is false}} id="modifier-{{ criterion_code }}" name="modifier-{{ criterion_code }}" class="form-control form-select">
                           <option value="" {% if not modifier %}selected{% endif %}>Strength modifier...</option>
                           {% for level in "Strong", "Moderate", "Supporting" %}
                             {% if(level != evidence) %}
@@ -89,10 +94,10 @@
                         </select>
                       </div>
                       <div class="row">
-                        <textarea {{ 'disabled' if evaluation }} class="form-control"
+                        <textarea {{ 'disabled' if evaluation and edit is false }} class="form-control"
                           name="comment-{{ criterion_code }}" rows="3" placeholder="Comment (optional)">{{ comment }}</textarea>
                       </div>
-                      <input type="url" {{ 'disabled' if evaluation }} class="form-control" name="link-{{ criterion_code }}"
+                      <input type="url" {{ 'disabled' if evaluation and edit is false }} class="form-control" name="link-{{ criterion_code }}"
                         placeholder="{{ link or 'Supporting link (optional)' }}" value="">
                     </div>
                   </div>
@@ -120,6 +125,11 @@
   {{ super() }}
 
   <script>
+
+    window.onload=function() {
+        update_classification();
+    }
+
     $(function () {
       $('[data-bs-toggle="tooltip"]').tooltip();
 
@@ -130,7 +140,6 @@
         } else {
           el.collapse('hide');
         }
-
         update_classification()
       });
 

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

@@ -49,14 +49,19 @@
         {% endif %}
       </span>
     </div>
-    <small class="text-muted">
-      <form action="{{ url_for('variant.evaluation', evaluation_id=data._id) }}" method="POST">
+    <span>
+      <small class="text-muted">
       {{ data.user_name }} on {{ data.created_at.date() }}
       {% if current_variant %}
-        <button class="btn btn-xs btn-link">Delete</button>
+          <form action="{{ url_for('variant.evaluation', evaluation_id=data._id) }}" method="POST" style="display: inline-block;">
+            <button class="btn btn-xs btn-link" >Delete</button>
+          </form>
+          {% if data.criteria %}
+            <a class="btn btn-xs btn-link" href="{{ url_for('variant.evaluation', evaluation_id=data._id, edit=True) }}" data-bs-toggle="tooltip" title="Editing this classification will result in a new classification">Edit</a>
+          {% endif %}
       {% endif %}
-      </form>
-    </small>
+      </small>
+    </span>
   </li>
 {% endmacro %}
 
@@ -90,7 +95,7 @@
             {% endif %}
             </div>
           {% endfor %}
-          {% if config.SQLALCHEMY_DATABASE_URI %}
+          {% 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) }}">

scout/server/blueprints/variant/views.py

@@ -13,7 +13,7 @@ from flask import (
 from flask_login import current_user
 from markupsafe import Markup
 
-from scout.constants import ACMG_CRITERIA, ACMG_MAP
+from scout.constants import ACMG_CRITERIA, ACMG_MAP, ACMG_OPTIONS
 from scout.server.blueprints.variant.controllers import check_reset_variant_classification
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
 from scout.server.blueprints.variant.controllers import observations, str_variant_reviewer
@@ -308,7 +308,7 @@ def variant_update(institute_id, case_name, variant_id):
 @variant_bp.route("/evaluations/<evaluation_id>", methods=["GET", "POST"])
 @templated("variant/acmg.html")
 def evaluation(evaluation_id):
-    """Show or delete an ACMG evaluation."""
+    """Show, edit or delete an ACMG evaluation."""
 
     evaluation_obj = store.get_evaluation(evaluation_id)
     if evaluation_obj is None:
@@ -328,12 +328,15 @@ def evaluation(evaluation_id):
             flash("Cleared ACMG classification.", "info")
 
         return redirect(link)
+
     return dict(
         evaluation=evaluation_obj,
+        edit=bool(request.args.get("edit")),
         institute=evaluation_obj["institute"],
         case=evaluation_obj["case"],
         variant=evaluation_obj["variant"],
         CRITERIA=ACMG_CRITERIA,
+        ACMG_OPTIONS=ACMG_OPTIONS,
     )
 
 

scout/server/blueprints/variants/controllers.py

@@ -3,12 +3,10 @@ import logging
 import re
 from typing import Any, Dict, List, Optional
 
-import bson
 from flask import Response, flash, session, url_for
 from flask_login import current_user
 from markupsafe import Markup
 from pymongo.cursor import CursorType
-from pymongo.errors import DocumentTooLarge
 from werkzeug.datastructures import Headers, ImmutableMultiDict, MultiDict
 from wtforms import DecimalField
 
@@ -513,7 +511,7 @@ def update_variant_genes(store, variant_obj, genome_build):
 
     if variant_genes is not None:
         for gene_obj in variant_genes:
-            # If there is no hgnc id there is nothin we can do
+            # If there is no hgnc id there is nothing we can do
             if not gene_obj["hgnc_id"]:
                 continue
             # Else we collect the gene object and check the id
@@ -530,27 +528,6 @@ def update_variant_genes(store, variant_obj, genome_build):
     return has_changed
 
 
-def update_variant_store(store, variant_obj):
-    """
-    Update variants in db store if anything changed.
-    Args:
-        store(scout.adapter.MongoAdapter)
-        variant_obj(scout.models.Variant)
-
-        update(boolean): upsert only if this is set true
-
-        get_compounds(bool): if compounds should be added to added to the returned variant object
-
-    """
-    try:
-        variant_obj = store.update_variant(variant_obj)
-    except DocumentTooLarge:
-        flash(
-            f"An error occurred while updating info for variant: {variant_obj['_id']} (pymongo_errors.DocumentTooLarge: {len(bson.BSON.encode(variant_obj))})",
-            "warning",
-        )
-
-
 def _compound_follow_filter_freq(compound, compound_var_obj, query_form):
     """When compound follow filter is selected, apply relevant settings from the query filter onto dismissing compounds.
 
@@ -895,11 +872,18 @@ def parse_variant(
     compounds_have_changed = False
     if get_compounds:
         compounds_have_changed = update_compounds(store, variant_obj, case_dismissed_vars)
+        if update and compounds_have_changed:
+            store.variant_update_field(
+                variant_id=variant_obj["_id"],
+                field_name="compounds",
+                field_value=variant_obj["compounds"],
+            )
 
     genes_have_changed = update_variant_genes(store, variant_obj, genome_build)
-
-    if update and (compounds_have_changed or genes_have_changed):
-        update_variant_store(store, variant_obj)
+    if update and genes_have_changed:
+        store.variant_update_field(
+            variant_id=variant_obj["_id"], field_name="genes", field_value=variant_obj["genes"]
+        )
 
     variant_obj["comments"] = store.events(
         institute_obj,
@@ -1996,7 +1980,7 @@ def activate_case(store, institute_obj, case_obj, current_user):
         store.update_status(institute_obj, case_obj, user_obj, "active", case_link)
 
 
-def reset_all_dimissed(store, institute_obj, case_obj):
+def reset_all_dismissed(store, institute_obj, case_obj):
     """Reset all dismissed variants for a case.
 
     Args:

scout/server/blueprints/variants/views.py

@@ -47,7 +47,7 @@ variants_bp = Blueprint(
 def reset_dismissed(institute_id, case_name):
     """Reset all dismissed variants for a case"""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
-    controllers.reset_all_dimissed(store, institute_obj, case_obj)
+    controllers.reset_all_dismissed(store, institute_obj, case_obj)
     return redirect(request.referrer)