Fixed bug where Exac and thousand genomes settings were not shown in …

…frequency tab for GRCh37.

Closes: #597
Related-Issue: #597
Projected-Results-Impact: none

HISTORY.rst

@@ -35,6 +35,7 @@ End-User Summary
 - Adding feature to enable and configure link-out to HGMD (#576).
 - Small variant filtration results now allow to easily look up second hits in the same gene (#573).
 - Structural filtration results now allow to easily look up second hits in the same gene (#574).
+- Fixed bug where Exac and thousand genomes settings were not shown in frequency tab for GRCh37 (#597).
 
 Full Change List
 ================
@@ -69,6 +70,7 @@ Full Change List
 - Small variant filtration results now allow to easily look up second hits in the same gene (#573).
 - Structural filtration results now allow to easily look up second hits in the same gene (#574).
 - Bugfix broken SV filter (#587).
+- Fixed bug where Exac and thousand genomes settings were not shown in frequency tab for GRCh37 (#597).
 
 ------
 v1.2.0

variants/forms.py

@@ -1478,21 +1478,6 @@ def __init__(self, *args, **kwargs):
             self.fields["cohort"] = forms.CharField(
                 widget=forms.HiddenInput(), initial=str(cohort.sodar_uuid)
             )
-        self.genomebuild = self._get_genomebuild()
-
-    def _get_genomebuild(self):
-        """Return genome build for case or cohort or project"""
-        if isinstance(self.project_or_cohort, Cohort):
-            cases = [
-                case
-                for case in self.project_or_cohort.get_accessible_cases_for_user(self.superuser)
-            ]
-        else:  # project
-            cases = [case for case in self.project_or_cohort.case_set.all()]
-        if not cases:
-            return "GRCh37"
-        else:
-            return cases[0].release
 
     def get_pedigree(self):
         """Return ``list`` of ``dict`` with pedigree information."""

variants/templates/variants/filter_form/frequency.html

@@ -9,7 +9,7 @@
   The checkboxes enable (<i class="iconify" data-icon="fa-regular:check-square"></i>) or disable (<i class="iconify" data-icon="fa-regular:square"></i>) filtration based on the population frequencies of the given database.
   You can provide the number of carriers with maximal heterozygous/homozygous (respectively: -plasmid) state or population frequencies.
   For the in-house DB, you can only filter based on carrier state as currently it is tracked how many carriers have sufficient coverage for each variant.
-  {% if form.genomebuild != "GRCh37" %}Thousand genomes and ExAC frequencies are only available GRCh37 cases.{% endif %}
+  {% if genomebuild != "GRCh37" %}Thousand genomes and ExAC frequencies are only available GRCh37 cases.{% endif %}
 </div>
 
 <table class="table table-striped table-hover sodar-card-table compact-form-groups">
@@ -24,15 +24,18 @@
     </tr>
   </thead>
   <tbody>
-    <tr{% if form.genomebuild != "GRCh37" %} style="display: none;"{% endif %}>
+    <tr>
+      <td colspan="6">{{ genomebuild }}</td>
+    </tr>
+    <tr{% if genomebuild != "GRCh37" %} style="display: none;"{% endif %}>
       <td>{{ form.thousand_genomes_enabled|as_crispy_field }}</td>
       <td data-toggle="tooltip" title="Phase 3 data (healthy individuals)">1000 Genomes <small class="text-muted">(samples: 1000)</small></td>
       <td>{{ form.thousand_genomes_homozygous|as_crispy_field }}</td>
       <td>{{ form.thousand_genomes_heterozygous|as_crispy_field }}</td>
       <td>{{ form.thousand_genomes_hemizygous|as_crispy_field }}</td>
       <td>{{ form.thousand_genomes_frequency|as_crispy_field }}</td>
     </tr>
-    <tr{% if form.genomebuild != "GRCh37" %} style="display: none;"{% endif %}>
+    <tr{% if genomebuild != "GRCh37" %} style="display: none;"{% endif %}>
       <td>{{ form.exac_enabled|as_crispy_field }}</td>
       <td data-toggle="tooltip" title="Exomes; project attempts to exclude pediatric disease cases">ExAC <small class="text-muted">(samples: 60,706)</small></td>
       <td>{{ form.exac_homozygous|as_crispy_field }}</td>

variants/views.py

@@ -2172,6 +2172,7 @@ def get_context_data(self, **kwargs):
         """Put the ``Case`` object into the context."""
         context = super().get_context_data(**kwargs)
         context["object"] = self.get_case_object()
+        context["genomebuild"] = context["object"].release
         context["num_small_vars"] = context["object"].num_small_vars
         context["variant_set_exists"] = (
             context["object"].smallvariantset_set.filter(state="active").exists()
@@ -2782,13 +2783,28 @@ def get_initial(self):
                     result[key] = value
         return result
 
+    def _get_genomebuild(self, project_or_cohort):
+        """Return genome build for case or cohort or project"""
+        if isinstance(project_or_cohort, Cohort):
+            cases = [
+                case for case in project_or_cohort.get_accessible_cases_for_user(self.request.user)
+            ]
+        else:  # project
+            cases = [case for case in project_or_cohort.case_set.all()]
+        if not cases:
+            return "GRCh37"
+        else:
+            return cases[0].release
+
     def get_context_data(self, **kwargs):
         context = super().get_context_data(**kwargs)
         context["cohort"] = self.get_cohort()
         if context["cohort"]:
             context["case_count"] = context["cohort"].cases.count()
+            context["genomebuild"] = self._get_genomebuild(context["cohort"])
         else:
             context["case_count"] = context["project"].case_set.count()
+            context["genomebuild"] = self._get_genomebuild(context["project"])
         context["num_small_vars"] = context["project"].num_small_vars()
         context["variant_set_exists"] = (
             context["project"].case_set.filter(smallvariantset__state="active").exists()