issue #1152 - classify from tag - get cohort genotype query to work a…

…cross common/uncommon and autocomplete to work
SACGF · Sep 4, 2024 · 87cf5a9 · 87cf5a9
1 parent f704b0a
commit 87cf5a9
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Showing 4 changed files with 21 additions and 22 deletions.
diff --git a/analysis/forms/forms.py b/analysis/forms/forms.py
@@ -354,15 +354,6 @@ def save(self, commit=True):
         return obj
 
 
-class InputSamplesForm(forms.Form):
-    sample = forms.ModelChoiceField(queryset=Sample.objects.none(), required=True)
-
-    def __init__(self, *args, **kwargs):
-        samples = kwargs.pop("samples")
-        super().__init__(*args, **kwargs)
-        self.fields['sample'].queryset = Sample.objects.filter(pk__in=[sample.pk for sample in samples])
-
-
 class VCFLocusFilterForm(forms.Form):
 
     def __init__(self, *args, **kwargs):

diff --git a/analysis/views/views.py b/analysis/views/views.py
@@ -29,7 +29,7 @@
 from analysis import forms
 from analysis.analysis_templates import populate_analysis_from_template_run
 from analysis.exceptions import NonFatalNodeError, NodeOutOfDateException
-from analysis.forms import SelectGridColumnForm, UserTrioWizardForm, VCFLocusFilterForm, InputSamplesForm, \
+from analysis.forms import SelectGridColumnForm, UserTrioWizardForm, VCFLocusFilterForm, \
     AnalysisChoiceForm, AnalysisTemplateTypeChoiceForm, AnalysisTemplateVersionForm, AnalysisTemplateForm
 from analysis.graphs.column_boxplot_graph import ColumnBoxplotGraph
 from analysis.grids import VariantGrid
@@ -55,6 +55,7 @@
 from library.utils import full_class_name, defaultdict_to_dict
 from library.utils.database_utils import run_sql, queryset_to_sql
 from pedigree.models import Pedigree
+from snpdb.forms import SampleChoiceForm
 from snpdb.graphs import graphcache
 from snpdb.models import UserSettings, Sample, \
     Cohort, CohortSample, ImportStatus, VCF, get_igv_data, Trio, Variant, GenomeBuild
@@ -944,8 +945,9 @@ def _get_sample_form(self):
                 samples = self.variant_tag.analysis.get_samples()
 
         if samples:
-            form = InputSamplesForm(samples=samples)
+            form = SampleChoiceForm()
             form.fields['sample'].required = False
+            form.fields['sample'].queryset = Sample.objects.filter(pk__in=[s.pk for s in samples])
         else:
             form = super()._get_sample_form()
         return form

diff --git a/classification/templates/classification/create_classification_for_variant.html b/classification/templates/classification/create_classification_for_variant.html
@@ -211,15 +211,15 @@ <h3>Create Classification Record for {{ variant }}</h3>
 
                 {% labelled label="Sample" %}
                     <div class='value'>
-                    {{ variant_sample_autocomplete_form.sample }} <span id='zygosity'></span>
-                    {{ variant_sample_autocomplete_form.media }}
-                    <div id='no-sample-link' class='hidden'>
-                        <a href="javascript:allowNoSample()">My sample isn't here</a>
-                    </div>
-                    <div id='no-sample-text' class='hidden'>
-                        <p>Please find or upload the sample if you have it, as it allows us to link classifications together, and auto-fill fields.
-                        <p>Please remember to set the SampleID field in the classification form manually.
-                    </div>
+                        {{ variant_sample_autocomplete_form.sample }} <span id='zygosity'></span>
+                        {{ variant_sample_autocomplete_form.media }}
+                        <div id='no-sample-link' class='hidden'>
+                            <a href="javascript:allowNoSample()">My sample isn't here</a>
+                        </div>
+                        <div id='no-sample-text' class='hidden'>
+                            <p>Please find or upload the sample if you have it, as it allows us to link classifications together, and auto-fill fields.
+                            <p>Please remember to set the SampleID field in the classification form manually.
+                        </div>
                     </div>
                 {% endlabelled %}
 

diff --git a/snpdb/models/models_vcf.py b/snpdb/models/models_vcf.py
@@ -372,10 +372,16 @@ def cohort_genotype_collection(self):
         return self.vcf.cohort.cohort_genotype_collection
 
     def get_genotype(self, variant: Variant) -> 'SampleGenotype':
+        from snpdb.models import CohortGenotype
+
+        cgc = self.cohort_genotype_collection
+        collections = [cgc]
+        if cgc.common_collection:
+            collections.append(cgc.common_collection)
         try:
-            cg = self.cohort_genotype_collection.cohortgenotype_set.get(variant=variant)
+            cg = CohortGenotype.objects.filter(collection__in=collections).get(variant=variant)
             sample_genotype = cg.get_sample_genotype(self)
-        except ObjectDoesNotExist:
+        except CohortGenotype.DoesNotExist:
             sample_genotype = None
         return sample_genotype