def clean(self):
cleaned_data = super(MendelianVariantSearchForm, self).clean()
if cleaned_data['search_mode'] not in ['standard_inheritance', 'custom_inheritance', 'gene_burden', 'allele_count', 'all_variants']:
raise forms.ValidationError("Invalid search mode: {}".format(cleaned_data['search_mode']))
if cleaned_data['search_mode'] == 'standard_inheritance' and not cleaned_data.get('inheritance_mode'):
raise forms.ValidationError("Inheritance mode is required for standard search. ")
parse_variant_filter(cleaned_data)
parse_quality_filter(cleaned_data)
parse_genotype_filter(cleaned_data)
parse_burden_filter(cleaned_data)
parse_allele_count_filter(cleaned_data)
search_spec = MendelianVariantSearchSpec()
search_spec.search_mode = cleaned_data['search_mode']
search_spec.inheritance_mode = cleaned_data.get('inheritance_mode')
search_spec.genotype_inheritance_filter = cleaned_data.get('genotype_filter')
search_spec.gene_burden_filter = cleaned_data.get('gene_burden_filter')
search_spec.allele_count_filter = cleaned_data.get('allele_count_filter')
search_spec.variant_filter = cleaned_data.get('variant_filter')
search_spec.genotype_quality_filter = cleaned_data.get('quality_filter')
cleaned_data['search_spec'] = search_spec
return cleaned_data
def clean(self):
cleaned_data = super(MendelianVariantSearchForm, self).clean()
if cleaned_data['search_mode'] not in ['standard_inheritance', 'custom_inheritance', 'gene_burden', 'allele_count', 'all_variants']:
raise forms.ValidationError("Invalid search mode: {}".format(cleaned_data['search_mode']))
if cleaned_data['search_mode'] == 'standard_inheritance' and not cleaned_data.get('inheritance_mode'):
raise forms.ValidationError("Inheritance mode is required for standard search. ")
parse_variant_filter(cleaned_data)
parse_quality_filter(cleaned_data)
parse_genotype_filter(cleaned_data)
parse_burden_filter(cleaned_data)
parse_allele_count_filter(cleaned_data)
search_spec = MendelianVariantSearchSpec()
search_spec.search_mode = cleaned_data['search_mode']
search_spec.inheritance_mode = cleaned_data.get('inheritance_mode')
search_spec.genotype_inheritance_filter = cleaned_data.get('genotype_filter')
search_spec.gene_burden_filter = cleaned_data.get('burden_filter')
search_spec.allele_count_filter = cleaned_data.get('allele_count_filter')
search_spec.variant_filter = cleaned_data.get('variant_filter')
search_spec.quality_filter = cleaned_data.get('quality_filter')
cleaned_data['search_spec'] = search_spec
return cleaned_data
def clean(self):
cleaned_data = super(CohortVariantSearchForm, self).clean()
if cleaned_data['search_mode'] not in [
'custom_inheritance', 'gene_burden'
]:
raise forms.ValidationError("Invalid search mode: {}".format(
cleaned_data['search_mode']))
parse_variant_filter(cleaned_data)
parse_quality_filter(cleaned_data)
parse_genotype_filter(cleaned_data)
parse_burden_filter(cleaned_data)
search_spec = MendelianVariantSearchSpec()
search_spec.search_mode = cleaned_data['search_mode']
search_spec.inheritance_mode = cleaned_data.get('inheritance_mode')
search_spec.genotype_inheritance_filter = cleaned_data.get(
'genotype_filter')
search_spec.gene_burden_filter = cleaned_data.get('gene_burden_filter')
search_spec.allele_count_filter = cleaned_data.get(
'allele_count_filter')
search_spec.variant_filter = cleaned_data.get('variant_filter')
search_spec.genotype_quality_filter = cleaned_data.get(
'quality_filter')
cleaned_data['search_spec'] = search_spec
return cleaned_data
def clean(self):
cleaned_data = super(CohortVariantSearchForm, self).clean()
parse_variant_filter(cleaned_data)
parse_quality_filter(cleaned_data)
search_spec = MendelianVariantSearchSpec()
search_spec.search_mode = cleaned_data['search_mode']
search_spec.inheritance_mode = cleaned_data.get('inheritance_mode')
search_spec.variant_filter = cleaned_data.get('variant_filter')
search_spec.quality_filter = cleaned_data.get('quality_filter')
cleaned_data['search_spec'] = search_spec
return cleaned_data
def clean(self):
cleaned_data = super(CohortVariantSearchForm, self).clean()
parse_variant_filter(cleaned_data)
parse_quality_filter(cleaned_data)
search_spec = MendelianVariantSearchSpec()
search_spec.search_mode = cleaned_data['search_mode']
search_spec.inheritance_mode = cleaned_data.get('inheritance_mode')
search_spec.variant_filter = cleaned_data.get('variant_filter')
search_spec.quality_filter = cleaned_data.get('quality_filter')
cleaned_data['search_spec'] = search_spec
return cleaned_data