def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
raise PermissionDenied
if not family.has_data('variation'):
return render(request, 'analysis_unavailable.html', {
'reason': 'This family does not have any variant data.'
})
elif project.project_status == Project.NEEDS_MORE_PHENOTYPES and not request.user.is_staff:
return render(request, 'analysis_unavailable.html', {
'reason': 'Awaiting phenotype data.'
})
has_gene_search = get_project_datastore(project_id).project_collection_is_loaded(project_id)
gene_lists = [project_gene_list.gene_list.toJSON(details=True) for project_gene_list in ProjectGeneList.objects.filter(project=project)]
sys.stderr.write("returning mendelian_variant_search page for %(project_id)s %(family_id)s. has_gene_search = %(has_gene_search)s\n " % locals() )
return render(request, 'mendelian_variant_search.html', {
'gene_lists': json.dumps(gene_lists),
'project': project,
'family': family,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
'has_gene_search': has_gene_search or get_elasticsearch_dataset(project_id) is not None
})
def has_variant_data(self):
"""
Can we do cohort variant analyses
So all individuals must have variant data
"""
if get_elasticsearch_dataset(self.project.project_id) is not None:
return True
return all(individual.has_variant_data()
for individual in self.get_individuals())
def has_variant_data(self):
"""
Can we do family variant analyses on this family
So True if any of the individuals have any variant data
"""
if get_elasticsearch_dataset(self.project.project_id,
family_id=self.family_id) is not None:
return True
return any(individual.has_variant_data()
for individual in self.get_individuals())
def get_data_status(self):
if get_elasticsearch_dataset(self.project.project_id) is not None:
return "loaded"
if not self.has_variant_data():
return 'no_variants'
elif not get_datastore(self.project.project_id).family_exists(
self.project.project_id, self.cohort_id):
return 'not_loaded'
else:
return get_datastore(self.project.project_id).get_family_status(
self.project.project_id, self.cohort_id)
def add_extra_info_to_variants_project(reference, project, variants):
"""
Add other info to a variant list that client might want to display:
- disease annotations
- coding_gene_ids
"""
project_id = project.project_id
if get_elasticsearch_dataset(project_id) is not None:
#raise ValueError("Project is in elasticsearch: " + str(project_id))
return
add_gene_names_to_variants(reference, variants)
add_disease_genes_to_variants(project, variants)
add_gene_databases_to_variants(variants)
add_gene_info_to_variants(variants)
add_clinical_info_to_variants(variants)
def add_extra_info_to_variants_family(reference, family, variants):
"""
Add other info to a variant list that client might want to display:
- disease annotations
- coding_gene_ids
"""
project_id = family.project.project_id
if get_elasticsearch_dataset(project_id, family.family_id) is not None:
#raise ValueError("Project is in elasticsearch: " + str(project_id))
return
add_gene_names_to_variants(reference, variants)
add_disease_genes_to_variants(family.project, variants)
add_gene_databases_to_variants(variants)
add_gene_info_to_variants(variants)
add_notes_to_variants_family(family, variants)
#add_populations_to_variants(variants, settings.ANNOTATOR_REFERENCE_POPULATION_SLUGS)
#add_custom_populations_to_variants(variants, family.project.private_reference_population_slugs())
add_clinical_info_to_variants(variants)
def project_home(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_view(request.user):
raise PermissionDenied
project.set_accessed()
if project.can_admin(request.user):
auth_level = 'admin'
elif project.can_edit(request.user):
auth_level = 'editor'
elif project.is_public:
auth_level = 'public'
elif project.can_view(request.user):
auth_level = 'viewer'
else:
raise Exception("Authx - how did we get here?!?")
phenotips_supported = True
if settings.PROJECTS_WITHOUT_PHENOTIPS is not None and project_id in settings.PROJECTS_WITHOUT_PHENOTIPS:
phenotips_supported = False
return render(
request, 'project.html', {
'phenotips_supported':
phenotips_supported,
'project':
project,
'auth_level':
auth_level,
'can_edit':
project.can_edit(request.user),
'is_manager':
project.can_admin(request.user),
'has_gene_search':
get_project_datastore(project_id).project_collection_is_loaded(
project_id) or
(get_elasticsearch_dataset(project_id) is not None)
})
def has_variant_data(self):
if get_elasticsearch_dataset(
self.project.project_id,
family_id=self.family.family_id) is not None:
return True
return self.vcf_files.all().count() > 0