def _process_variants(variants, families):
genes = _saved_variant_genes(variants)
# TODO add locus lists on the client side (?)
# TODO handle multiple projects
_add_locus_lists(families.first().project, variants, genes)
saved_variants_by_guid = _get_saved_variants(variants)
return {
'searchedVariants': variants,
'savedVariantsByGuid': saved_variants_by_guid,
'genesById': genes,
}
def _process_variants(variants, families):
prefetch_related_objects(families, 'project')
genes = _saved_variant_genes(variants)
# TODO add locus lists on the client side (?)
projects = {family.project for family in families}
_add_locus_lists(projects, variants, genes)
saved_variants_by_guid = _get_saved_variants(variants)
return {
'searchedVariants': variants,
'savedVariantsByGuid': saved_variants_by_guid,
'genesById': genes,
}
def _process_variants(variants, families):
prefetch_related_objects(families, 'project')
genes = _saved_variant_genes(variants)
# TODO add locus lists on the client side (?)
projects = {family.project for family in families}
_add_locus_lists(projects, variants, genes)
saved_variants_by_guid = _get_saved_variants(variants)
return {
'searchedVariants': variants,
'savedVariantsByGuid': saved_variants_by_guid,
'genesById': genes,
}
def _process_variants(variants, families, user):
prefetch_related_objects(families, 'project')
genes = _saved_variant_genes(variants)
# TODO add locus lists on the client side (?)
projects = {family.project for family in families}
_add_locus_lists(projects, variants, genes)
response_json, _ = _get_saved_variants(
variants, families, include_discovery_tags=user.is_staff)
response_json.update({
'searchedVariants': variants,
'genesById': genes,
})
return response_json
def saved_variants(request, tag):
tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
saved_variant_models = SavedVariant.objects.filter(varianttag__variant_tag_type=tag_type, family__isnull=False)
saved_variants = get_json_for_saved_variants(saved_variant_models, add_tags=True, add_details=True, user=request.user)
project_models_by_guid = {variant.project.guid: variant.project for variant in saved_variant_models}
families = {variant.family for variant in saved_variant_models}
individuals = Individual.objects.filter(family__in=families)
genes = _saved_variant_genes(saved_variants)
locus_list_guids = _add_locus_lists(project_models_by_guid.values(), saved_variants, genes)
projects_json = get_json_for_projects(project_models_by_guid.values(), user=request.user, add_project_category_guids_field=False)
functional_tag_types = get_json_for_variant_functional_data_tag_types()
for project_json in projects_json:
project_json.update({
'locusListGuids': locus_list_guids,
'variantTagTypes': get_project_variant_tag_types(project_models_by_guid[project_json['projectGuid']]),
'variantFunctionalTagTypes': functional_tag_types,
})
families_json = _get_json_for_families(list(families), user=request.user, add_individual_guids_field=True)
individuals_json = _get_json_for_individuals(individuals, user=request.user)
locus_lists_by_guid = {locus_list['locusListGuid']: locus_list for locus_list in
get_json_for_locus_lists(LocusList.objects.filter(guid__in=locus_list_guids), request.user)}
return create_json_response({
'savedVariantsByGuid': {variant['variantGuid']: variant for variant in saved_variants},
'genesById': genes,
'projectsByGuid': {project['projectGuid']: project for project in projects_json},
'familiesByGuid': {family['familyGuid']: family for family in families_json},
'individualsByGuid': {indiv['individualGuid']: indiv for indiv in individuals_json},
'locusListsByGuid': locus_lists_by_guid,
})
def saved_variants_page(request, tag):
gene = request.GET.get('gene')
if tag == 'ALL':
saved_variant_models = SavedVariant.objects.exclude(varianttag=None)
else:
tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
saved_variant_models = SavedVariant.objects.filter(varianttag__variant_tag_type=tag_type)
saved_variant_models = saved_variant_models.filter(family__project__in=get_projects_user_can_view(request.user))
if gene:
saved_variant_models = saved_variant_models.filter(saved_variant_json__transcripts__has_key=gene)
elif saved_variant_models.count() > MAX_SAVED_VARIANTS:
return create_json_response({'error': 'Select a gene to filter variants'}, status=400)
prefetch_related_objects(saved_variant_models, 'family__project')
response_json = get_json_for_saved_variants_with_tags(saved_variant_models, add_details=True, include_missing_variants=True)
project_models_by_guid = {variant.family.project.guid: variant.family.project for variant in saved_variant_models}
families = {variant.family for variant in saved_variant_models}
individuals = Individual.objects.filter(family__in=families)
saved_variants = list(response_json['savedVariantsByGuid'].values())
genes = saved_variant_genes(saved_variants)
locus_lists_by_guid = _add_locus_lists(list(project_models_by_guid.values()), genes, include_all_lists=True)
projects_json = get_json_for_projects(list(project_models_by_guid.values()), user=request.user, add_project_category_guids_field=False)
functional_tag_types = get_json_for_variant_functional_data_tag_types()
variant_tag_types = VariantTagType.objects.filter(Q(project__in=project_models_by_guid.values()) | Q(project__isnull=True))
prefetch_related_objects(variant_tag_types, 'project')
variant_tags_json = _get_json_for_models(variant_tag_types)
tag_projects = {vt.guid: vt.project.guid for vt in variant_tag_types if vt.project}
for project_json in projects_json:
project_guid = project_json['projectGuid']
project_variant_tags = [
vt for vt in variant_tags_json if tag_projects.get(vt['variantTagTypeGuid'], project_guid) == project_guid]
project_json.update({
'locusListGuids': list(locus_lists_by_guid.keys()),
'variantTagTypes': sorted(project_variant_tags, key=lambda variant_tag_type: variant_tag_type['order'] or 0),
'variantFunctionalTagTypes': functional_tag_types,
})
families_json = _get_json_for_families(list(families), user=request.user, add_individual_guids_field=True)
individuals_json = _get_json_for_individuals(individuals, add_hpo_details=True, user=request.user)
for locus_list in get_json_for_locus_lists(LocusList.objects.filter(guid__in=locus_lists_by_guid.keys()), request.user):
locus_lists_by_guid[locus_list['locusListGuid']].update(locus_list)
response_json.update({
'genesById': genes,
'projectsByGuid': {project['projectGuid']: project for project in projects_json},
'familiesByGuid': {family['familyGuid']: family for family in families_json},
'individualsByGuid': {indiv['individualGuid']: indiv for indiv in individuals_json},
'locusListsByGuid': locus_lists_by_guid,
})
return create_json_response(response_json)
def _process_variants(variants, families, user):
if not variants:
return {'searchedVariants': variants}
prefetch_related_objects(families, 'project')
genes = _saved_variant_genes(variants)
projects = {family.project for family in families}
locus_lists_by_guid = _add_locus_lists(projects, genes)
response_json, _ = _get_saved_variants(variants, families, include_discovery_tags=user.is_staff)
response_json.update({
'searchedVariants': variants,
'genesById': genes,
'locusListsByGuid': locus_lists_by_guid,
})
return response_json
def saved_variants_page(request, tag):
gene = request.GET.get('gene')
tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
saved_variant_models = SavedVariant.objects.filter(
varianttag__variant_tag_type=tag_type)
if gene:
saved_variant_models = saved_variant_models.filter(
saved_variant_json__transcripts__has_key=gene)
if saved_variant_models.count() > 10000 and not gene:
return create_json_response(
{'message': 'Select a gene to filter variants'}, status=400)
prefetch_related_objects(saved_variant_models, 'family__project')
saved_variants = get_json_for_saved_variants(saved_variant_models,
add_tags=True,
add_details=True)
project_models_by_guid = {
variant.family.project.guid: variant.family.project
for variant in saved_variant_models
}
families = {variant.family for variant in saved_variant_models}
individuals = Individual.objects.filter(family__in=families)
genes = _saved_variant_genes(saved_variants)
locus_list_guids = _add_locus_lists(project_models_by_guid.values(),
saved_variants, genes)
projects_json = get_json_for_projects(
project_models_by_guid.values(),
user=request.user,
add_project_category_guids_field=False)
functional_tag_types = get_json_for_variant_functional_data_tag_types()
variant_tag_types = VariantTagType.objects.filter(
Q(project__in=project_models_by_guid.values())
| Q(project__isnull=True))
prefetch_related_objects(variant_tag_types, 'project')
variant_tags_json = _get_json_for_models(variant_tag_types)
tag_projects = {
vt.guid: vt.project.guid
for vt in variant_tag_types if vt.project
}
for project_json in projects_json:
project_guid = project_json['projectGuid']
project_variant_tags = [
vt for vt in variant_tags_json if tag_projects.get(
vt['variantTagTypeGuid'], project_guid) == project_guid
]
project_json.update({
'locusListGuids':
locus_list_guids,
'variantTagTypes':
sorted(project_variant_tags,
key=lambda variant_tag_type: variant_tag_type['order']),
'variantFunctionalTagTypes':
functional_tag_types,
})
families_json = _get_json_for_families(list(families),
user=request.user,
add_individual_guids_field=True)
individuals_json = _get_json_for_individuals(individuals,
user=request.user)
locus_lists_by_guid = {
locus_list['locusListGuid']: locus_list
for locus_list in get_json_for_locus_lists(
LocusList.objects.filter(guid__in=locus_list_guids), request.user)
}
return create_json_response({
'savedVariantsByGuid':
{variant['variantGuid']: variant
for variant in saved_variants},
'genesById': genes,
'projectsByGuid':
{project['projectGuid']: project
for project in projects_json},
'familiesByGuid':
{family['familyGuid']: family
for family in families_json},
'individualsByGuid':
{indiv['individualGuid']: indiv
for indiv in individuals_json},
'locusListsByGuid': locus_lists_by_guid,
})
