def query_variants_handler(request, search_hash):
"""Search variants.
"""
page = int(request.GET.get('page') or 1)
per_page = int(request.GET.get('per_page') or 100)
sort = request.GET.get('sort') or XPOS_SORT_KEY
if sort == PATHOGENICTY_SORT_KEY and request.user.is_staff:
sort = PATHOGENICTY_HGMD_SORT_KEY
try:
results_model = _get_or_create_results_model(search_hash, json.loads(request.body or '{}'), request.user)
except Exception as e:
logger.error(e)
return create_json_response({'error': e.message}, status=400, reason=e.message)
_check_results_permission(results_model, request.user)
try:
variants, total_results = get_es_variants(results_model, sort=sort, page=page, num_results=per_page)
except InvalidIndexException as e:
logger.error('InvalidIndexException: {}'.format(e))
return create_json_response({'error': e.message}, status=400, reason=e.message)
except ConnectionTimeout:
return create_json_response({}, status=504, reason='Query Time Out')
response = _process_variants(variants or [], results_model.families.all(), request.user)
response['search'] = _get_search_context(results_model)
response['search']['totalResults'] = total_results
return create_json_response(response)
def query_variants_handler(request, search_hash):
"""Search variants.
"""
page = int(request.GET.get('page') or 1)
per_page = int(request.GET.get('per_page') or 100)
sort = request.GET.get('sort') or XPOS_SORT_KEY
if sort == PATHOGENICTY_SORT_KEY and user_is_analyst(request.user):
sort = PATHOGENICTY_HGMD_SORT_KEY
search_context = json.loads(request.body or '{}')
try:
results_model = _get_or_create_results_model(search_hash,
search_context,
request.user)
except Exception as e:
return create_json_response({'error': str(e)},
status=400,
reason=str(e))
_check_results_permission(results_model, request.user)
is_all_project_search = _is_all_project_family_search(search_context)
variants, total_results = get_es_variants(
results_model,
sort=sort,
page=page,
num_results=per_page,
skip_genotype_filter=is_all_project_search,
user=request.user)
response_context = {}
if is_all_project_search and len(variants) == total_results:
# For all project search only save the relevant families
family_guids = set()
for variant in variants:
family_guids.update(variant['familyGuids'])
families = results_model.families.filter(guid__in=family_guids)
results_model.families.set(families)
projects = Project.objects.filter(family__in=families).distinct()
response_context = _get_projects_details(projects, request.user)
response = _process_variants(variants or [], results_model.families.all(),
request.user)
response['search'] = _get_search_context(results_model)
response['search']['totalResults'] = total_results
response.update(response_context)
return create_json_response(response)
def export_variants_handler(request, search_hash):
results_model = VariantSearchResults.objects.get(search_hash=search_hash)
_check_results_permission(results_model, request.user)
families = results_model.families.all()
family_ids_by_guid = {family.guid: family.family_id for family in families}
variants, _ = get_es_variants(results_model, page=1, load_all=True)
variants = _flatten_variants(variants)
json, variants_to_saved_variants = _get_saved_variants(variants, families)
max_families_per_variant = max([len(variant['familyGuids']) for variant in variants])
max_samples_per_variant = max([len(variant['genotypes']) for variant in variants])
rows = []
for variant in variants:
row = [_get_field_value(variant, config) for config in VARIANT_EXPORT_DATA]
for i in range(max_families_per_variant):
family_guid = variant['familyGuids'][i] if i < len(variant['familyGuids']) else ''
variant_guid = variants_to_saved_variants.get(variant['variantId'], {}).get(family_guid, '')
family_tags = {
'family_id': family_ids_by_guid.get(family_guid),
'tags': [tag for tag in json['variantTagsByGuid'].values() if variant_guid in tag['variantGuids']],
'notes': [note for note in json['variantNotesByGuid'].values() if variant_guid in note['variantGuids']],
}
row += [_get_field_value(family_tags, config) for config in VARIANT_FAMILY_EXPORT_DATA]
genotypes = variant['genotypes'].values()
for i in range(max_samples_per_variant):
if i < len(genotypes):
row.append('{sampleId}:{numAlt}:{gq}:{ab}'.format(**genotypes[i]))
else:
row.append('')
rows.append(row)
header = [config['header'] for config in VARIANT_EXPORT_DATA]
for i in range(max_families_per_variant):
header += ['{}_{}'.format(config['header'], i+1) for config in VARIANT_FAMILY_EXPORT_DATA]
header += ['sample_{}:num_alt_alleles:gq:ab'.format(i+1) for i in range(max_samples_per_variant)]
file_format = request.GET.get('file_format', 'tsv')
return export_table('search_results_{}'.format(search_hash), header, rows, file_format, titlecase_header=False)