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
results_model = VariantSearchResults.objects.filter(
search_hash=search_hash).first()
if not results_model:
if not request.body:
return create_json_response(
{},
status=400,
reason='Invalid search hash: {}'.format(search_hash))
search_context = json.loads(request.body)
project_families = search_context.get('projectFamilies')
if not project_families:
return create_json_response(
{},
status=400,
reason='Invalid search: no projects/ families specified')
search_dict = search_context.get('search', {})
search_model = VariantSearch.objects.filter(search=search_dict).filter(
Q(created_by=request.user) | Q(name__isnull=False)).first()
if not search_model:
search_model = VariantSearch.objects.create(
created_by=request.user, search=search_dict)
results_model = VariantSearchResults.objects.create(
search_hash=search_hash, variant_search=search_model)
all_families = set()
for project_family in project_families:
all_families.update(project_family['familyGuids'])
results_model.families.set(
Family.objects.filter(guid__in=all_families))
_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:
return create_json_response({}, status=400, reason=e.message)
except ConnectionTimeout as e:
return create_json_response({}, status=504, reason='Query Time Out')
response = _process_variants(variants, results_model.families.all())
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 request.user.is_staff:
sort = PATHOGENICTY_HGMD_SORT_KEY
results_model = VariantSearchResults.objects.filter(
search_hash=search_hash).first()
if not results_model:
if not request.body:
return create_json_response(
{},
status=400,
reason='Invalid search hash: {}'.format(search_hash))
search_context = json.loads(request.body)
project_families = search_context.get('projectFamilies')
if not project_families:
return create_json_response(
{},
status=400,
reason='Invalid search: no projects/ families specified')
search_model = VariantSearch.objects.create(created_by=request.user,
search=search_context.get(
'search', {}))
results_model = VariantSearchResults.objects.create(
search_hash=search_hash, variant_search=search_model, sort=sort)
# TODO handle multiple projects
results_model.families.set(
Family.objects.filter(guid__in=project_families[0]['familyGuids']))
elif results_model.sort != sort:
families = results_model.families.all()
results_model, created = VariantSearchResults.objects.get_or_create(
search_hash=search_hash,
variant_search=results_model.variant_search,
sort=sort)
if created:
results_model.families.set(families)
_check_results_permission(results_model, request.user)
try:
variants = get_es_variants(results_model,
page=page,
num_results=per_page)
except InvalidIndexException as e:
return create_json_response({}, status=400, reason=e.message)
response = _process_variants(variants, results_model.families)
response['search'] = _get_search_context(results_model)
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 request.user.is_staff:
sort = PATHOGENICTY_HGMD_SORT_KEY
results_model = VariantSearchResults.objects.filter(search_hash=search_hash).first()
if not results_model:
if not request.body:
return create_json_response({}, status=400, reason='Invalid search hash: {}'.format(search_hash))
search_context = json.loads(request.body)
project_families = search_context.get('projectFamilies')
if not project_families:
return create_json_response({}, status=400, reason='Invalid search: no projects/ families specified')
search_dict = search_context.get('search', {})
search_model = VariantSearch.objects.filter(search=search_dict).filter(Q(created_by=request.user) | Q(name__isnull=False)).first()
if not search_model:
search_model = VariantSearch.objects.create(created_by=request.user, search=search_dict)
results_model = VariantSearchResults.objects.create(search_hash=search_hash, variant_search=search_model)
all_families = set()
for project_family in project_families:
all_families.update(project_family['familyGuids'])
results_model.families.set(Family.objects.filter(guid__in=all_families))
_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:
return create_json_response({}, status=400, reason=e.message)
except ConnectionTimeout as e:
return create_json_response({}, status=504, reason='Query Time Out')
response = _process_variants(variants, results_model.families.all())
response['search'] = _get_search_context(results_model)
response['search']['totalResults'] = total_results
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)
family_ids_by_guid = {family.guid: family.family_id for family in results_model.families.all()}
variants, _ = get_es_variants(results_model, page=1, load_all=True)
saved_variants_by_guid = _get_saved_variants(variants)
saved_variants_by_family = defaultdict(dict)
for var in saved_variants_by_guid.values():
for family_guid in var['familyGuids']:
saved_variants_by_family[family_guid]['{}-{}-{}'.format(var['xpos'], var['ref'], var['alt'])] = var
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 ''
family_tags = saved_variants_by_family[family_guid].get('{}-{}-{}'.format(variant['xpos'], variant['ref'], variant['alt'])) or {}
family_tags['family_id'] = family_ids_by_guid.get(family_guid)
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):
genotype = genotypes[i] if i < len(genotypes) else {}
row += [_get_field_value(genotype, config) for config in VARIANT_GENOTYPE_EXPORT_DATA]
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]
for i in range(max_samples_per_variant):
header += ['{}_{}'.format(config['header'], i+1) for config in VARIANT_GENOTYPE_EXPORT_DATA]
file_format = request.GET.get('file_format', 'tsv')
return export_table('search_results_{}'.format(search_hash), header, rows, file_format, titlecase_header=False)
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:
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:
return create_json_response({'error': e.message},
status=400,
reason=e.message)
except ConnectionTimeout as e:
return create_json_response({}, status=504, reason='Query Time Out')
response = _process_variants(variants, results_model.families.all())
response['search'] = _get_search_context(results_model)
response['search']['totalResults'] = total_results
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)
saved_variants_by_guid, 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 ''
family_tags = saved_variants_by_guid.get(
variants_to_saved_variants.get(variant['variantId'], {}).get(
family_guid, '')) or {}
family_tags['family_id'] = family_ids_by_guid.get(family_guid)
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)