def variant_resource(variant, chromosome=None):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, reveal = apiu._get_basic_arguments(
args)
study = apiu._retrieve_endpoint_arguments(args, "study_accession")
except ValueError as error:
logging.debug("/chromosomes/" + chromosome + "/associations/" +
variant + ". " + (str(error)))
raise BadUserRequest(str(error))
searcher = search.Search(apiu.properties)
try:
datasets, index_marker = searcher.search_snp(
snp=variant,
chromosome=chromosome,
start=start,
size=size,
pval_interval=pval_interval,
study=study)
data_dict = apiu._get_array_to_display(datasets=datasets,
variant=variant,
reveal=reveal)
params = {'variant_id': variant, 'study_accession': study}
if chromosome is not None:
params['chromosome'] = chromosome
response = apiu._create_resource_response(data_dict=data_dict,
params=params)
return simplejson.dumps(response, ignore_nan=True)
except (NotFoundError, SubgroupError) as error:
logging.debug(str(error))
raise RequestedNotFound(str(error))
def trait_associations(trait):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, reveal = apiu._get_basic_arguments(
args)
except ValueError as error:
logging.error("/traits/" + trait + ". " + (str(error)))
raise BadUserRequest(str(error))
searcher = search.Search(apiu.properties)
try:
datasets, index_marker = searcher.search_trait(
trait=trait, start=start, size=size, pval_interval=pval_interval)
data_dict = apiu._get_array_to_display(datasets=datasets,
reveal=reveal)
params = dict(trait=trait, p_lower=p_lower, p_upper=p_upper)
response = apiu._create_response(method_name='api.get_trait_assocs',
start=start,
size=size,
index_marker=index_marker,
data_dict=data_dict,
params=params)
return simplejson.dumps(response, ignore_nan=True)
except NotFoundError as error:
logging.error("/traits/" + trait + ". " + (str(error)))
raise RequestedNotFound(str(error))
def trait_associations(trait):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, quant_method, snp, tissue, gene, study, _ , paginate, links, qtl_group = apiu._get_basic_arguments(args)
except ValueError as error:
logging.error("/molecular_phenotypes/" + trait + ". " + (str(error)))
raise BadUserRequest(str(error))
searcher = search.Search(apiu.properties)
try:
datasets, index_marker, paginate = searcher.search(trait=trait, start=start, size=size, pval_interval=pval_interval, quant_method=quant_method,
tissue=tissue, gene=gene, study=study, snp=snp, paginate=paginate, qtl_group=qtl_group)
data_dict = apiu._get_array_to_display(datasets=datasets, links=links)
params = dict(molecular_trait_id=trait, p_lower=p_lower, p_upper=p_upper, quant_method=quant_method, tissue=tissue, gene_id=gene, study=study, variant_id=snp, qtl_group=qtl_group, links=links)
response = apiu._create_response(method_name='api.get_trait_assocs', start=start, size=size,
index_marker=index_marker,
data_dict=data_dict, params=params)
return simplejson.dumps(response, ignore_nan=True)
except NotFoundError as error:
logging.error("/molecular_phenotypes/" + trait + ". " + (str(error)))
raise RequestedNotFound(str(error))
def variant_resource(variant, chromosome=None):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, quant_method, _, tissue, gene, study, trait, paginate, links, qtl_group = apiu._get_basic_arguments(args)
except ValueError as error:
logging.debug("/chromosomes/" + chromosome + "/associations/" + variant + ". " + (str(error)))
raise BadUserRequest(str(error))
searcher = search.Search(apiu.properties)
try:
datasets, index_marker, paginate = searcher.search(snp=variant, chromosome=chromosome, start=start, size=size,
pval_interval=pval_interval, study=study, quant_method=quant_method,
tissue=tissue, gene=gene, trait=trait, paginate=paginate, qtl_group=qtl_group)
data_dict = apiu._get_array_to_display(datasets=datasets, variant=variant, links=links)
params = {'variant_id': variant, 'study': study, 'quant_method': quant_method, 'tissue': tissue, 'gene_id': gene, 'molecular_trait_id': trait, 'qtl_group': qtl_group, 'links': links}
if chromosome is not None:
params['chromosome'] = chromosome
response = apiu._create_resource_response(data_dict=data_dict, params=params)
print(response)
return simplejson.dumps(response, ignore_nan=True)
except (NotFoundError, SubgroupError) as error:
logging.debug(str(error))
raise RequestedNotFound(str(error))
def chromosome_associations(chromosome):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, quant_method, snp, tissue, gene, study, trait, paginate, links, qtl_group = apiu._get_basic_arguments(args)
bp_lower, bp_upper, bp_interval = apiu._get_bp_arguments(args)
except ValueError as error:
logging.error("/chromosomes/" + chromosome + ". " + (str(error)))
raise BadUserRequest(str(error))
searcher = search.Search(apiu.properties)
try:
datasets, index_marker, paginate = searcher.search(chromosome=chromosome,
start=start, size=size, study=study, snp=snp,
pval_interval=pval_interval, bp_interval=bp_interval,
quant_method=quant_method, tissue=tissue, gene=gene,
trait=trait, paginate=paginate, qtl_group=qtl_group)
data_dict = apiu._get_array_to_display(datasets=datasets, chromosome=chromosome, links=links)
return _create_chromosome_response(dict(chromosome=chromosome, data_dict=data_dict, start=start, size=size,
index_marker=index_marker, bp_lower=bp_lower, bp_upper=bp_upper, variant_id=snp,
p_lower=p_lower, p_upper=p_upper, study=study, quant_method=quant_method,
tissue=tissue, gene=gene, trait=trait, qtl_group=qtl_group, links=links))
except NotFoundError as error:
logging.error("/chromosomes/" + chromosome + ". " + (str(error)))
raise RequestedNotFound(str(error))
except SubgroupError:
# we have not found bp in chromosome, return empty collection
data_dict = {}
index_marker = 0
return _create_chromosome_response(dict(chromosome=chromosome, data_dict=data_dict, start=start, size=size,
index_marker=index_marker, bp_lower=bp_lower, bp_upper=bp_upper, variant_id=snp,
p_lower=p_lower, p_upper=p_upper, study=study, quant_method=quant_method,
tissue=tissue, gene=gene, trait=trait, qtl_group=qtl_group, links=links))
def chromosome_associations(chromosome):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, reveal = apiu._get_basic_arguments(
args)
bp_lower, bp_upper, bp_interval = apiu._get_bp_arguments(args)
study = apiu._retrieve_endpoint_arguments(args, 'study_accession')
except ValueError as error:
logging.error("/chromosomes/" + chromosome + ". " + (str(error)))
raise BadUserRequest(str(error))
searcher = search.Search(apiu.properties)
try:
datasets, index_marker = searcher.search_chromosome(
chromosome=chromosome,
start=start,
size=size,
study=study,
pval_interval=pval_interval,
bp_interval=bp_interval)
data_dict = apiu._get_array_to_display(datasets=datasets,
chromosome=chromosome,
reveal=reveal)
return _create_chromosome_response(
dict(chromosome=chromosome,
data_dict=data_dict,
start=start,
size=size,
index_marker=index_marker,
bp_lower=bp_lower,
bp_upper=bp_upper,
p_lower=p_lower,
p_upper=p_upper,
study=study))
except NotFoundError as error:
logging.error("/chromosomes/" + chromosome + ". " + (str(error)))
raise RequestedNotFound(str(error))
except SubgroupError:
# we have not found bp in chromosome, return empty collection
data_dict = {}
index_marker = 0
return _create_chromosome_response(
dict(chromosome=chromosome,
data_dict=data_dict,
start=start,
size=size,
index_marker=index_marker,
bp_lower=bp_lower,
bp_upper=bp_upper,
p_lower=p_lower,
p_upper=p_upper,
study=study))
def tissue_study_associations(study, tissue=None):
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, quant_method, snp, _, gene, _, trait, paginate, links, qtl_group = apiu._get_basic_arguments(args)
except ValueError as error:
logging.error("/studies/" + study + ". " + (str(error)))
raise BadUserRequest(str(error))
try:
#trait = apiu._find_study_info(study=study, trait=trait)
searcher = search.Search(apiu.properties)
#datasets, index_marker = searcher.search_study(trait=trait, study=study,
# start=start, size=size, pval_interval=pval_interval)
if tissue:
datasets, index_marker, paginate = searcher.search(tissue=tissue, study=study, trait=trait, gene=gene, snp=snp,
start=start, size=size, pval_interval=pval_interval,
quant_method=quant_method, paginate=paginate, qtl_group=qtl_group)
data_dict = apiu._get_array_to_display(datasets=datasets, links=links)
params = dict(tissue=tissue, molecular_trait_id=trait, variant_id=snp, study=study, p_lower=p_lower, p_upper=p_upper, gene_id=gene, quant_method=quant_method, qtl_group=qtl_group, links=links)
else:
datasets, index_marker, paginate = searcher.search(study=study, gene=gene, snp=snp, trait=trait, start=start, size=size,
pval_interval=pval_interval, quant_method=quant_method, paginate=paginate, qtl_group=qtl_group)
data_dict = apiu._get_array_to_display(datasets=datasets, links=links)
params = dict(study=study, p_lower=p_lower, p_upper=p_upper, variant_id=snp, gene_id=gene, molecular_trait_id=trait, quant_method=quant_method, qtl_group=qtl_group, links=links)
response = apiu._create_response(method_name='api.get_tissue_study_assocs', start=start, size=size,
index_marker=index_marker,
data_dict=data_dict, params=params)
return simplejson.dumps(response, ignore_nan=True)
except (NotFoundError, SubgroupError) as error:
logging.error("/studies/" + study + ". " + (str(error)))
raise RequestedNotFound(str(error))
def setup_method(self):
# initialize searcher with local path
properties.h5files_path = "./outputchr"
self.searcher = search.Search(properties)
