def _trait_has_no_children_left(self, trait):
explorer = ex.Explorer(config_properties=self.properties)
studies = explorer.get_list_of_studies_for_trait(trait)
if len(studies) == 1 and studies[0] == self.study:
return True
else:
return False
def studies_for_trait(trait):
args = request.args.to_dict()
try:
start, size = apiu._get_start_size(args)
except ValueError as error:
logging.error("/traits/" + trait + "/studies. " + (str(error)))
raise BadUserRequest(str(error))
try:
explorer = ex.Explorer(apiu.properties)
studies = explorer.get_list_of_studies_for_trait(trait)
study_list = apiu._create_study_info_for_trait(studies, trait)
end = min(start + size, len(study_list))
response = apiu._create_response(
collection_name='studies',
method_name='api.get_studies_for_trait',
start=start,
size=size,
index_marker=size,
data_dict=study_list[start:end],
params=dict(trait=trait))
return simplejson.dumps(response)
except NotFoundError as error:
logging.error("/traits/" + trait + "/studies. " + (str(error)))
raise RequestedNotFound(str(error))
def setup_method(self):
# initialize explorer with local path
properties.h5files_path = "./outputexplorer"
self.explorer = ex.Explorer(properties)
self.loaded_traits = ['t1', 't2', 't3']
self.loaded_studies = ['s1', 's2', 's11', 's12', 's3', 's4', 's5']
self.loaded_studies_t1 = ['s1', 's2', 's11', 's12']
self.loaded_studies_t3 = ['s5']
def trait(trait):
try:
explorer = ex.Explorer(config_properties=properties)
if explorer.has_trait(trait):
response = apiu._create_info_for_trait(trait)
return simplejson.dumps(response, ignore_nan=True)
except NotFoundError as error:
logging.error("/traits/" + trait + ". " + (str(error)))
raise RequestedNotFound(str(error))
def _create_chromosome_info(chromosome):
explorer = ex.Explorer(apiu.properties)
if explorer.has_chromosome(chromosome):
chromosome_info = {'chromosome': chromosome,
'_links': {'self': apiu._create_href(method_name='api.get_chromosome',
params={'chromosome': chromosome}),
'associations': apiu._create_href(method_name='api.get_chromosome_assocs',
params={'chromosome': chromosome})}}
return chromosome_info
raise NotFoundError("Chromosome " + str(chromosome))
def qtl_group(qtl_group):
try:
explorer = ex.Explorer(config_properties=properties)
if explorer.get_studies_of_tissue(tissue):
response = apiu._create_info_for_tissue(tissue)
return simplejson.dumps(response, ignore_nan=True)
else:
raise RequestedNotFound("Tissue: {} not found".format(tissue))
except NotFoundError as error:
logging.error("/tissue/" + tissue + ". " + (str(error)))
raise RequestedNotFound(str(error))
def tissue_study(study, tissue=None):
try:
explorer = ex.Explorer(apiu.properties)
if explorer.check_study(study):
response = apiu._create_info_for_study(study=study, tissue=tissue)
return simplejson.dumps(response, ignore_nan=True)
else:
raise RequestedNotFound("Study: {}.".format(study))
except (NotFoundError, SubgroupError) as error:
logging.error("/studies/" + study + ". " + (str(error)))
raise RequestedNotFound(str(error))
def genes():
args = request.args.to_dict()
try:
start, size = apiu._get_start_size(args)
except ValueError as error:
logging.error("/genes. " + (str(error)))
raise BadUserRequest(str(error))
explorer = ex.Explorer(apiu.properties)
genes = explorer.get_list_of_genes()
gene_list = apiu._get_gene_list(genes=genes, start=start, size=size)
response = apiu._create_response(collection_name='gene', method_name='api.get_genes',
start=start, size=size, index_marker=size, data_dict=gene_list)
return simplejson.dumps(response)
def chromosomes():
chromosomes_list = []
for chromosome in range(1, (properties.available_chromosomes + 1)):
try:
explorer = ex.Explorer(apiu.properties)
explorer.has_chromosome(chromosome)
# adding plus one to include the available_chromosomes number
chromosome_info = _create_chromosome_info(chromosome)
chromosomes_list.append(chromosome_info)
except NotFoundError:
logging.debug("Chromosome %s does not have data...",
str(chromosome))
response = OrderedDict({'_embedded': {'chromosomes': chromosomes_list}})
return simplejson.dumps(response)
def qtl_groups():
args = request.args.to_dict()
try:
start, size, p_lower, p_upper, pval_interval, quant_method, snp, _, gene, study, trait, paginate, links, qtl_group = apiu._get_basic_arguments(args)
except ValueError as error:
logging.error("/qtl_groups. " + (str(error)))
raise BadUserRequest(str(error))
explorer = ex.Explorer(apiu.properties)
qtls = explorer.get_qtl_list()
qtl_list = apiu._get_qtl_list(qtls=qtls, start=start, size=size, links=links)
response = apiu._create_response(collection_name='qtl_groups', method_name='api.get_qtl_groups',
start=start, size=size, index_marker=size, data_dict=qtl_list)
return simplejson.dumps(response)
def study_list():
args = request.args.to_dict()
try:
start, size = apiu._get_start_size(args)
except ValueError as error:
logging.error("/study_list. " + (str(error)))
raise BadUserRequest(str(error))
explorer = ex.Explorer(apiu.properties)
studies = explorer.get_list_of_studies()
# default size is max unless specified:
if 'size' not in args:
size = len(studies)
study_list = apiu._get_study_list_no_info(studies=studies, start=start, size=size)
response = apiu._create_response(collection_name='studies', method_name='api.get_studies',
start=start, size=size, index_marker=size, data_dict=study_list)
return simplejson.dumps(response)
def traits():
args = request.args.to_dict()
#need to add in study to url if present
try:
start, size = apiu._get_start_size(args)
study = apiu._retrieve_endpoint_arguments(args, "study")
except ValueError as error:
logging.error("/molecular_phenotypes. " + (str(error)))
raise BadUserRequest(str(error))
explorer = ex.Explorer(apiu.properties)
if study:
traits = explorer.get_trait_of_study(study_to_find=study)
trait_list = apiu._get_trait_list(traits=traits)
response = apiu._create_response(collection_name='molecular_trait_id', method_name='api.get_traits', params={'study': study},
start=start, size=size, index_marker=size, data_dict=trait_list)
else:
traits = explorer.get_list_of_traits()
trait_list = apiu._get_trait_list(traits=traits, start=start, size=size)
response = apiu._create_response(collection_name='molecular_trait_id', method_name='api.get_traits',
start=start, size=size, index_marker=size, data_dict=trait_list)
return simplejson.dumps(response)
def _find_study_info(study, trait=None):
if trait is None:
explorer = ex.Explorer(config_properties=properties)
trait = explorer.get_trait_of_study(study)
return trait
def _get_all_traits(self):
explorer = ex.Explorer(self.properties)
return explorer.get_list_of_traits()
def main(): # pragma: no cover
args = argument_parser(sys.argv[1:]) # pragma: no cover
trait, study, chromosome, bp_interval, snp, pval_interval = au.convert_search_args(
args) # pragma: no cover
find_all = args.all # pragma: no cover
start = args.start # pragma: no cover
if start is None: # pragma: no cover
start = 0
else:
start = int(start)
size = args.size # pragma: no cover
if size is None: # pragma: no cover
size = 20
else:
size = int(size)
search = Search(properties) # pragma: no cover
if find_all: # pragma: no cover
result, index_marker = search.search_all_assocs(
start=start, size=size, pval_interval=pval_interval)
elif trait is not None:
if study is not None:
result, index_marker = search.search_study(
trait=trait,
study=study,
start=start,
size=size,
pval_interval=pval_interval)
else:
result, index_marker = search.search_trait(
trait=trait,
start=start,
size=size,
pval_interval=pval_interval)
elif study is not None:
explorer = ex.Explorer(properties)
trait = explorer.get_trait_of_study(study)
result, index_marker = search.search_study(trait=trait,
study=study,
start=start,
size=size,
pval_interval=pval_interval)
elif chromosome is not None:
if snp is not None:
result, index_marker = search.search_snp(
snp=snp,
start=start,
size=size,
study=study,
pval_interval=pval_interval,
chromosome=chromosome)
else:
result, index_marker = search.search_chromosome(
chromosome=chromosome,
start=start,
size=size,
bp_interval=bp_interval,
study=study,
pval_interval=pval_interval)
elif snp is not None:
result, index_marker = search.search_snp(snp=snp,
start=start,
size=size,
study=study,
pval_interval=pval_interval)
else:
raise ValueError("Input is wrong!")
if result is not None: # pragma: no cover
for name, dataset in result.items():
print(name, dataset)
else:
print("Result is empty!")