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 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 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 variants(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) #if study is not None: # return variant_resource(variant=variant, chromosome=chromosome) 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, 'p_lower': p_lower, 'p_upper': p_upper, 'study': study, 'quant_method': quant_method, 'tissue': tissue, 'gene_id': gene, 'molecular_trait_id': trait, 'qtl_group': qtl_group, 'links': links} if chromosome is None: method_name = 'api.get_variant' else: params['chromosome'] = chromosome method_name = 'api.get_chromosome_variants' response = apiu._create_response(method_name=method_name, 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.debug(str(error)) raise RequestedNotFound(str(error))
def _create_chromosome_response(search_info): params = dict(chromosome=search_info['chromosome'], p_lower=search_info['p_lower'], p_upper=search_info['p_upper'], bp_lower=search_info['bp_lower'], bp_upper=search_info['bp_upper'], study=search_info['study'], links=search_info['links']) response = apiu._create_response(method_name='api.get_chromosome_assocs', start=search_info['start'], size=search_info['size'], index_marker=search_info['index_marker'], data_dict=search_info['data_dict'], params=params) return simplejson.dumps(response, ignore_nan=True)
def variants(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") if study is not None: return variant_resource(variant=variant, chromosome=chromosome) 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, 'p_lower': p_lower, 'p_upper': p_upper, 'study_accession': study } if chromosome is None: method_name = 'api.get_variant' else: params['chromosome'] = chromosome method_name = 'api.get_chromosome_variants' response = apiu._create_response(method_name=method_name, 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.debug(str(error)) raise RequestedNotFound(str(error))
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 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 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 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))