def get(self, gene_ensembl_id): ''' Get gene expression value ''' parser = reqparse.RequestParser() arguments = { 'project_name': str, 'subproject_name': str, 'loader': str, 'show_gene_ensembl': bool, 'show_clinical_data_id': bool, 'show_samples_data_id': bool, 'show_phenotype_data_id': bool } parser = add_argument(parser, arguments) app.logger.info('获取%s数据' % gene_ensembl_id) args = parser.parse_args() project_name = args.project_name subproject_name = args.subproject_name del args['project_name'] del args['subproject_name'] error, message, expr_info = get_expr_by_project( project_name, subproject_name, gene_ensembl_id, GeneExpr, **args) if not expr_info: expr_info = {} expr_info['gene_ensembl_id'] = gene_ensembl_id expr_info['api_uri'] = url('api.gene', absolute=True, gene_ensembl_id=gene_ensembl_id, project_name=project_name) expr_info['message'] = message expr_info = call_loader(args.get('loader'), json_obj=expr_info) app.logger.info("expr_info: %s" % expr_info) return jsonify(expr_info)
def get(self, expr_info_id=None, query_condition_md5=None): parser = reqparse.RequestParser() arguments = {'loader': str} parser = add_argument(parser, arguments) args = parser.parse_args() if expr_info_id: error, message, expr_info = get_exprtemp_info(id=expr_info_id) else: error, message, expr_info = get_exprtemp_info( query_condition_md5=query_condition_md5) app.logger.debug("expr_info<ExprTemp>: %s" % expr_info.source_type_lst) if error: app.logger.debug("error: %s" % error) expr_info = {} error_code = '0' message = 'success' template_str = render_template(exprtemp_info_j2_file, expr_value=expr_info, show_id=True, error_code=error_code, message=message) app.logger.debug("Jinja2 Template: %s" % template_str) expr_info = json.loads( template_str.strip("'<>() ").replace('\'', '\"')) app.logger.debug("loader: %s" % args.get('loader')) expr_info = call_loader(args.get('loader'), json_obj=expr_info) app.logger.debug("expr_info: %s" % expr_info) return jsonify(expr_info)
def get(self, gene_ensembl_id): parser = reqparse.RequestParser() arguments = { 'project_name': str, 'subproject_name': str, 'loader': str, 'show_transcript_ensembl': bool, 'show_clinical_data_id': bool, 'show_samples_data_id': bool, 'show_phenotype_data_id': bool } parser = add_argument(parser, arguments) args = parser.parse_args() args['gene_ensembl_id'] = gene_ensembl_id if gene_ensembl_id and args.get('project_name'): error, message, mutation_info = get_mutation_by_project(**args) if error: app.logger.debug("error: %s" % message) return {"message": message}, 404 mutation_info['message'] = message mutation_info = call_loader(args.get('loader'), json_obj=mutation_info) app.logger.debug("mutation_info: %s" % mutation_info) return jsonify(mutation_info) else: return {"message": 'No ensembl id'}, 400
def get(self, project_name): ''' Get project information ''' # 定义argument parser = reqparse.RequestParser() arguments = { 'project_name': str, 'loader': str, 'show_src_project': bool, 'show_analysis_program': bool } parser = add_argument(parser, arguments) app.logger.info('获取%s数据' % project_name) args = parser.parse_args() del args['project_name'] error, message, project_info = get_project_info(project_name, **args) project_info['project_name'] = project_name project_info['api_uri'] = url('api.project', absolute=True, project_name=project_name) project_info['message'] = message if error and not message: project_info['message'] = '' project_info = call_loader(args.get('loader'), json_obj=project_info) app.logger.info("project_info: %s" % project_info) return jsonify(project_info)
def get(self): parser = reqparse.RequestParser() app.logger.info('获取测试数据') args = parser.parse_args() welcome_page = { "name": "YJC", "version": '1.0', "tagline": "You Know, for Gene Data" } welcome_page = call_loader(args.get('loader'), json_obj=welcome_page) app.logger.info(welcome_page) return jsonify(welcome_page)