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)