def search_init(): res_obj = {} try: res_obj = apilib.search_init(config_obj) except Exception, e: res_obj = errorlib.get_error_obj("idmapping_search_init", traceback.format_exc(), path_obj)
def search(): form_dict = cgi.FieldStorage() record_type = form_dict["recordtype"].value input_namespace = form_dict["input_namespace"].value output_namespace = form_dict["output_namespace"].value input_idlist = [] if "userfile" in form_dict: file_buffer = form_dict["userfile"].file.read() file_buffer = file_buffer.replace("\r", "\n") file_buffer = file_buffer.replace("\n\n", "\n") line_list = file_buffer.split("\n") for line in line_list: if line.strip() != "" and line.strip() not in input_idlist: input_idlist.append(line.strip()) if "input_idlist" in form_dict: if form_dict["input_idlist"].value.strip() != "": for word in form_dict["input_idlist"].value.split(","): if word.strip() not in input_idlist: input_idlist.append(word.strip()) query_obj = {"input_idlist":input_idlist, "recordtype":record_type, "input_namespace":input_namespace, "output_namespace":output_namespace} res_obj = {} try: res_obj = apilib.search(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("idmapping_search", traceback.format_exc(), path_obj)
def protein_search_init(): res_obj = {} try: res_obj = apilib.protein_search_init(config_obj) except Exception, e: res_obj = errorlib.get_error_obj("protein_search_init", traceback.format_exc(), path_obj)
def typeahead(): res_obj = [] try: query_value = util.get_arg_value("query", request.method) if query_value == "": res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]} elif util.is_valid_json(query_value) == False: res_obj = {"error_list":[{"error_code": "invalid-query-json"}]} else: query_obj = json.loads(query_value) util.trim_object(query_obj) field_list_one = ["glytoucan_ac", "motif_name", "enzyme_uniprot_canonical_ac", "glycan_pmid", "enzyme"] field_list_two = ["uniprot_canonical_ac", "uniprot_id", "refseq_ac", "protein_name", "gene_name", "pathway_id", "pathway_name", "disease_name","disease_id", "go_id", "go_term", "protein_pmid"] tmp_obj_one, tmp_obj_two = [], [] if query_obj["field"] in field_list_one: tmp_obj_one = apilib.glycan_typeahead(query_obj, config_obj) if query_obj["field"] in field_list_two: tmp_obj_two = apilib.protein_typeahead(query_obj, config_obj) if "error_list" in tmp_obj_one: res_obj = tmp_obj_one elif "error_list" in tmp_obj_two: res_obj = tmp_obj_two else: res_obj = tmp_obj_one + tmp_obj_two except Exception, e: res_obj = errorlib.get_error_obj("typeahead", traceback.format_exc(), path_obj)
def misc_messagelist(): res_obj = {} try: res_obj = apilib.messagelist(config_obj) except Exception, e: res_obj = errorlib.get_error_obj("misc_messagelist", traceback.format_exc(), path_obj)
def home_init(): res_obj = {} try: res_obj = apilib.home_init(config_obj) except Exception, e: res_obj = errorlib.get_error_obj("home_init", traceback.format_exc(), path_obj)
def protein_detail(uniprot_canonical_ac): res_obj = {} try: if uniprot_canonical_ac in ["", "empty"]: res_obj = {"error_list":[{"error_code":"missing-parameter", "field":"uniprot_canonical_ac"}]} else: query_obj = {"uniprot_canonical_ac":uniprot_canonical_ac} util.trim_object(query_obj) res_obj = apilib.protein_detail(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("protein_detail", traceback.format_exc(), path_obj)
def idmapping_list(): res_obj = {} try: query_value = util.get_arg_value("query", request.method) if query_value == "": res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]} elif util.is_valid_json(query_value) == False: res_obj = {"error_list":[{"error_code": "invalid-query-json"}]} else: query_obj = json.loads(query_value) util.trim_object(query_obj) res_obj = util.get_cached_records_direct(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("idmapping_list", traceback.format_exc(), path_obj)
def glycan_to_biosynthesis_enzymes(): res_obj = {} try: query_value = util.get_arg_value("query", request.method) if query_value == "": res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]} elif util.is_valid_json(query_value) == False: res_obj = {"error_list":[{"error_code": "invalid-query-json"}]} else: query_obj = json.loads(query_value) util.trim_object(query_obj) res_obj = apilib.glycan_to_biosynthesis_enzymes(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("glycan_to_biosynthesis_enzymes_direct", traceback.format_exc(), path_obj)
def protein_search(): res_obj = {} try: query_value = util.get_arg_value("query", request.method) if query_value == "": res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]} elif util.is_valid_json(query_value) == False: res_obj = {"error_list":[{"error_code": "invalid-query-json"}]} else: query_obj = json.loads(query_value) util.trim_object(query_obj) res_obj = apilib.protein_search(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("protein_search", traceback.format_exc(), path_obj)
def site_detail(site_id): res_obj = {} try: if site_id in ["", "empty"]: res_obj = { "error_list": [{ "error_code": "missing-parameter", "field": "site_id" }] } else: query_obj = {"site_id": site_id} util.trim_object(query_obj) res_obj = apilib.site_detail(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("site_detail", traceback.format_exc(), path_obj)
def glycan_image(glytoucan_ac): res_obj = {} try: if glytoucan_ac in ["", "empty"]: res_obj = { "error_list": [{ "error_code": "missing-parameter", "field": "glytoucan_ac" }] } else: query_obj = {"glytoucan_ac": glytoucan_ac} img_file = apilib.glycan_image(query_obj, config_obj) return send_file(img_file, mimetype='image/png') except Exception, e: res_obj = errorlib.get_error_obj("glycan_image", traceback.format_exc(), path_obj)
def glycan_detail(glytoucan_ac): res_obj = {} try: if glytoucan_ac in ["", "empty"]: res_obj = { "error_list": [{ "error_code": "missing-parameter", "field": "glytoucan_ac" }] } else: query_obj = {"glytoucan_ac": glytoucan_ac} util.trim_object(query_obj) res_obj = apilib.glycan_detail(query_obj, config_obj) except Exception, e: res_obj = errorlib.get_error_obj("glycan_detail", traceback.format_exc(), path_obj)
def categorized_typeahead(): res_obj = [] try: query_value = util.get_arg_value("query", request.method) if query_value == "": res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]} elif util.is_valid_json(query_value) == False: res_obj = {"error_list":[{"error_code": "invalid-query-json"}]} else: query_obj = json.loads(query_value) util.trim_object(query_obj) tmp_obj = apilib.categorized_typeahead(query_obj, config_obj) if "error_list" in tmp_obj: res_obj = tmp_obj else: res_obj = tmp_obj except Exception, e: res_obj = errorlib.get_error_obj("categorized_typeahead", traceback.format_exc(), path_obj)