def main(args): if args.aid_file is None: aidlist = args.aid.split(",") else: aidlist = readfile.getListFromFile(args.aid_file) aidliststring = ",".join(aidlist) url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/" + aidliststring + "/cids/xml" print('The constructed REST URL is: %s' % url) dic = rest_tool_functions.get_dict_key_value(url, "AID", "CID") rest_tool_functions.write_to_sf(dic, args.outfile, "\t")
def main(args): if args.aid_file is None: aidlist = args.aid.split(",") else: aidlist = readfile.getListFromFile(args.aid_file) aidliststring = ",".join(aidlist) url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/xml" print('The constructed REST URL is: %s' % url) dic = rest_tool_functions.get_dict_key_value(url, "AID", "CID") rest_tool_functions.write_to_sf(dic, args.outfile, "\t")
def main(args): url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/%s/%s/" % (args.type, args.id_type) # check if we are POST then skip this part otherwise insert the ids into the url if not args.id_type in post_id_types: if args.id_type == id_dict[args.type]: url += readfile.getListString(args) + "/" else: url += args.id_value + "/" url += args.operation + "/" if args.operation in ["target", "property", "xrefs"]: url += args.operation_value + "/" create_dict_tsv = False if args.operation == "xrefs": if "," in args.operation_value: url += "xml" else: url += "txt" else: if args.operation in check_for_id_type: # dont create dictionary if they are the same if dic_key_value_type[args.type] == dic_key_value_operation[ args.operation]: url += "txt" else: url += "xml" create_dict_tsv = True else: url += dict_output[args.operation] if args.operation in check_for_id_type and args.id_type not in post_id_types: url += "?%s_type=%s" % (args.operation, args.ids_operation_type) print('The constructed REST URL is: %s' % url) if args.id_type in post_id_types: postfile = open(args.id_value, "r") post_value = postfile.read() post_dict = {args.id_type: post_value} #print(post_dict) readfile.store_result_post(url, post_dict, args.outfile) # check if we have to create a tsv file elif create_dict_tsv == True: key = dic_key_value_type[args.type] value = dic_key_value_operation[args.operation] dic = rest_tool_functions.get_dict_key_value(url, key, value) rest_tool_functions.write_to_sf(dic, args.outfile, "\t") else: readfile.store_result_get(url, args.outfile)
def main(args): url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/" url+=args.id_type+"/" # check if we are post then skip this part otherwise put the ids in the url if not args.id_type in post_id_types: if args.id_type ==id_dict[args.type]: url+=readfile.getListString(args)+"/" else: url+=args.id_value+"/" url+=args.operation+"/" if args.operation == "target" or args.operation == "property" or args.operation == "xrefs": url+=args.operation_value+"/" create_dict_tsv=False if args.operation == "xrefs": if "," in args.operation_value: url+="xml" else: url+="txt" else: if args.operation in check_for_id_type: # dont create dictionary if they are the same if dic_key_value_type[args.type] == dic_key_value_operation[args.operation]: url+="txt" else: url+="xml" create_dict_tsv=True else: url+=dict_output[args.operation] if args.operation in check_for_id_type and args.id_type not in post_id_types: url+="?%s_type=%s" % (args.operation, args.ids_operation_type) print(url) if args.id_type in post_id_types: postfile=open(args.id_value,"r") post_value=postfile.read() post_dict={args.id_type : post_value} print(post_dict) readfile.store_result_post(url, post_dict, args.outfile) # check if have to create a tsv file elif create_dict_tsv == True: key=dic_key_value_type[args.type] value=dic_key_value_operation[args.operation] dic=rest_tool_functions.get_dict_key_value(url, key, value) rest_tool_functions.write_to_sf(dic, args.outfile, "\t") else: readfile.store_result_get(url, args.outfile)