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)
