Mercurial > repos > bernhardlutz > rest_tool

comparison rest_tool_advanced.py @ 9:80bf0039c0dc draft

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Uploaded
author bernhardlutz
date Fri, 02 May 2014 18:16:36 -0400
parents 3c1e862e8cd6
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8:3c1e862e8cd6 9:80bf0039c0dc
5 5
6 import readfile 6 import readfile
7 7
8 #dicitionary for the output format 8 #dicitionary for the output format
9 9
10 dict_output={"cids" :"txt", "aids" : "txt", "sids" : "txt", "description": "xml", "summary" : "xml", "record" : "csv", "classification": "xml", "targets" : "txt", "xrefs" : "txt", "synonyms" : "txt", "property": "csv" } 10 dict_output={"cids" :"txt", "aids" : "txt", "sids" : "txt", "description": "xml", "summary" : "xml", "record" : "csv", "classification": "xml", "targets" : "txt", "xrefs" : "txt", "synonyms" : "txt", "property": "csv", "doseresponse" : "csv" }
11 11
12 #alles andere ist xml 12 #alles andere ist xml
13 check_for_id_type=["cids", "aids", "sids"] 13 check_for_id_type=["cids", "aids", "sids"]
14
15 post_id_types=["inchi", "sdf", "smiles"]
14 16
15 id_dict={"compound": "cid", "assay": "aid", "substance" : "sid" } 17 id_dict={"compound": "cid", "assay": "aid", "substance" : "sid" }
16 18
17 def getListString(args): 19 def getListString(args):
18 if args.id_type_ff == "file": 20 if args.id_type_ff == "file":
19 #build comma list 21 #build comma list
20 list_string=",".join(getListFromFile(open(args.id_value,"r"))) 22 list_string=",".join(getListFromFile(open(args.id_value,"r")))
21 else: 23 else:
22 list_string=args.id_value 24 print (args.id_value)
25 list_string=args.id_value.strip().replace("__cr____cn__", ",")
23 return list_string 26 return list_string
24 27
25 28
26 def main(args): 29 def main(args):
27
28 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/" 30 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
29 url+=args.id_type+"/" 31 url+=args.id_type+"/"
30 if args.id_type ==id_dict[args.type]: 32 # check if we are post then skip this part otherwise put the ids in the url
31 url+=getListString(args)+"/" 33 if not args.id_type in post_id_types:
32 else: 34 if args.id_type ==id_dict[args.type]:
33 url+=args.id_value+"/" 35 url+=getListString(args)+"/"
36 else:
37 url+=args.id_value+"/"
38
34 url+=args.operation+"/" 39 url+=args.operation+"/"
35 if args.operation == "target" or args.operation == "property" or args.operation == "xrefs": 40 if args.operation == "target" or args.operation == "property" or args.operation == "xrefs":
36 url+=args.operation_value+"/" 41 url+=args.operation_value+"/"
37 42
38 url+=dict_output[args.operation] 43 if args.operation == "xrefs":
39 if args.operation in check_for_id_type: 44 if "," in args.operation_value:
40 url+="?"+args.operation+"_type="+args.ids_operation_type 45 url+="xml"
46 else:
47 url+="txt"
48 else:
49 url+=dict_output[args.operation]
50 if args.operation in check_for_id_type and args.id_type not in post_id_types:
51 url+="?%s_type=%s" % (args.operation, args.ids_operation_type)
41 print(url) 52 print(url)
42 readfile.store_result(url, args.outfile) 53 if args.id_type in post_id_types:
43 54 postfile=open(args.id_value,"r")
44 55 post_value=postfile.read()
45 56 post_dict={args.id_type : post_value}
46 57 print(post_dict)
58 readfile.store_result_post(url, post_dict, args.outfile)
59 else:
60 readfile.store_result_get(url, args.outfile)
47 if __name__ == "__main__": 61 if __name__ == "__main__":
48 parser = argparse.ArgumentParser() 62 parser = argparse.ArgumentParser()
49 parser.add_argument('--type', type=str, required=True, 63 parser.add_argument('--type', type=str, required=True,
50 help="That you want BioAssay Compund ...") 64 help="That you want BioAssay Compund ...")
51 parser.add_argument('--id-type', type=str, 65 parser.add_argument('--id-type', type=str,