Mercurial > repos > bernhardlutz > rest_tool
view rest_tool_advanced.py @ 9:80bf0039c0dc draft
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author | bernhardlutz |
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date | Fri, 02 May 2014 18:16:36 -0400 |
parents | 3c1e862e8cd6 |
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#!/usr/bin/env python import sys, os import argparse import readfile #dicitionary for the output format 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" } #alles andere ist xml check_for_id_type=["cids", "aids", "sids"] post_id_types=["inchi", "sdf", "smiles"] id_dict={"compound": "cid", "assay": "aid", "substance" : "sid" } def getListString(args): if args.id_type_ff == "file": #build comma list list_string=",".join(getListFromFile(open(args.id_value,"r"))) else: print (args.id_value) list_string=args.id_value.strip().replace("__cr____cn__", ",") return list_string 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+=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+"/" if args.operation == "xrefs": if "," in args.operation_value: url+="xml" else: url+="txt" 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) else: readfile.store_result_get(url, args.outfile) if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('--type', type=str, required=True, help="That you want BioAssay Compund ...") parser.add_argument('--id-type', type=str, help="Specify the ID type") parser.add_argument('--operation', type=str, required=True, help="Specify the operation") parser.add_argument('--operation-value', dest="operation_value", type=str, required=False, help="Specify the additional operation value") parser.add_argument('--xref-operation-value', dest="xref_operation_value", type=str, required=False, help="Specify the xref operation ") parser.add_argument('--ids-operation-type', dest="ids_operation_type", type=str, required=False, help="all inactive ...") parser.add_argument('--xref', dest="xref", type=str, help="use xref to identify the searched thing") parser.add_argument('--xref-value', dest="xref_value", type=str, help="Specify the xref") parser.add_argument('--property-value', dest="property_value", type=str, help="Specify the property value") parser.add_argument('--id-type-ff', dest="id_type_ff", type=str, help="file or field") parser.add_argument('--id-value', dest="id_value", type=str, required=True, help="Specify the id") parser.add_argument('--outfile', type=argparse.FileType('w'), required=True, help="Specify the output file") if len(sys.argv) < 8: print "Too few arguments..." parser.print_help() exit(1) args = parser.parse_args() main( args )