def usecases_search_init(): res_obj = {} try: res_obj = apilib.usecases_search_init(db_obj) except Exception, e: res_obj = apilib.get_error_obj("usecases_search_init", traceback.format_exc(), path_obj)
def glycan_to_enzyme_gene_loci(tax_id, glytoucan_ac): res_obj = {} try: if glytoucan_ac in ["", "empty"] or tax_id in ["", "empty"]: res_obj = {"error_code": "missing-parameter"} else: query_obj = {"glytoucan_ac": glytoucan_ac, "tax_id": int(tax_id)} trim_object(query_obj) res_obj = apilib.glycan_to_enzyme_gene_loci(query_obj, db_obj) except Exception, e: res_obj = apilib.get_error_obj("glycan_to_enzyme_gene_loci", traceback.format_exc(), path_obj)
def species_to_glycoproteins(tax_id, evidence_type): res_obj = {} try: if evidence_type in ["", "empty"] or tax_id in ["", "empty"]: res_obj = {"error_code": "missing-parameter"} else: query_obj = {"evidence_type": evidence_type, "tax_id": int(tax_id)} trim_object(query_obj) res_obj = apilib.species_to_glycoproteins(query_obj, db_obj) except Exception, e: res_obj = apilib.get_error_obj("species_to_glycoproteins", traceback.format_exc(), path_obj)
def species_to_glycohydrolases(tax_id): res_obj = {} try: if tax_id in ["", "empty"]: res_obj = {"error_code": "missing-parameter"} else: query_obj = {"tax_id": int(tax_id)} trim_object(query_obj) res_obj = apilib.species_to_glycohydrolases(query_obj, db_obj) except Exception, e: res_obj = apilib.get_error_obj("species_to_glycohydrolases", traceback.format_exc(), path_obj)
def protein_to_orthologs(uniprot_canonical_ac): res_obj = {} try: if uniprot_canonical_ac in ["", "empty"]: res_obj = {"error_code": "missing-parameter"} else: query_obj = {"uniprot_canonical_ac": uniprot_canonical_ac} trim_object(query_obj) res_obj = apilib.protein_to_orthologs(query_obj, db_obj) except Exception, e: res_obj = apilib.get_error_obj("protein_to_orthologs", traceback.format_exc(), path_obj)
def biosynthesis_enzyme_to_glycans(tax_id, uniprot_canonical_ac): res_obj = {} try: if uniprot_canonical_ac in ["", "empty"] or tax_id in ["", "empty"]: res_obj = {"error_code": "missing-parameter"} else: query_obj = { "uniprot_canonical_ac": uniprot_canonical_ac, "tax_id": int(tax_id) } trim_object(query_obj) res_obj = apilib.biosynthesis_enzyme_to_glycans(query_obj, db_obj) except Exception, e: res_obj = apilib.get_error_obj("biosynthesis_enzyme_to_glycans", traceback.format_exc(), path_obj)
def ortholog_list(): res_obj = {} try: query_value = get_arg_value("query", request.method) if query_value == "": res_obj = {"error_code": "missing-query-key-in-query-json"} elif apilib.is_valid_json(query_value) == False: res_obj = {"error_code": "invalid-query-json"} else: query_obj = json.loads(query_value) trim_object(query_obj) res_obj = apilib.ortholog_list(query_obj, db_obj) except Exception, e: res_obj = apilib.get_error_obj("ortholog_list", traceback.format_exc(), path_obj)
def main(): usage = "\n%prog [options]" parser = OptionParser(usage, version="%prog version___") parser.add_option("-s", "--svctype", action="store", dest="svctype", help="SVC name") parser.add_option("-q", "--queryfile", action="store", dest="queryfile", help="Query JSON file") (options, args) = parser.parse_args() for key in ([options.queryfile, options.svctype]): if not (key): parser.print_help() sys.exit(0) global config_obj global path_obj config_obj = json.loads(open("./conf/config.json", "r").read()) path_obj = config_obj[config_obj["server"]]["pathinfo"] db_obj = config_obj[config_obj["server"]]["dbinfo"] res_obj = {} query_obj = json.loads(open(options.queryfile, "r").read()) svc_type = options.svctype try: if svc_type == "search_init": res_obj = apilib.protein_search_init(db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "glycan_to_biosynthesis_enzymes": res_obj = apilib.glycan_to_biosynthesis_enzymes(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "glycan_to_glycoproteins": res_obj = apilib.glycan_to_glycoproteins(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "species_to_glycosyltransferases": res_obj = apilib.species_to_glycosyltransferases(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "species_to_glycohydrolases": res_obj = apilib.species_to_glycohydrolases(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "species_to_glycoproteins": res_obj = apilib.species_to_glycoproteins(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "disease_to_glycosyltransferases": res_obj = apilib.disease_to_glycosyltransferases(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "protein_to_orthologs": res_obj = apilib.protein_to_orthologs(query_obj, db_obj) print json.dumps(res_obj, indent=4) elif svc_type == "glycan_to_enzyme_gene_loci": res_obj = apilib.glycan_to_enzyme_gene_loci(query_obj, db_obj) print json.dumps(res_obj, indent=4) except Exception, e: res_obj = apilib.get_error_obj("proteinsearch", traceback.format_exc(), path_obj) print traceback.format_exc()