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()
