def search_init():
res_obj = {}
try:
res_obj = apilib.search_init(config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("idmapping_search_init", traceback.format_exc(), path_obj)
def search():
form_dict = cgi.FieldStorage()
record_type = form_dict["recordtype"].value
input_namespace = form_dict["input_namespace"].value
output_namespace = form_dict["output_namespace"].value
input_idlist = []
if "userfile" in form_dict:
file_buffer = form_dict["userfile"].file.read()
file_buffer = file_buffer.replace("\r", "\n")
file_buffer = file_buffer.replace("\n\n", "\n")
line_list = file_buffer.split("\n")
for line in line_list:
if line.strip() != "" and line.strip() not in input_idlist:
input_idlist.append(line.strip())
if "input_idlist" in form_dict:
if form_dict["input_idlist"].value.strip() != "":
for word in form_dict["input_idlist"].value.split(","):
if word.strip() not in input_idlist:
input_idlist.append(word.strip())
query_obj = {"input_idlist":input_idlist, "recordtype":record_type,
"input_namespace":input_namespace, "output_namespace":output_namespace}
res_obj = {}
try:
res_obj = apilib.search(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("idmapping_search", traceback.format_exc(), path_obj)
def protein_search_init():
res_obj = {}
try:
res_obj = apilib.protein_search_init(config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("protein_search_init", traceback.format_exc(), path_obj)
def typeahead():
res_obj = []
try:
query_value = util.get_arg_value("query", request.method)
if query_value == "":
res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]}
elif util.is_valid_json(query_value) == False:
res_obj = {"error_list":[{"error_code": "invalid-query-json"}]}
else:
query_obj = json.loads(query_value)
util.trim_object(query_obj)
field_list_one = ["glytoucan_ac", "motif_name", "enzyme_uniprot_canonical_ac",
"glycan_pmid", "enzyme"]
field_list_two = ["uniprot_canonical_ac", "uniprot_id", "refseq_ac",
"protein_name", "gene_name", "pathway_id", "pathway_name",
"disease_name","disease_id",
"go_id", "go_term", "protein_pmid"]
tmp_obj_one, tmp_obj_two = [], []
if query_obj["field"] in field_list_one:
tmp_obj_one = apilib.glycan_typeahead(query_obj, config_obj)
if query_obj["field"] in field_list_two:
tmp_obj_two = apilib.protein_typeahead(query_obj, config_obj)
if "error_list" in tmp_obj_one:
res_obj = tmp_obj_one
elif "error_list" in tmp_obj_two:
res_obj = tmp_obj_two
else:
res_obj = tmp_obj_one + tmp_obj_two
except Exception, e:
res_obj = errorlib.get_error_obj("typeahead", traceback.format_exc(), path_obj)
def misc_messagelist():
res_obj = {}
try:
res_obj = apilib.messagelist(config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("misc_messagelist", traceback.format_exc(), path_obj)
def home_init():
res_obj = {}
try:
res_obj = apilib.home_init(config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("home_init", traceback.format_exc(),
path_obj)
def protein_detail(uniprot_canonical_ac):
res_obj = {}
try:
if uniprot_canonical_ac in ["", "empty"]:
res_obj = {"error_list":[{"error_code":"missing-parameter", "field":"uniprot_canonical_ac"}]}
else:
query_obj = {"uniprot_canonical_ac":uniprot_canonical_ac}
util.trim_object(query_obj)
res_obj = apilib.protein_detail(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("protein_detail", traceback.format_exc(), path_obj)
def idmapping_list():
res_obj = {}
try:
query_value = util.get_arg_value("query", request.method)
if query_value == "":
res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]}
elif util.is_valid_json(query_value) == False:
res_obj = {"error_list":[{"error_code": "invalid-query-json"}]}
else:
query_obj = json.loads(query_value)
util.trim_object(query_obj)
res_obj = util.get_cached_records_direct(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("idmapping_list", traceback.format_exc(), path_obj)
def glycan_to_biosynthesis_enzymes():
res_obj = {}
try:
query_value = util.get_arg_value("query", request.method)
if query_value == "":
res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]}
elif util.is_valid_json(query_value) == False:
res_obj = {"error_list":[{"error_code": "invalid-query-json"}]}
else:
query_obj = json.loads(query_value)
util.trim_object(query_obj)
res_obj = apilib.glycan_to_biosynthesis_enzymes(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("glycan_to_biosynthesis_enzymes_direct", traceback.format_exc(), path_obj)
def protein_search():
res_obj = {}
try:
query_value = util.get_arg_value("query", request.method)
if query_value == "":
res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]}
elif util.is_valid_json(query_value) == False:
res_obj = {"error_list":[{"error_code": "invalid-query-json"}]}
else:
query_obj = json.loads(query_value)
util.trim_object(query_obj)
res_obj = apilib.protein_search(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("protein_search", traceback.format_exc(), path_obj)
def site_detail(site_id):
res_obj = {}
try:
if site_id in ["", "empty"]:
res_obj = {
"error_list": [{
"error_code": "missing-parameter",
"field": "site_id"
}]
}
else:
query_obj = {"site_id": site_id}
util.trim_object(query_obj)
res_obj = apilib.site_detail(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("site_detail", traceback.format_exc(),
path_obj)
def glycan_image(glytoucan_ac):
res_obj = {}
try:
if glytoucan_ac in ["", "empty"]:
res_obj = {
"error_list": [{
"error_code": "missing-parameter",
"field": "glytoucan_ac"
}]
}
else:
query_obj = {"glytoucan_ac": glytoucan_ac}
img_file = apilib.glycan_image(query_obj, config_obj)
return send_file(img_file, mimetype='image/png')
except Exception, e:
res_obj = errorlib.get_error_obj("glycan_image",
traceback.format_exc(), path_obj)
def glycan_detail(glytoucan_ac):
res_obj = {}
try:
if glytoucan_ac in ["", "empty"]:
res_obj = {
"error_list": [{
"error_code": "missing-parameter",
"field": "glytoucan_ac"
}]
}
else:
query_obj = {"glytoucan_ac": glytoucan_ac}
util.trim_object(query_obj)
res_obj = apilib.glycan_detail(query_obj, config_obj)
except Exception, e:
res_obj = errorlib.get_error_obj("glycan_detail",
traceback.format_exc(), path_obj)
def categorized_typeahead():
res_obj = []
try:
query_value = util.get_arg_value("query", request.method)
if query_value == "":
res_obj = {"error_list":[{"error_code": "missing-query-key-in-query-json"}]}
elif util.is_valid_json(query_value) == False:
res_obj = {"error_list":[{"error_code": "invalid-query-json"}]}
else:
query_obj = json.loads(query_value)
util.trim_object(query_obj)
tmp_obj = apilib.categorized_typeahead(query_obj, config_obj)
if "error_list" in tmp_obj:
res_obj = tmp_obj
else:
res_obj = tmp_obj
except Exception, e:
res_obj = errorlib.get_error_obj("categorized_typeahead", traceback.format_exc(), path_obj)
