def schemas():
byc = initialize_service()
create_empty_service_response(byc)
s_path = path.join( pkg_path, "schemas" )
s_files = [ f.name for f in scandir(s_path) if f.is_file() ]
s_files = [ f for f in s_files if f.endswith(".yaml") ]
s_files = [ f for f in s_files if not f.startswith("_") ]
# commenting beacon since remote $ref are not handled yet
# s_files = [ f for f in s_files if not f.startswith("beacon") ]
schema_name = rest_path_value("schemas")
if schema_name is not False:
for s_f in s_files:
f_name = os.path.splitext( s_f )[0]
if f_name == schema_name:
s = read_schema_files(f_name, "")
if "$id" in s:
byc["service_response"]["meta"]["returned_schemas"] = [ s["$id"] ]
populate_service_response(byc, [s])
cgi_print_json_response( byc, 200 )
exit()
response_add_error(byc, 422, "No correct schema name provided!")
cgi_print_json_response( byc, 422 )
def geolocations():
byc = initialize_service()
# for the geolocs database, not the provenance object
byc["geoloc_definitions"]["geo_root"] = "geo_location"
create_empty_service_response(byc)
query, geo_pars = geo_query(**byc)
for g_k, g_v in geo_pars.items():
response_add_parameter(byc, g_k, g_v)
if len(query.keys()) < 1:
response_add_error(
byc, 422, "No query generated - missing or malformed parameters")
cgi_break_on_errors(byc)
results, e = mongo_result_list(byc["geo_db"], byc["geo_coll"], query,
{'_id': False})
if e:
response_add_error(byc, 422, e)
cgi_break_on_errors(byc)
populate_service_response(byc, results)
cgi_print_json_response(byc, 200)
def info():
byc = initialize_service()
parse_beacon_schema(byc)
create_empty_service_response(byc)
byc["beacon_info"].update({"datasets": datasets_update_latest_stats(byc)})
populate_service_response(byc, [byc["beacon_info"]])
cgi_print_json_response(byc, 200)
def services(service):
set_debug_state(debug=0)
uri = environ.get('REQUEST_URI')
these_prefs = read_local_prefs("service_mappings", dir_path)
rest_base_name = "services"
if path in these_prefs["service_names"]:
service_name = path
else:
service_name = rest_path_value(rest_base_name)
if service_name in these_prefs["service_names"]:
f = these_prefs["service_names"][service_name]
# dynamic package/function loading
try:
mod = import_module(f)
serv = getattr(mod, f)
serv()
exit()
except Exception as e:
print('Content-Type: text')
print('status:422')
print()
print('Service {} error: {}'.format(f, e))
exit()
if service_name in these_prefs["rewrites"]:
pat = re.compile(rf"^.+\/{service_name}\/?(.*?)$")
if pat.match(uri):
stuff = pat.match(uri).group(1)
cgi_print_rewrite_response(these_prefs["rewrites"][service_name],
stuff)
cgi_print_json_response(
{
"service_response": {
"response": {
"error": {
"error_code":
422,
"error_message":
"No correct service path provided. Please refer to the documentation at http://info.progenetix.org/tags/services"
},
}
}
}, 422)
def datasets():
byc = initialize_service()
parse_beacon_schema(byc)
select_dataset_ids(byc)
check_dataset_ids(byc)
_get_history_depth(byc)
create_empty_service_response(byc)
results = datasets_update_latest_stats(byc)
populate_service_response(byc, results)
cgi_print_json_response(byc, 200)
def dbstats():
byc = initialize_service()
select_dataset_ids(byc)
check_dataset_ids(byc)
if "statsNumber" in byc["form_data"]:
s_n = byc["form_data"].getvalue("statsNumber")
try:
s_n = int(s_n)
except:
pass
if type(s_n) == int:
if s_n > 0:
byc["stats_number"] = s_n
create_empty_service_response(byc)
ds_stats = dbstats_return_latest(byc)
results = []
for stat in ds_stats:
byc["service_response"]["response"]["info"].update(
{"date": stat["date"]})
for ds_id, ds_vs in stat["datasets"].items():
if len(byc["dataset_ids"]) > 0:
if not ds_id in byc["dataset_ids"]:
continue
dbs = {"dataset_id": ds_id}
for k in byc["these_prefs"]["methods"][byc["method"]]:
dbs.update({k: ds_vs[k]})
results.append(dbs)
populate_service_response(byc, results)
cgi_print_json_response(byc, 200)