500 Server Error and JSONDecodeError When Querying chr05 with MultiQuery

[lyangfan]

Description

When executing the following code using the pyrice library's MultiQuery class to query a genomic region on chromosome 5, the program encountered 500 Server Errors from external services and a subsequent JSONDecodeError during result parsing.

Steps to Reproduce

1. Import the MultiQuery class and initialize an instance.
2. Execute a genomic region query for chromosome 5 (positions 4,319,844 to 4,519,844) with the specified databases:

   from pyrice.multi_query import MultiQuery
   
   query = MultiQuery()
   result = query.query_by_chromosome(
       chro="chr05",
       start_pos="4319844",
       end_pos="4519844",
       number_process=1,
       multi_processing=False,
       multi_threading=False,
       dbs=['oryzabase', 'rapdb', 'gramene', 'funricegene_faminfo', 'funricegene_geneinfo']
   )

Error Output

Server Error: 500
For url:https://snp-seek.irri.org/ws/genomics/gene/osnippo/chr05?start=4319844&end=4519844&model=rap
Server Error: 500
For url:https://snp-seek.irri.org/ws/genomics/gene/osnippo/chr05?start=4319844&end=4519844&model=msu7
---------------------------------------------------------------------------
JSONDecodeError                           Traceback (most recent call last)
[<ipython-input-2-0b35b801d254>](https://localhost:8080/#) in <cell line: 0>()
      2 
      3 query = MultiQuery()
----> 4 result = query.query_by_chromosome(chro="chr05", start_pos="4319844", end_pos="4519844", 
      5                                    number_process = 1, multi_processing=False,
      6                                    multi_threading=False, dbs=['oryzabase', 'rapdb', 'gramene', 'funricegene_faminfo', 'funricegene_geneinfo'])

10 frames
[/usr/local/lib/python3.11/dist-packages/pyrice/multi_query.py](https://localhost:8080/#) in query_by_chromosome(self, chro, start_pos, end_pos, number_process, multi_processing, multi_threading, dbs, query_expansion)
    464         #Query in multi_database
    465         i=1
--> 466         file_id = self.search_on_chromosome(chro=chro,start_pos=start_pos,end_pos=end_pos,number_process = number_process)
    467         self.result = dict()
    468         if query_expansion:

[/usr/local/lib/python3.11/dist-packages/pyrice/multi_query.py](https://localhost:8080/#) in search_on_chromosome(self, chro, start_pos, end_pos, number_process, save_path, dbs)
   1096             p = ThreadPoolExecutor(max_workers=number_process)
   1097             tmp = p.map(self.query,list_key,list_dbs,list_ids)
-> 1098             for t in tmp:
   1099                 if t != None:
   1100                     self.result[t[0]].setdefault(t[1], t[2])

[/usr/lib/python3.11/concurrent/futures/_base.py](https://localhost:8080/#) in result_iterator()
    617                     # Careful not to keep a reference to the popped future
    618                     if timeout is None:
--> 619                         yield _result_or_cancel(fs.pop())
    620                     else:
    621                         yield _result_or_cancel(fs.pop(), end_time - time.monotonic())

[/usr/lib/python3.11/concurrent/futures/_base.py](https://localhost:8080/#) in _result_or_cancel(***failed resolving arguments***)
    315     try:
    316         try:
--> 317             return fut.result(timeout)
    318         finally:
    319             fut.cancel()

[/usr/lib/python3.11/concurrent/futures/_base.py](https://localhost:8080/#) in result(self, timeout)
    454                     raise CancelledError()
    455                 elif self._state == FINISHED:
--> 456                     return self.__get_result()
    457                 else:
    458                     raise TimeoutError()

[/usr/lib/python3.11/concurrent/futures/_base.py](https://localhost:8080/#) in __get_result(self)
    399         if self._exception:
    400             try:
--> 401                 raise self._exception
    402             finally:
    403                 # Break a reference cycle with the exception in self._exception

[/usr/lib/python3.11/concurrent/futures/thread.py](https://localhost:8080/#) in run(self)
     56 
     57         try:
---> 58             result = self.fn(*self.args, **self.kwargs)
     59         except BaseException as exc:
     60             self.future.set_exception(exc)

[/usr/local/lib/python3.11/dist-packages/pyrice/multi_query.py](https://localhost:8080/#) in query(self, iricname, db, qfields, verbose)
    113             if len(res.content) > 3:
    114                 if iricname == "snpseek":
--> 115                     return [iricname,qfields[-1],json.loads(res.content.decode('utf-8'))]
    116                 elif db == "ic4r":
    117                     return [iricname,db,json.loads(res.content.decode('utf-8'))[0][1]]

[/usr/lib/python3.11/json/__init__.py](https://localhost:8080/#) in loads(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    344             parse_int is None and parse_float is None and
    345             parse_constant is None and object_pairs_hook is None and not kw):
--> 346         return _default_decoder.decode(s)
    347     if cls is None:
    348         cls = JSONDecoder

[/usr/lib/python3.11/json/decoder.py](https://localhost:8080/#) in decode(self, s, _w)
    335 
    336         """
--> 337         obj, end = self.raw_decode(s, idx=_w(s, 0).end())
    338         end = _w(s, end).end()
    339         if end != len(s):

[/usr/lib/python3.11/json/decoder.py](https://localhost:8080/#) in raw_decode(self, s, idx)
    353             obj, end = self.scan_once(s, idx)
    354         except StopIteration as err:
--> 355             raise JSONDecodeError("Expecting value", s, err.value) from None
    356         return obj, end

JSONDecodeError: Expecting value: line 1 column 1 (char 0)