JetBrains-Research / pubtrends

Scientific literature explorer. Runs a Pubmed or Semantic Scholar search and allows user to explore high-level structure of result papers
Apache License 2.0
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ValueError: zero-size array to reduction operation maximum which has no identity #313

Open olegs opened 2 years ago

olegs commented 2 years ago
[2022-06-02 04:03:50,890: INFO/MainProcess] Received task: analyze_search_terms[5a3f682d-4a5a-4f1b-b64f-73f72e7e16f3]  
[2022-06-02 04:03:50,892: INFO/ForkPoolWorker-2] Analyzing search query
[2022-06-02 04:03:50,893: INFO/ForkPoolWorker-2] Searching 1000 most cited publications matching "pan genome" software
[2022-06-02 04:03:51,237: INFO/ForkPoolWorker-2] Found 2 publications in the database
[2022-06-02 04:03:51,238: INFO/ForkPoolWorker-2] Expanding related papers by references
[2022-06-02 04:03:51,242: WARNING/ForkPoolWorker-2] /home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
[2022-06-02 04:03:51,242: WARNING/ForkPoolWorker-2] /home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
[2022-06-02 04:03:51,242: WARNING/ForkPoolWorker-2] /home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/_methods.py:262: RuntimeWarning: Degrees of freedom <= 0 for slice
  ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
[2022-06-02 04:03:51,242: WARNING/ForkPoolWorker-2] /home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/_methods.py:222: RuntimeWarning: invalid value encountered in true_divide
  arrmean = um.true_divide(arrmean, div, out=arrmean, casting='unsafe',
[2022-06-02 04:03:51,242: WARNING/ForkPoolWorker-2] /home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
[2022-06-02 04:03:51,244: ERROR/ForkPoolWorker-2] Task analyze_search_terms[5a3f682d-4a5a-4f1b-b64f-73f72e7e16f3] raised unexpected: ValueError('zero-size array to reduction operation maximum which has no identity')
Traceback (most recent call last):
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/celery/app/trace.py", line 385, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/celery/app/trace.py", line 650, in __protected_call__
    return self.run(*args, **kwargs)
  File "/home/user/pysrc/celery/tasks_main.py", line 37, in analyze_search_terms
    ids = expand_ids(loader=loader, ids=ids, single_paper=False,
  File "/home/user/pysrc/papers/analysis/expand.py", line 45, in expand_ids
    cit_mean, cit_std = estimate_citations(ids, single_paper, loader,
  File "/home/user/pysrc/papers/analysis/expand.py", line 142, in estimate_citations
    logger.debug(f'Filtered citations min={np.mean(filtered)}, max={np.max(filtered)}, mean={mean}, std={std}')
  File "<__array_function__ internals>", line 5, in amax
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 2754, in amax
    return _wrapreduction(a, np.maximum, 'max', axis, None, out,
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation maximum which has no identity