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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zero-size array to reduction operation maximum which has no identity #323

Closed olegs closed 1 year ago

olegs commented 1 year ago

Query to reproduce: hematology oncology cannabis

[2023-01-16 08:31:59,009: INFO/MainProcess] Received task: analyze_search_terms[615dbe17-af53-419d-b5a9-1023ba2cfa55]  
[2023-01-16 08:31:59,011: INFO/ForkPoolWorker-12] Analyzing search query
[2023-01-16 08:31:59,012: INFO/ForkPoolWorker-12] Searching 1000 most cited publications matching hematology oncology cannabis
[2023-01-16 08:32:01,117: INFO/ForkPoolWorker-12] Found 2 publications in the database
[2023-01-16 08:32:01,118: INFO/ForkPoolWorker-12] Expanding related papers by references
[2023-01-16 08:32:01,120: WARNING/ForkPoolWorker-12] /home/user/miniconda3/envs/pubtrends/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3474: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
[2023-01-16 08:32:01,121: WARNING/ForkPoolWorker-12] /home/user/miniconda3/envs/pubtrends/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
[2023-01-16 08:32:01,121: WARNING/ForkPoolWorker-12] /home/user/miniconda3/envs/pubtrends/lib/python3.10/site-packages/numpy/core/_methods.py:264: RuntimeWarning: Degrees of freedom <= 0 for slice
  ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
[2023-01-16 08:32:01,121: WARNING/ForkPoolWorker-12] /home/user/miniconda3/envs/pubtrends/lib/python3.10/site-packages/numpy/core/_methods.py:222: RuntimeWarning: invalid value encountered in true_divide
  arrmean = um.true_divide(arrmean, div, out=arrmean, casting='unsafe',
[2023-01-16 08:32:01,121: WARNING/ForkPoolWorker-12] /home/user/miniconda3/envs/pubtrends/lib/python3.10/site-packages/numpy/core/_methods.py:256: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
[2023-01-16 08:32:01,122: ERROR/ForkPoolWorker-12] Task analyze_search_terms[615dbe17-af53-419d-b5a9-1023ba2cfa55] 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/python3.10/site-packages/celery/app/trace.py", line 385, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.10/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 40, 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 180, in amax
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 2791, in amax
    return _wrapreduction(a, np.maximum, 'max', axis, None, out,
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.10/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