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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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Failed to analyze fresh paper without any references or citations in the PubMed database #309

Closed olegs closed 2 years ago

olegs commented 2 years ago

Paper title: Semi-supervised peak calling with SPAN and JBR Genome Browser

[2022-01-24 13:10:25,676: ERROR/ForkPoolWorker-2] Task analyze_search_paper[56244586-c2cd-4ba5-a67a-d20ecf3e79e9] raised unexpected: ValueError('Out of range float values are not JSON compliant')
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 149, in analyze_search_paper
    return _analyze_id_list(
  File "/home/user/pysrc/celery/tasks_main.py", line 128, in _analyze_id_list
    visualization = visualize_analysis(analyzer)
  File "/home/user/pysrc/papers/plot/plotter.py", line 66, in visualize_analysis
    most_cited_per_year_papers=[components(plotter.plot_most_cited_per_year_papers())],
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/bokeh/embed/standalone.py", line 217, in components
    (docs_json, [render_item]) = standalone_docs_json_and_render_items(models)
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/bokeh/embed/util.py", line 294, in standalone_docs_json_and_render_items
    docs_json[docid] = doc.to_json()
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/bokeh/document/document.py", line 882, in to_json
    doc_json = self.to_json_string()
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/bokeh/document/document.py", line 911, in to_json_string
    return serialize_json(json, indent=indent)
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/site-packages/bokeh/core/json_encoder.py", line 166, in serialize_json
    return json.dumps(obj, cls=BokehJSONEncoder, allow_nan=False, indent=indent, separators=separators, sort_keys=True, **kwargs)
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/json/__init__.py", line 234, in dumps
    return cls(
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/home/user/miniconda3/envs/pubtrends/lib/python3.8/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)