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Notebook NotJSONError #227

Closed avivajpeyi closed 2 years ago

avivajpeyi commented 2 years ago 
 cat july12_cat/log_pe/pe_28112378_502.log
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
[00:00:05 - TESS-ATLAS-RUNNER] run_toi(626)
Traceback (most recent call last):
  File "/fred/oz200/avajpeyi/envs/tess/lib/python3.8/site-packages/nbformat/reader.py", line 14, in parse_json
    nb_dict = json.loads(s, **kwargs)
  File "/apps/sandybridge/software/Python/3.8.5-gni-2020.0/lib/python3.8/json/__init__.py", line 357, in loads
    return _default_decoder.decode(s)
  File "/apps/sandybridge/software/Python/3.8.5-gni-2020.0/lib/python3.8/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/apps/sandybridge/software/Python/3.8.5-gni-2020.0/lib/python3.8/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/fred/oz200/avajpeyi/envs/tess/bin/run_toi", line 11, in <module>
    load_entry_point('tess-atlas', 'console_scripts', 'run_toi')()
  File "/fred/oz200/avajpeyi/projects/tess-atlas/src/tess_atlas/notebook_preprocessors/run_toi.py", line 109, in main
    success, run_duration = run_toi(toi_number, outdir, quickrun, setup)
  File "/fred/oz200/avajpeyi/projects/tess-atlas/src/tess_atlas/notebook_preprocessors/run_toi.py", line 79, in run_toi
    execution_successful = execute_ipynb(notebook_filename)
  File "/fred/oz200/avajpeyi/projects/tess-atlas/src/tess_atlas/notebook_preprocessors/notebook_executor.py", line 17, in execute_ipynb
    notebook = nbformat.read(f, as_version=4)
  File "/fred/oz200/avajpeyi/envs/tess/lib/python3.8/site-packages/nbformat/__init__.py", line 143, in read
    return reads(buf, as_version, **kwargs)
  File "/fred/oz200/avajpeyi/envs/tess/lib/python3.8/site-packages/nbformat/__init__.py", line 73, in reads
    nb = reader.reads(s, **kwargs)
  File "/fred/oz200/avajpeyi/envs/tess/lib/python3.8/site-packages/nbformat/reader.py", line 58, in reads
    nb_dict = parse_json(s, **kwargs)
  File "/fred/oz200/avajpeyi/envs/tess/lib/python3.8/site-packages/nbformat/reader.py", line 17, in parse_json
    raise NotJSONError(("Notebook does not appear to be JSON: %r" % s)[:77] + "...") from e
nbformat.reader.NotJSONError: Notebook does not appear to be JSON: ''...
srun: error: john14: task 0: Exited with exit code 1
srun: launch/slurm: _step_signal: Terminating StepId=28116418.0