Pharmacokinetics exception in codeine/Loetsch2006

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INFO Upload /var/git/pkdb_data/studies/codeine/Loetsch2006
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INFO Start indexing PKDB00098
INFO - 0.25 [s] : Created TSVs ['Fig2', 'Tab1']
INFO - 0.08 [s] : Upload references
INFO - 0.24 [s] : Upload files
INFO - 0.13 [s] : Upload core study
INFO - 0.46 [s] : Upload groups
INFO Finished indexing PKDB00098 in 1.44 [s]
INFO - 1.20 [s] : Upload individuals
INFO Finished indexing PKDB00097 in 6.90 [s]
WARNING 
{
  "pharmacokinetics exception": "Traceback (most recent call last):\n  File \"/code/pkdb_app/outputs/serializers.py\", line 381, in create\n    outputs = pkoutputs_from_timecourse(timecourse)\n  File \"/code/pkdb_app/outputs/pk_calculation.py\", line 42, in pkoutputs_from_timecourse\n    pkinf = pharmacokinetics.TimecoursePKNoDosing(**variables)\n  File \"/src/pkdb-analysis/pkdb_analysis/pk/pharmacokinetics.py\", line 87, in __init__\n    self._init(time, concentration, ureg, substance, min_treshold, **kwargs)\n  File \"/src/pkdb-analysis/pkdb_analysis/pk/pharmacokinetics.py\", line 110, in _init\n    cmin = np.nanmin(concentration[np.nonzero(concentration)])  # only take non-zero values\n  File \"<__array_function__ internals>\", line 6, in nanmin\n  File \"/usr/local/lib/python3.7/site-packages/pint/quantity.py\", line 1552, in __array_function__\n    return numpy_wrap(\"function\", func, args, kwargs, types)\n  File \"/usr/local/lib/python3.7/site-packages/pint/numpy_func.py\", line 893, in numpy_wrap\n    return handled[name](*args, **kwargs)\n  File \"/usr/local/lib/python3.7/site-packages/pint/numpy_func.py\", line 727, in implementation\n    ret = func(*bound_args.args, **bound_args.kwargs)\n  File \"<__array_function__ internals>\", line 6, in nanmin\n  File \"/usr/local/lib/python3.7/site-packages/numpy/lib/nanfunctions.py\", line 321, in nanmin\n    res = np.fmin.reduce(a, axis=axis, out=out, **kwargs)\nValueError: zero-size array to reduction operation fmin which has no identity\n"
}
matthiaskoenig / pkdb

Pharmacokinetics exception in codeine/Loetsch2006 #571
