codeine/Loetsch2006 and glucose/Prager1986 not uploading

[janekg89]

Bug probably in pharmacokinetics.

[matthiaskoenig]

Could you add the detailed error report.

[janekg89]

(pkdb_data) janek@dell-desktop:~/Dev/pkdb_data$ upload_study -s studies/codeine/Loetsch2006/
INFO --------------------------------------------------------------------------------
INFO Upload studies/codeine/Loetsch2006/
INFO --------------------------------------------------------------------------------
INFO - 0.16 [s] : Created TSVs ['Fig2', 'Tab1', 'TabData']
INFO - 0.11 [s] : Upload references
INFO - 0.39 [s] : Upload files
INFO - 0.10 [s] : Upload core study
INFO - 0.31 [s] : Upload groups
INFO - 0.82 [s] : Upload individuals
WARNING 
{
  "pharmacokinetics exception": "Traceback (most recent call last):\n  File \"/code/pkdb_app/data/serializers.py\", line 76, in calculate_pks_from_timecourses\n    outputs = pkoutputs_from_timecourse(subset)\n  File \"/code/pkdb_app/outputs/pk_calculation.py\", line 49, in pkoutputs_from_timecourse\n    pkinf = pharmacokinetics.TimecoursePKNoDosing(**variables)\n  File \"/usr/local/lib/python3.7/site-packages/pkdb_analysis/pk/pharmacokinetics.py\", line 87, in __init__\n    self._init(time, concentration, ureg, substance, min_treshold, **kwargs)\n  File \"/usr/local/lib/python3.7/site-packages/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 1578, 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 904, in numpy_wrap\n    return handled[name](*args, **kwargs)\n  File \"/usr/local/lib/python3.7/site-packages/pint/numpy_func.py\", line 736, 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 319, 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"
}
ERROR UPLOAD ERROR (check errors and warnings)

[matthiaskoenig]

I am pretty sure this is just a vector with all NaNs on which pharmacokinetics should be calculated.

On Tue, Jul 28, 2020 at 5:24 PM Jan Grzegorzewski notifications@github.com wrote:

(pkdb_data) janek@dell-desktop:~/Dev/pkdb_data$ upload_study -s studies/codeine/Loetsch2006/ INFO -------------------------------------------------------------------------------- INFO Upload studies/codeine/Loetsch2006/ INFO -------------------------------------------------------------------------------- INFO - 0.16 [s] : Created TSVs ['Fig2', 'Tab1', 'TabData'] INFO - 0.11 [s] : Upload references INFO - 0.39 [s] : Upload files INFO - 0.10 [s] : Upload core study INFO - 0.31 [s] : Upload groups INFO - 0.82 [s] : Upload individuals WARNING { "pharmacokinetics exception": "Traceback (most recent call last):\n File \"/code/pkdb_app/data/serializers.py\", line 76, in calculate_pks_from_timecourses\n outputs = pkoutputs_from_timecourse(subset)\n File \"/code/pkdb_app/outputs/pk_calculation.py\", line 49, in pkoutputs_from_timecourse\n pkinf = pharmacokinetics.TimecoursePKNoDosing(variables)\n File \"/usr/local/lib/python3.7/site-packages/pkdb_analysis/pk/pharmacokinetics.py\", line 87, in init\n self._init(time, concentration, ureg, substance, min_treshold, kwargs)\n File \"/usr/local/lib/python3.7/site-packages/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 1578, 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 904, in numpy_wrap\n return handled[name](*args, *kwargs)\n File \"/usr/local/lib/python3.7/site-packages/pint/numpy_func.py\", line 736, 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 319, 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" } ERROR UPLOAD ERROR (check errors and warnings)

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-- Matthias König, PhD. Junior Group Leader LiSyM - Systems Medicine of the Liver Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology https://livermetabolism.com konigmatt@googlemail.com https://twitter.com/konigmatt https://github.com/matthiaskoenig Tel: +49 30 2093 98435

[matthiaskoenig]

Same issue for studies/glucose/Prager1986