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Validator: handle undefined observables more gracefully #300

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dweindl opened this issue Feb 18, 2020 · 0 comments · Fixed by #357
Closed

Validator: handle undefined observables more gracefully #300

dweindl opened this issue Feb 18, 2020 · 0 comments · Fixed by #357
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dweindl commented Feb 18, 2020 •
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What happens if measurement table contains an observableId that is not defined in the observables table:

  File "PEtab/petab/lint.py", line 127, in check_measurement_df
    trafo = observable_df.loc[obs_id, OBSERVABLE_TRANSFORMATION]
  File "lib/python3.7/site-packages/pandas/core/indexing.py", line 1761, in __getitem__
    return self._getitem_tuple(key)
  File "lib/python3.7/site-packages/pandas/core/indexing.py", line 1271, in _getitem_tuple
    return self._getitem_lowerdim(tup)
  File "lib/python3.7/site-packages/pandas/core/indexing.py", line 1388, in _getitem_lowerdim
    section = self._getitem_axis(key, axis=i)
  File "lib/python3.7/site-packages/pandas/core/indexing.py", line 1964, in _getitem_axis
    return self._get_label(key, axis=axis)
  File "lib/python3.7/site-packages/pandas/core/indexing.py", line 624, in _get_label
    return self.obj._xs(label, axis=axis)
  File "lib/python3.7/site-packages/pandas/core/generic.py", line 3537, in xs
    loc = self.index.get_loc(key)
  File "lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1618, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1626, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'K27me0K36me0'

What should have happened:
A more informative message should be printed (and potentially validation should continue)
@dweindl dweindl added good first issue Good for newcomers pythonlib labels Feb 18, 2020
@dweindl dweindl added this to the v0.1.3 milestone Feb 28, 2020
@dweindl dweindl self-assigned this Feb 28, 2020
dweindl added a commit that referenced this issue Feb 28, 2020
@dweindl
Validator: handle undefined observables more gracefully (Closes #300)
2674e4d
dweindl added a commit that referenced this issue Feb 28, 2020
@dweindl
Validator: handle undefined observables more gracefully (Closes #300) (…
5da4527 
…#351)
@dweindl dweindl mentioned this issue Feb 28, 2020
Merged
dweindl added a commit that referenced this issue Feb 28, 2020
@dweindl
Merge pull request #357 from PEtab-dev/release_0.1.3
7b9d189 
Release 0.1.3

File format:

* Updated documentation
* Observables table in YAML file now mandatory in schema (was implicitly 
  mandatory before, as observable table was required already)

Library:
* petablint:
  * Fix: allow specifying observables file via CLI (Closes #302)
  * Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes #303)
  * Fix: handle undefined observables more gracefully (Closes #300) (#351)
* Parameter mapping: 
  * Fix / refactor parameter mapping (breaking change) (#344)
    (now performing parameter value and scale mapping together)
  * check optional measurement cols in mapping (#350)
* allow calculating llhs (#349), chi2 values (#348) and residuals (#345)
* Visualization
  * Basic Scatterplots & lot of bar plot fixes (#270)
  * Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas 
    (Closes #322)
* make libcombine optional (#338)
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Release 0.1.3 PEtab-dev/PEtab
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