[BUG] in integration test of wikidata

[miguelgfierro]

Description

============================= test session starts ==============================
platform linux -- Python 3.6.8, pytest-5.0.1, py-1.8.0, pluggy-0.12.0
rootdir: /data/home/recocat/cicd/7/s
collected 29 items / 12 deselected / 17 selected

tests/integration/test_criteo.py .                                       [  5%]
tests/integration/test_movielens.py .........                            [ 58%]
tests/integration/test_notebooks_python.py ......F                       [100%]

=================================== FAILURES ===================================
__________________________ test_wikidata_integration ___________________________

self = Index(['name', 'value', 'type', 'filename'], dtype='object')
key = 'lenght_result', method = None, tolerance = None

    @Appender(_index_shared_docs['get_loc'])
    def get_loc(self, key, method=None, tolerance=None):
        if method is None:
            if tolerance is not None:
                raise ValueError('tolerance argument only valid if using pad, '
                                 'backfill or nearest lookups')
            try:
>               return self._engine.get_loc(key)

/anaconda/envs/nightly_reco_base/lib/python3.6/site-packages/pandas/core/indexes/base.py:2657: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???

pandas/_libs/index.pyx:108: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???

pandas/_libs/index.pyx:132: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???

pandas/_libs/hashtable_class_helper.pxi:1601: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   KeyError: 'lenght_result'

pandas/_libs/hashtable_class_helper.pxi:1608: KeyError

During handling of the above exception, another exception occurred:

notebooks = {'als_deep_dive': '/data/home/recocat/cicd/7/s/notebooks/02_model/als_deep_dive.ipynb', 'als_pyspark': '/data/home/rec...baseline_deep_dive.ipynb', 'data_split': '/data/home/recocat/cicd/7/s/notebooks/01_prepare_data/data_split.ipynb', ...}
tmp = '/tmp/pytest-of-recocat/pytest-1082/tmpwyijg271'

    @pytest.mark.integration
    def test_wikidata_integration(notebooks, tmp):
        notebook_path = notebooks["wikidata_KG"]
        MOVIELENS_SAMPLE_SIZE = 5
        pm.execute_notebook(notebook_path, OUTPUT_NOTEBOOK, kernel_name=KERNEL_NAME,
                            parameters=dict(MOVIELENS_DATA_SIZE='100k',
                                            MOVIELENS_SAMPLE=True,
                                            MOVIELENS_SAMPLE_SIZE=MOVIELENS_SAMPLE_SIZE))
    
>       result = pm.read_notebook(OUTPUT_NOTEBOOK).dataframe["lenght_result"]

@almudenasanz please check when you are available

In which platform does it happen?

How do we replicate the issue?

Expected behavior (i.e. solution)

Other Comments

[miguelgfierro]

hey @almudenasanz, there is another error in the same test:

tests/integration/test_notebooks_python.py ......F                       [100%]

=================================== FAILURES ===================================
__________________________ test_wikidata_integration ___________________________

notebooks = {'als_deep_dive': '/data/home/recocat/cicd/7/s/notebooks/02_model/als_deep_dive.ipynb', 'als_pyspark': '/data/home/rec...baseline_deep_dive.ipynb', 'data_split': '/data/home/recocat/cicd/7/s/notebooks/01_prepare_data/data_split.ipynb', ...}
tmp = '/tmp/pytest-of-recocat/pytest-1104/tmpyx54eslt'

    @pytest.mark.integration
    def test_wikidata_integration(notebooks, tmp):
        notebook_path = notebooks["wikidata_KG"]
        MOVIELENS_SAMPLE_SIZE = 5
        pm.execute_notebook(notebook_path, OUTPUT_NOTEBOOK, kernel_name=KERNEL_NAME,
                            parameters=dict(MOVIELENS_DATA_SIZE='100k',
                                            MOVIELENS_SAMPLE=True,
                                            MOVIELENS_SAMPLE_SIZE=MOVIELENS_SAMPLE_SIZE))
    
        results = pm.read_notebook(OUTPUT_NOTEBOOK).dataframe.set_index("name")["value"]
>       assert results["lenght_result"] == MOVIELENS_SAMPLE_SIZE
E       assert 184 == 5

[almudenasanz]

Totally normal, I was not exporting the right variable for the assert. Just did a PR

[miguelgfierro]

hey @almudenasanz

tests/integration/test_criteo.py .                                       [  5%]
tests/integration/test_movielens.py .........                            [ 58%]
tests/integration/test_notebooks_python.py ......F                       [100%]

=================================== FAILURES ===================================
__________________________ test_wikidata_integration ___________________________

notebooks = {'als_deep_dive': '/data/home/recocat/cicd/7/s/notebooks/02_model/als_deep_dive.ipynb', 'als_pyspark': '/data/home/rec...baseline_deep_dive.ipynb', 'data_split': '/data/home/recocat/cicd/7/s/notebooks/01_prepare_data/data_split.ipynb', ...}
tmp = '/tmp/pytest-of-recocat/pytest-1122/tmpx00synt0'

    @pytest.mark.integration
    def test_wikidata_integration(notebooks, tmp):
        notebook_path = notebooks["wikidata_KG"]
        MOVIELENS_SAMPLE_SIZE = 5
        pm.execute_notebook(notebook_path, OUTPUT_NOTEBOOK, kernel_name=KERNEL_NAME,
                            parameters=dict(MOVIELENS_DATA_SIZE='100k',
                                            MOVIELENS_SAMPLE=True,
>                                           MOVIELENS_SAMPLE_SIZE=MOVIELENS_SAMPLE_SIZE))

tests/integration/test_notebooks_python.py:173: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/anaconda/envs/nightly_reco_base/lib/python3.6/site-packages/papermill/execute.py:94: in execute_notebook
    raise_for_execution_errors(nb, output_path)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

nb = {'cells': [{'cell_type': 'code', 'metadata': {'inputHidden': True, 'hide_input': True}, 'execution_count': None, 'sour...nd_time': '2019-07-31T12:48:30.058293', 'duration': 15.144893, 'exception': True}}, 'nbformat': 4, 'nbformat_minor': 2}
output_path = 'output.ipynb'

    def raise_for_execution_errors(nb, output_path):
        """Assigned parameters into the appropriate place in the input notebook
    
        Parameters
        ----------
        nb : NotebookNode
           Executable notebook object
        output_path : str
           Path to write executed notebook
        """
        error = None
        for cell in nb.cells:
            if cell.get("outputs") is None:
                continue
    
            for output in cell.outputs:
                if output.output_type == "error":
                    error = PapermillExecutionError(
                        exec_count=cell.execution_count,
                        source=cell.source,
                        ename=output.ename,
                        evalue=output.evalue,
                        traceback=output.traceback,
                    )
                    break
    
        if error:
            # Write notebook back out with the Error Message at the top of the Notebook.
            error_msg = ERROR_MESSAGE_TEMPLATE % str(error.exec_count)
            error_msg_cell = nbformat.v4.new_code_cell(
                source="%%html\n" + error_msg,
                outputs=[
                    nbformat.v4.new_output(output_type="display_data", data={"text/html": error_msg})
                ],
                metadata={"inputHidden": True, "hide_input": True},
            )
            nb.cells = [error_msg_cell] + nb.cells
            write_ipynb(nb, output_path)
>           raise error
E           papermill.exceptions.PapermillExecutionError: 
E           ---------------------------------------------------------------------------
E           Exception encountered at "In [19]":
E           ---------------------------------------------------------------------------
E           ImportError                               Traceback (most recent call last)
E           /anaconda/envs/nightly_reco_base/lib/python3.6/site-packages/tqdm/_tqdm.py in pandas(tclass, *targs, **tkwargs)
E               612             # pandas>=0.23.0
E           --> 613             from pandas.core.groupby.groupby import DataFrameGroupBy, \
E               614                 SeriesGroupBy, GroupBy, PanelGroupBy
E           
E           ImportError: cannot import name 'DataFrameGroupBy'
E           
E           During handling of the above exception, another exception occurred:
E           
E           ImportError                               Traceback (most recent call last)
E           <ipython-input-19-6ccb9974139b> in <module>
E           ----> 1 tqdm().pandas(desc="Number of movies completed")
E                 2 result = pd.concat(list(movies.progress_apply(lambda x: wikidata_KG_from_movielens(x), axis=1)))
E           
E           /anaconda/envs/nightly_reco_base/lib/python3.6/site-packages/tqdm/_tqdm.py in pandas(tclass, *targs, **tkwargs)
E               614                 SeriesGroupBy, GroupBy, PanelGroupBy
E               615         except ImportError:
E           --> 616             from pandas.core.groupby import DataFrameGroupBy, \
E               617                 SeriesGroupBy, GroupBy, PanelGroupBy
E               618 
E           
E           ImportError: cannot import name 'PanelGroupBy'

/anaconda/envs/nightly_reco_base/lib/python3.6/site-packages/papermill/execute.py:241: PapermillExecutionError

can you take a look?

[almudenasanz]

Seems related to this tqdm issue: tqdm/tqdm#780

[almudenasanz]

I will avoid using tqdm in the notebook until the issue is resolved

[miguelgfierro]

@almudenasanz :-)

tests/integration/test_notebooks_python.py ......F                       [100%]

=================================== FAILURES ===================================
__________________________ test_wikidata_integration ___________________________

notebooks = {'als_deep_dive': '/data/home/recocat/cicd/7/s/notebooks/02_model/als_deep_dive.ipynb', 'als_pyspark': '/data/home/rec...baseline_deep_dive.ipynb', 'data_split': '/data/home/recocat/cicd/7/s/notebooks/01_prepare_data/data_split.ipynb', ...}
tmp = '/tmp/pytest-of-recocat/pytest-1197/tmpaqmy5olp'

    @pytest.mark.integration
    def test_wikidata_integration(notebooks, tmp):
        notebook_path = notebooks["wikidata_KG"]
        MOVIELENS_SAMPLE_SIZE = 5
        pm.execute_notebook(notebook_path, OUTPUT_NOTEBOOK, kernel_name=KERNEL_NAME,
                            parameters=dict(MOVIELENS_DATA_SIZE='100k',
                                            MOVIELENS_SAMPLE=True,
                                            MOVIELENS_SAMPLE_SIZE=MOVIELENS_SAMPLE_SIZE))
    
        results = pm.read_notebook(OUTPUT_NOTEBOOK).dataframe.set_index("name")["value"]
>       assert results["lenght_result"] == MOVIELENS_SAMPLE_SIZE
E       assert 4 == 5