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Add tests for ingestion of files with missing columns #128

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diskontinuum opened this issue Sep 29, 2020 · 2 comments
Open

Add tests for ingestion of files with missing columns #128

diskontinuum opened this issue Sep 29, 2020 · 2 comments

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@diskontinuum
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diskontinuum commented Sep 29, 2020 •
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See also pycytominer/issues/79.
@diskontinuum diskontinuum changed the title Add testTest ingestion of files with missing Add tests for ingestion of files with missing Sep 29, 2020
@diskontinuum diskontinuum changed the title Add tests for ingestion of files with missing Add tests for ingestion of files with missing columns Sep 29, 2020
@diskontinuum
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Please ignore several involuntary enter-typos for the title above ;)

@diskontinuum
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The current cytominer-database version (only with the --parquet option) deals with missing columns explicitly by aligning dataframes (that will be concatenated and written to a Parquet file) with a specific reference dataframe:
`aligned_df, ref_df = df.align(ref_df, axis=1)``

Missing columns will be added as NaN-valued columns by default (with same column name and type as the reference frame). To choose a specific value, we could add the parameter fill_value to pandas.dataframe.align() .

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