Updating the extract galaxy tools script to add two more columns one for reduced EDAM operation and one for reduced EDAM topic

[EngyNasr]

Adding the Jupyter notebook and R scripts that are responsible for updating the tools.tsv to include a reduced EDAM operation column and to produce some figures, more updates and figures are to follow

[paulzierep]

Tu use this in the CI could you please:

• Remove notebook

• Add a function here: https://github.com/galaxyproject/galaxy_tool_metadata_extractor/blob/main/bin/extract_galaxy_tools.py

func(df) -> df (with 2 new columns having reduced terms)

• Use the function here: https://github.com/galaxyproject/galaxy_tool_metadata_extractor/blob/a9a6902dd4f998e5a4e31cbd4ea2ee7c5922cd77/bin/extract_galaxy_tools.py#L519

[paulzierep]

Thanks @EngyNasr
I did run this locally, and it seems to work.
But can you please:

• fix linting
• add comments and function docstring
• look at

/home/paul/git/galaxyproject/galaxy_tool_extractor/bin/extract_galaxy_tools.py:532: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
  return pd.Series([row[0], ', '.join(new_terms)])  # Combine the new terms with commas
/home/paul/git/galaxyproject/galaxy_tool_extractor/bin/extract_galaxy_tools.py:532: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
  return pd.Series([row[0], ', '.join(new_terms)])  # Combine the new terms with commas

[paulzierep]

please simplify as suggested

[paulzierep]

why ?

[paulzierep]

what errors are we getting ?

[paulzierep]

Sorry but this seems far to complicated. Can you not just do

df[["EDAM operation (reduced)", "EDAM topic (reduced)"]] = df[["EDAM operation", "EDAM topic"]].map(reduced_edam_term)

and reduced_edam_term is a function that takes the EDAM term as input and return the reduced form.

[paulzierep]

the test worked on my local branch: paulzierep@6a01007
Can we merge it @bebatut