Write method for adding KEGG Pathways into data frame, using KEGG compounds column.

[pkrog]

Use getPathwayIdsPerCompound().
Add a limitation to the number of pathways.
See ceabiodb/biodb#404
Add to the data frame:

• Pathway IDs.
• Pathway Names.
• Pathway Classes (the more specific if possible).
• Module IDs.
• Module names.
• Enzymes.
• Reaction IDs.

[pkrog]

Can we write a new Biodb general method to add new columns using entry fields from entries created from one of the column containing IDs.

addColsToDataframe=function(input.df, id.col, db, fields, limit=3)
":\n\n
\ninput.df: 
\nid.col: The column containing IDs.
\ndb: The biodb database name for the IDs contained in id.col.
\nfields: A character vector containing entry fields to add.
\nlimit: The maximum number of field values to write into new columns. Used for fields that can contain more than one value.
"

[pkrog]

Using such a general method for our use case may require to write new computing rules for fields.
Maybe we should restrict the current computing rules, by stating on which databases each rule applies.

[pkrog]

How to write such a general method that uses getPathwayIdsPerCompound()?

[pkrog]

Is it possible to override computeFields(fields) in KeggCompoundEntry and compute fields kegg.pathway.id?

Maybe, but how to compute pathway IDs for a specific organism?
---> Why not compute them in a second stage with the method KeggPathwayConn::convertToOrgPathways?

[pkrog]

All this seems too much complex. Why not just write a method KeggCompoundConn::addAnotations()?

[pkrog]

• Add limit parameter into Biodb::entriesToDataframe().
• Implement Biodb::entryIdsToDataframe() by making it call Biodb::entriesToDataframe().
• Implement the method Biodb::addColsToDataframe() by making it call Biodb::entryIdsToDataframe().
• Implement KeggCompoundConn::addAnotations() using Biodb::addColsToDataframe() and `Biodb::addColsToDataframe()``.