Alternatives for handling NA inputs

[stitam]

This PR is meant to contribute to the discussion on issue #224.

The interesing part is in chebi.R. The issue is that if the input is invalid, e.g. "balloon" (unknown chemical) or NA, the structure of the output will be different, which makes vectorisation difficult. As a reprex, chebi_comp_entity(c("CHEBI:89301","CHEBI:89302","balloon",NA)) will return a nicely formatted list for the first two entries and something else for the last two. This makes sapply(test, function(x) x[["properties"]]$inchikey) return NULL-s, and unable to coerse the output into a character vector.

My approach for handling invalid inputs is to return an empty object with the same structure but all NA-s. I tried two alternatives: in get_chebiid() I defined the structure twice within the function. In chebi_comp_entity() this would have been distrubingly complex, so I created a separate, non exported function, which generates an object with the correct structure, but all NA-s inside, and called this function in lines 226 and 251. Forcing to return an empty object for invalid inputs allowed sapply() to extract inchikeys and coerce the output to a character vector.

I think the second approach is more elegant and less error prone. What do you think about the these empty objects? Can you suggest other solutions?

PR task list:

• Update NEWS
• Add tests (if appropriate)
• Update documentation with devtools::document()
• Check package passed

[codecov-io]

Codecov Report

Merging #225 into master will not change coverage by %.
The diff coverage is 0.00%.

@@          Coverage Diff           @@
##           master    #225   +/-   ##
======================================
  Coverage    0.00%   0.00%           
======================================
  Files          19      19           
  Lines        1587    1675   +88     
======================================
- Misses       1587    1675   +88     

Impacted Files	Coverage Δ
R/alanwood.R	0.00% <0.00%> (ø)
R/chebi.R	0.00% <0.00%> (ø)

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[Aariq]

I'm a little confused by match == "na". Maybe you could clarify what that "does" or see if my suggestions allow you to get rid of that code entirely.