Florabank query

[hansvancalster]

I propose to add 3 functions to inborutils that facilitate some often required queries to the florabank.
See also this issue in inbo/tutorials

[hansvancalster]

Anyone know how to get rid of this note (after running Build check)?

> checking R code for possible problems ... NOTE
  florabank_traits: no visible global function definition for '%LIKE%'
  Undefined global functions or variables:
    %LIKE%

It happens when using an infix SQL function within a dbplyr filter statement. See dbplyr vignette section on infix functions

[hansvancalster]

The issue about the note can be solved as explained here

[hansvancalster]

Question: the functions possibly return lots of records (especially florabank_taxon_ifbl_year() can be 10^6). Should we actively return them (= current implementation), or only return a pointer to the query (lazy data)? This can be done by removing the final collect statement from the function using dbplyr syntax. However, for the functions using dbGetQuery I don't know a simple solution to do this.

[damianooldoni]

Maybe by using commandos dbBegin and dbExecute avoiding to commit (dBCommit) the query (same as collect() of dbplyr)?
https://github.com/trias-project/occ-processing/blob/master/src/belgium/assign_grid.Rmd#L122

But, the question is: do people really need to work locally on these data? Would it be an option to inform them about number of records they are going to get before to collect the data? A message like:

You are going to import a data.frame with x rows y columns. 
Press Enter to continue or any other key to abort.

[hansvancalster]

Thanks! I'll have a look at the documentation of these DBI functions. I'd rather not let the function be interactive with the user (not suitable for use in markdown knitted documents).

[ThierryO]

dbBegin and dbCommit are intended for queries that alter the database. Because you can dbRollback these changes to the status stored by dbBegin untill you dbCommit the changes.

dbplyr automatically replaces SELECT by SELECT TOP 10, unless collect() is specified.

[hansvancalster]

@ThierryO thanks for the review! Most of the comments are resolved. For some I need to take a closer look.

[florisvdh]

Glad to be learning from this code + reviewing @hansvancalster, @ThierryO , cool.

[hansvancalster]

@ThierryO I think all your comments are addressed. Can you approve?