Export option exceptions

[PatrickRWright]

I added a new directory with test exports to do this. NEWS.md explains what has been fixed. Basically, if the information to add the pat_id, visit_name or centre columns is missing they are simply not added.

One review should do but I will invite you both.

closes #67
closes #103
closes #105

[codecov-io]

Codecov Report

Merging #106 into master will decrease coverage by 0.25%.
The diff coverage is 84.84%.

@@            Coverage Diff             @@
##           master     #106      +/-   ##
==========================================
- Coverage   93.67%   93.41%   -0.26%     
==========================================
  Files          20       20              
  Lines         996     1018      +22     
==========================================
+ Hits          933      951      +18     
- Misses         63       67       +4

Impacted Files	Coverage Δ
R/labels_secuTrial.R	95% <0%> (ø)	⬆️
R/read_export_options.R	93.58% <100%> (+0.14%)	⬆️
R/read_export_table.R	97.43% <100%> (+0.06%)	⬆️
R/read_secuTrial_raw.R	94.54% <100%> (ø)	⬆️
R/read_secuTrial.R	81.81% <80.95%> (-18.19%)	⬇️

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[PatrickRWright]

I'm finished. Just thought of one more thing I wanted to test and added it while I was at it.

[aghaynes]

what does read_secutrial currently do? In my opinion, it would give warnings that the labels, etc are not applied, but still import the data. this could be done by checking if something is in the export options and then setting the 3 logicals to false if the setup stuff is not there...

[PatrickRWright]

Currently it will always try and add pat_id, centre and visit_name. This fails if the data for the procedure is missing.

I also considered adding warnings in this PR but decided not to.

I think that would be a work package related to #17. Once we have agreed on a set of suggested options (which will definitely include add-id, centre info and project setup) I suggest we tailor a verbose warning message for each option (if it differs from the suggestion) and point out what the effect is.

[aghaynes]

maybe it makes sense to skip factorize, dates and labels if project setup isn't available and give a warning (an if loop in read_secutrial would do i think)