Fix DOIs code especially for square brackets etc.

[GlazerMann]

mark_inactive_doi needs to be public not protected to call from API file

lots of url encoding for evil square bracket DOIs (and ending with -# is pure evil)

Add missing { } after if that lead to wrong code logic

[codecov]

Codecov Report

❗ No coverage uploaded for pull request base (master@543879b). Click here to learn what that means.
The diff coverage is 100%.

@@            Coverage Diff            @@
##             master     #751   +/-   ##
=========================================
  Coverage          ?   68.22%           
  Complexity        ?     1626           
=========================================
  Files             ?       12           
  Lines             ?     3286           
  Branches          ?        0           
=========================================
  Hits              ?     2242           
  Misses            ?     1044           
  Partials          ?        0

Impacted Files	Coverage Δ	Complexity Δ
Template.php	73.84% <100%> (ø)	1454 <4> (?)
apiFunctions.php	70.02% <100%> (ø)	0 <0> (?)

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