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Make sure that only returns the commands that are actually active.

@antgonza this will fix the issue that we are seeing with generating BIOM summaries

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Codecov Report

Merging #2431 into dev will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev    #2431      +/-   ##
==========================================
+ Coverage   94.09%   94.09%   +<.01%     
==========================================
  Files         163      163              
  Lines       19335    19345      +10     
==========================================
+ Hits        18193    18203      +10     
  Misses       1142     1142
Impacted Files Coverage Δ
qiita_db/software.py 97.98% <ø> (ø) ⬆️
qiita_db/test/test_software.py 99.81% <100%> (ø) ⬆️

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@antgonza antgonza merged commit cd2746b into qiita-spots:dev Dec 13, 2017
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3 participants