Merge pull request #782 from wurmlab/tt/consider-paths

Consider path configuration when extracting tasks
wurmlab · Aug 13, 2024 · 17c3bb6 · 17c3bb6
2 parents 269a429 + 312cf1d
commit 17c3bb6
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diff --git a/lib/sequenceserver/blast/tasks.rb b/lib/sequenceserver/blast/tasks.rb
@@ -6,7 +6,7 @@ module Tasks
 
       def self.to_h
         @to_h ||= ALGORITHMS.map do |algorithm|
-          help_text = `#{algorithm} -help`
+          help_text, = SequenceServer.sys("#{algorithm} -help", path: SequenceServer.config[:bin])
           [algorithm, extract_tasks(help_text)]
         end.to_h
       end

diff --git a/spec/features/search_and_results_spec.rb b/spec/features/search_and_results_spec.rb
@@ -258,7 +258,7 @@ def nucleotide_query
     expect(File.basename(downloaded_file)).to eq('sequenceserver-xml_report.xml')
     clear_downloads
 
-    page.click_link('Full Pairwise report')
+    page.click_link('Full Text report')
     wait_for_download
     expect(File.basename(downloaded_file)).to eq('sequenceserver-pairwise_report.txt')
     clear_downloads