test/test_helper.rb in macroape-3.3.3 vs test/test_helper.rb in macroape-3.3.4

@@ -1,12 +1,71 @@
 $lib_folder = File.dirname(__FILE__) + '/../lib'
 $LOAD_PATH.unshift $lib_folder
 require 'test/unit'
+require 'stringio'
+
+require 'macroape/cli/find_threshold'
+require 'macroape/cli/find_pvalue'
+require 'macroape/cli/eval_similarity'
+require 'macroape/cli/eval_alignment'
+require 'macroape/cli/preprocess_collection'
+require 'macroape/cli/scan_collection'
+require 'macroape/cli/align_motifs'
  
 module Helpers
+  # from minitest
+  def self.capture_io(&block)
+    orig_stdout, orig_stderr = $stdout, $stderr
+    captured_stdout, captured_stderr = StringIO.new, StringIO.new
+    $stdout, $stderr = captured_stdout, captured_stderr
+    yield
+    return {stdout: captured_stdout.string, stderr: captured_stderr.string}
+  ensure
+    $stdout = orig_stdout
+    $stderr = orig_stderr
+  end
+  
+  # Method stubs $stdin not STDIN !
+  def self.provide_stdin(input, &block)
+    orig_stdin = $stdin
+    $stdin = StringIO.new(input)
+    yield
+  ensure  
+    $stdin = orig_stdin
+  end
+  
+  def self.capture_output(&block)
+    capture_io(&block)[:stdout]
+  end
+  def self.capture_stderr(&block)
+    capture_io(&block)[:stderr]
+  end
+  
   def self.obtain_pvalue_by_threshold(args)
-    IO.popen("ruby -I #{$lib_folder} #{$lib_folder}/macroape/exec/find_pvalue.rb #{args}",&:read).strip.split.last
+    find_pvalue_output(args).strip.split.last
   end
   def self.exec_cmd(executable, param_list)
-    "ruby -I #{$lib_folder} #{$lib_folder}/macroape/exec/#{executable}.rb #{param_list}"
+    "ruby -I #{$lib_folder} #{$lib_folder}/../bin/#{executable} #{param_list}"
   end
+  def self.find_threshold_output(param_list)
+    capture_output{ Macroape::CLI::FindThreshold.main(param_list.split) }
+  end
+  def self.align_motifs_output(param_list)
+    capture_output{ Macroape::CLI::AlignMotifs.main(param_list.split) }
+  end
+  def self.find_pvalue_output(param_list)
+    capture_output{ Macroape::CLI::FindPValue.main(param_list.split) }
+  end
+  def self.eval_similarity_output(param_list)
+    capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.split) }
+  end
+  def self.eval_alignment_output(param_list)
+    capture_output{ Macroape::CLI::EvalAlignment.main(param_list.split) }
+  end
+  def self.scan_collection_output(param_list)
+    capture_output{ Macroape::CLI::ScanCollection.main(param_list.split) }
+  end
+  def self.run_preprocess_collection(param_list)
+    Macroape::CLI::PreprocessCollection.main(param_list.split)
+  end
+
 end