test/test_helper.rb in macroape-3.3.7 vs test/test_helper.rb in macroape-3.3.8

@@ -10,11 +10,11 @@
 require_relative '../lib/macroape/cli/eval_similarity'
 require_relative '../lib/macroape/cli/eval_alignment'
 require_relative '../lib/macroape/cli/preprocess_collection'
 require_relative '../lib/macroape/cli/scan_collection'
 require_relative '../lib/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
@@ -23,54 +23,138 @@
     return {stdout: captured_stdout.string, stderr: captured_stderr.string}
   ensure
     $stdout = orig_stdout
     $stderr = orig_stderr
   end
-  
+
+  def self.suppress_output(&block)
+    orig_stdout, orig_stderr = $stdout, $stderr
+    captured_stdout, captured_stderr = StringIO.new, StringIO.new
+    $stdout, $stderr = captured_stdout, captured_stderr
+    yield
+  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  
+  ensure
     $stdin = orig_stdin
   end
-  
+
   def self.capture_output(&block)
     capture_io(&block)[:stdout]
   end
   def self.capture_stderr(&block)
     capture_io(&block)[:stderr]
   end
-  
+
+  # aaa\tbbb\nccc\tddd  ==>  [['aaa','bbb'],['ccc','ddd']]
+  def self.split_on_lines(str)
+    str.lines.map{|line| line.strip.split("\t")}
+  end
+
   def self.obtain_pvalue_by_threshold(args)
-    find_pvalue_output(args).strip.split.last
+    find_pvalue_output(args).last.last
   end
   def self.exec_cmd(executable, param_list)
     "ruby -I #{$lib_folder} #{$lib_folder}/../bin/#{executable} #{param_list}"
   end
   def self.find_threshold_output(param_list)
     capture_output{ Macroape::CLI::FindThreshold.main(param_list.shellsplit) }
   end
   def self.align_motifs_output(param_list)
-    capture_output{ Macroape::CLI::AlignMotifs.main(param_list.shellsplit) }
+    split_on_lines( capture_output{ Macroape::CLI::AlignMotifs.main(param_list.shellsplit)} )
   end
   def self.find_pvalue_output(param_list)
-    capture_output{ Macroape::CLI::FindPValue.main(param_list.shellsplit) }
+    capture_output{ Macroape::CLI::FindPValue.main(param_list.shellsplit)} .lines.to_a.map(&:strip).reject{|line| line.start_with? '#' }.reject(&:empty?).map{|line|line.split("\t")}
   end
   def self.eval_similarity_output(param_list)
-    capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.shellsplit) }
+    capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.shellsplit)}
   end
   def self.eval_alignment_output(param_list)
-    capture_output{ Macroape::CLI::EvalAlignment.main(param_list.shellsplit) }
+    capture_output{ Macroape::CLI::EvalAlignment.main(param_list.shellsplit)}
   end
   def self.scan_collection_output(param_list)
-    capture_output{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
+    capture_output{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }.lines.to_a.map(&:strip).reject{|line| line.start_with? '#' }.reject(&:empty?).join("\n")
   end
   def self.scan_collection_stderr(param_list)
     capture_stderr{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
   end
   def self.run_preprocess_collection(param_list)
-    Macroape::CLI::PreprocessCollection.main(param_list.shellsplit)
+    suppress_output{ Macroape::CLI::PreprocessCollection.main(param_list.shellsplit) }
+  end
+
+  def parse_similarity_infos_string(info_string)
+    infos = {}
+    info_string.lines.map(&:strip).reject{|line| line.start_with?('#')}.reject(&:empty?).each do |line|
+      key, value = line.split
+      case key
+        when 'S'  then infos[:similarity] = value
+        when 'D'  then infos[:distance] = value
+        when 'L'  then infos[:length] = value
+        when 'SH'  then infos[:shift] = value
+        when 'OR'  then infos[:orientation] = value
+        when 'W'  then infos[:words_recognized_by_both] = value
+
+        when 'W1' then infos[:words_recognized_by_first] = value
+        when 'P1' then infos[:pvalue_recognized_by_first] = value
+        when 'T1' then infos[:threshold_first] = value
+
+        when 'W2' then infos[:words_recognized_by_second] = value
+        when 'P2' then infos[:pvalue_recognized_by_second] = value
+        when 'T2' then infos[:threshold_second] = value
+
+        when 'A1'  then infos[:matrix_first_alignment] = value
+        when 'A2'  then infos[:matrix_second_alignment] = value
+
+        when 'V' then infos[:discretization] = value
+      end
+    end
+    infos
+  end
+
+  def assert_similarity_info_output(expected_info, info_string)
+    infos = parse_similarity_infos_string(info_string)
+    expected_info.each do |key, value|
+      assert_equal value.to_s, infos[key]
+    end
+  end
+
+  def parse_threshold_infos_string(infos_string)
+    infos = []
+    infos_string.lines.map(&:strip).reject{|line| line.start_with?('#')}.reject(&:empty?).each do |line|
+      info_data = line.split
+      if info_data.size == 4
+        requested_pvalue, real_pvalue, number_of_recognized_words, threshold = info_data
+        info = {requested_pvalue: requested_pvalue,
+                real_pvalue: real_pvalue,
+                number_of_recognized_words: number_of_recognized_words,
+                threshold: threshold }
+      elsif info_data.size == 3
+        requested_pvalue, real_pvalue, threshold = info_data
+        info = {requested_pvalue: requested_pvalue,
+                real_pvalue: real_pvalue,
+                threshold: threshold }
+      else
+        raise 'can\'t parse threshold infos table'
+      end
+      infos << info
+    end
+    infos
+  end
+
+  def assert_threshold_info_output(*expected_infos, info_string)
+    infos = parse_threshold_infos_string(info_string)
+    expected_infos.zip(infos).each do |expected_info, info|
+      assert_not_nil info
+      expected_info.each do |key, value|
+        assert_equal value.to_s, info[key]
+      end
+    end
   end
 
 end