msrun_spec.rb in ms-msrun-0.2.0

- old
+ new
@@ -1,158 +1,139 @@
 require File.expand_path(File.dirname(__FILE__) + '/../spec_helper.rb')
 
 require 'ms/msrun'
 
 module MsrunSpec
-  extend Shareable
 
-  before do
-    @file = nil  # you need to define this!
-    @key = nil   # <- do nothing with this.
-    @nums = (1..20).to_a  # define scan numbers
+  before_all = lambda do |file|
+    nums = (1..20).to_a  # define scan numbers
+    key = YAML.load_file(file + '.key.yml')
+    [key, nums]
   end
 
-  def key
-    @key || @key = YAML.load_file(@file + '.key.yml')
-  end
+  shared 'an msrun object' do
 
-  def hash_match(hash, obj)
-    #$DEBUG = 1
-    puts "SCAN: #{obj.num}" if $DEBUG && obj.respond_to?(:num)
-    hash.each do |k,v|
-      if v.is_a?(Hash)
-        hash_match(v, obj.send(k.to_sym))
-      else
-        puts "#{k}: #{v} but was #{obj.send(k.to_sym)}" if obj.send(k.to_sym) != v
-        obj.send(k.to_sym).must_equal v
+    it 'reads header information' do
+      Ms::Msrun.open(@file) do |ms|
+        @key['header'].each do |k,v|
+          #puts "K: #{k} Vexp: #{v} Vact: #{ms.send(k.to_sym)}"
+          ms.send(k.to_sym).is v
+        end
       end
     end
-  end
 
-  it 'reads header information' do
-    Ms::Msrun.open(@file) do |ms|
-      key['header'].each do |k,v|
-        #puts "K: #{k} Vexp: #{v} Vact: #{ms.send(k.to_sym)}"
-        ms.send(k.to_sym).must_equal v
+    it 'can access random scans' do
+      Ms::Msrun.open(@file) do |ms|
+        scan = ms.scan(20)
+        hash_match(@key['scans'][20], scan)
       end
     end
-  end
 
-  it 'can access random scans' do
-    Ms::Msrun.open(@file) do |ms|
-      scan = ms.scan(20)
-      hash_match(key['scans'][20], scan)
+    it 'can read all scans' do
+      num_required_scans = @key['scans'].size
+      Ms::Msrun.open(@file) do |ms|
+        ms.each do |scan|
+          if hash = @key['scans'][scan.num]
+            hash_match(hash, scan)
+            num_required_scans -= 1
+          end
+        end
+      end
+      num_required_scans.is 0
     end
-  end
 
-  it 'can read all scans' do
-    num_required_scans = key['scans'].size
-    Ms::Msrun.open(@file) do |ms|
-      ms.each do |scan|
-        if hash = key['scans'][scan.num]
-          hash_match(hash, scan)
-          num_required_scans -= 1
+    it 'can read scans of a certain ms_level' do
+      nums = [1,5,9,13,17]
+      Ms::Msrun.open(@file) do |ms|
+        ms.each(:ms_level => 1) do |scan|
+          scan.num.is nums.shift 
         end
       end
+      nums = [2,3,4,6,7,8,10,11,12,14,15,16,18,19,20]
+      Ms::Msrun.foreach(@file, :ms_level => 2) do |scan|
+        scan.num.is nums.shift 
+      end
     end
-    num_required_scans.must_equal 0
-  end
 
-  it 'can read scans of a certain ms_level' do
-    nums = [1,5,9,13,17]
-    Ms::Msrun.open(@file) do |ms|
-      ms.each(:ms_level => 1) do |scan|
-        scan.num.must_equal nums.shift 
+    it 'can avoid reading spectra' do 
+      nums = @nums.map
+      Ms::Msrun.foreach(@file, :spectrum => false) do |scan|
+        scan.spectrum.nil?.ok
+        scan.num.is nums.shift
       end
     end
-    nums = [2,3,4,6,7,8,10,11,12,14,15,16,18,19,20]
-    Ms::Msrun.foreach(@file, :ms_level => 2) do |scan|
-      scan.num.must_equal nums.shift 
-    end
-  end
 
-  it 'can avoid reading spectra' do 
-    nums = @nums.map
-    Ms::Msrun.foreach(@file, :spectrum => false) do |scan|
-      assert scan.spectrum.nil?
-      scan.num.must_equal nums.shift
+    it 'can avoid reading precursor information' do 
+      Ms::Msrun.foreach(@file, :precursor => false) do |scan|
+        scan.precursor.nil?.ok
+      end
     end
-  end
 
-  it 'can avoid reading precursor information' do 
-    Ms::Msrun.foreach(@file, :precursor => false) do |scan|
-      assert scan.precursor.nil?
+    it 'gives scan counts for different ms levels' do
+      Ms::Msrun.open(@file) do |ms|
+        @key['scan_count'].each do |index, count|
+          ms.scan_count(index).is count
+        end
+      end
     end
-  end
 
-  it 'gives scan counts for different ms levels' do
-    Ms::Msrun.open(@file) do |ms|
-      key['scan_count'].each do |index, count|
-        ms.scan_count(index).must_equal count
+    it 'gives start and end mz even if the information is not given' do
+      Ms::Msrun.open(@file) do |ms|
+        ms.start_and_end_mz_brute_force.is(@key['start_and_end_mz'][1])
       end
     end
   end
 
-  it 'gives start and end mz even if the information is not given' do
-    Ms::Msrun.open(@file) do |ms|
-      ms.start_and_end_mz_brute_force.must_equal(key['start_and_end_mz'][1])
+  describe 'reading an mzXML v1 file' do
+    @file = TESTFILES + '/opd1/000.v1.mzXML'
+    
+    (@key, @nums) = before_all.call(@file)
+
+
+    it 'can give start and end mz' do
+      # scan has attributes startMz endMz
+      Ms::Msrun.open(@file) do |ms|
+        #ms.start_and_end_mz.is([300.0, 1500.0])
+        ms.start_and_end_mz.is @key['start_and_end_mz'][1]
+      end
     end
-  end
 
-end
+    behaves_like 'an msrun object'
 
-class Mzxml_v1 < MiniTest::Spec
-  include MsrunSpec
-  before do
-    super
-    @file = TESTFILES + '/opd1/000.v1.mzXML'
   end
 
-  it 'can give start and end mz' do
-    # scan has attributes startMz endMz
-    Ms::Msrun.open(@file) do |ms|
-      #ms.start_and_end_mz.must_equal([300.0, 1500.0])
-      ms.start_and_end_mz.must_equal(key['start_and_end_mz'][1])
-    end
-  end
-end
-
-class Mzxml_v2_0 < MiniTest::Spec
-  include MsrunSpec
-  before do
-    super
+  describe 'reading an mzXML v2.0 file' do
     @file = TESTFILES + '/opd1/020.v2.0.readw.mzXML'
+    (@key, @nums) = before_all.call(@file)
+    behaves_like 'an msrun object'
   end
-end
 
-class Mzxml_v2_1 < MiniTest::Spec
-  include MsrunSpec
-  before do
-    super
+  describe 'reading an mzXML v2.1 file' do
     @file = TESTFILES + '/opd1/000.v2.1.mzXML'
-  end
+    (@key, @nums) = before_all.call(@file)
+    behaves_like 'an msrun object'
 
-  it 'gives nil if scans do not have start and end mz info' do
-    # scans do not have startMz endMz or filterLine
-    Ms::Msrun.open(@file) do |ms|
-      ms.start_and_end_mz.must_equal([nil, nil])
+    it 'gives nil if scans do not have start and end mz info' do
+      # scans do not have startMz endMz or filterLine
+      Ms::Msrun.open(@file) do |ms|
+        ms.start_and_end_mz.is([nil, nil])
+      end
     end
-  end
 
-  it 'gives start and end mz if filterLine present' do
-    newname = @file + ".TMP.mzXML"
-    File.open(newname, 'w') do |out|
-      IO.foreach(@file) do |line|
-        if line =~ /msLevel="1"/
-          out.puts %Q{        filterLine="FTMS + p NSI Full ms [300.00-1500.00]"}
+    it 'gives start and end mz if filterLine present' do
+      newname = @file + ".TMP.mzXML"
+      File.open(newname, 'w') do |out|
+        IO.foreach(@file) do |line|
+          if line =~ /msLevel="1"/
+            out.puts %Q{        filterLine="FTMS + p NSI Full ms [300.00-1500.00]"}
+          end
+          out.print line
         end
-        out.print line
       end
+      Ms::Msrun.open(newname) do |ms|
+        ms.start_and_end_mz.is([300.0, 1500.0])
+      end
+      File.unlink(newname) if File.exist?(newname)
     end
-    Ms::Msrun.open(newname) do |ms|
-      ms.start_and_end_mz.must_equal([300.0, 1500.0])
-    end
-    File.unlink(newname) if File.exist?(newname)
-  end
 
+  end
 end
-