mzml_spec.rb in mspire-0.6.9

- old
+ new

@@ -1,13 +1,13 @@
 require 'spec_helper'
+require 'builder'
 
 require 'ms/mzml'
 
-describe 'indexed, compressed peaks, mzML file' do
+describe MS::Mzml do
 
-  describe MS::Mzml do
-
+  describe 'reading an indexed, compressed peaks, mzML file' do
     describe 'reading a spectrum' do
 
       before do
         @file = TESTFILES + "/ms/mzml/j24z.idx_comp.3.mzML"
         @io = File.open(@file)
@@ -40,11 +40,72 @@
         mz_sizes = [20168, 315, 634]
         @mzml.each do |spec|
           spec.mzs.size.should == mz_sizes.shift
         end
       end
+    end
+  end
 
+  describe 'writing mzml' do 
+
+    def sanitize_version(string)
+      string.gsub(/"mspire" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})    
     end
+
+    it 'reads MS1 spectra and retention times' do
+
+      spec_params = ['MS:1000127', ['MS:1000511', 1]]
+
+      spec1 = MS::Mzml::Spectrum.new('scan=1', params: spec_params) do |spec|
+        spec.data_arrays = [[1,2,3], [4,5,6]]
+        spec.scan_list = MS::Mzml::ScanList.new do |sl|
+          scan = MS::Mzml::Scan.new do |scan|
+            # retention time of 42 seconds
+            scan.describe! ['MS:1000016', 40.0, 'UO:0000010']
+          end
+          sl << scan
+        end
+      end
+      spec2 = MS::Mzml::Spectrum.new('scan=2', params: spec_params) do |spec| 
+        spec.data_arrays = [[1,2,3.5], [5,6,5]]
+        spec.scan_list = MS::Mzml::ScanList.new do |sl|
+          scan = MS::Mzml::Scan.new do |scan|
+            # retention time of 42 seconds
+            scan.describe! ['MS:1000016', 45.0, 'UO:0000010']
+          end
+          sl << scan
+        end
+      end
+
+      mzml = MS::Mzml.new do |mzml|
+        mzml.id = 'the_little_one'
+        mzml.cvs = MS::Mzml::CV::DEFAULT_CVS
+        mzml.file_description = MS::Mzml::FileDescription.new  do |fd|
+          fd.file_content = MS::Mzml::FileContent.new
+          fd.source_files << MS::Mzml::SourceFile.new
+        end
+        default_instrument_config = MS::Mzml::InstrumentConfiguration.new("IC",[], params: ['MS:1000031'])
+        mzml.instrument_configurations << default_instrument_config
+        software = MS::Mzml::Software.new
+        mzml.software_list << software
+        default_data_processing = MS::Mzml::DataProcessing.new("did_nothing")
+        mzml.data_processing_list << default_data_processing
+        mzml.run = MS::Mzml::Run.new("little_run", default_instrument_config) do |run|
+          spectrum_list = MS::Mzml::SpectrumList.new(default_data_processing)
+          spectrum_list.push(spec1, spec2)
+          run.spectrum_list = spectrum_list
+        end
+      end
+
+      check = TESTFILES + '/ms/mzml/mspire_simulated.noidx.check.mzML'
+      tmpfile = TESTFILES + '/ms/mzml/mspire_simulated.TMP.mzML'
+      mzml.to_xml(tmpfile)
+      xml = sanitize_version(IO.read(tmpfile))
+      xml.should be_a(String)
+      sanitize_version(mzml.to_xml).should == xml
+      xml.should == sanitize_version(IO.read(check))
+      xml.should match(/<mzML/)
+      File.unlink(tmpfile)
+    end
   end
 end
-
 