spec/ms/mzml_spec.rb in mspire-0.6.22 vs spec/ms/mzml_spec.rb in mspire-0.6.24

- old
+ new

@@ -134,73 +134,16 @@ end #check = TESTFILES + '/ms/mzml/mspire_simulated.noidx.check.mzML' tmpfile = TESTFILES + '/ms/mzml/mspire_simulated.MSn.TMP.mzML' mzml.to_xml(tmpfile) - p 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 + as_string = mzml.to_xml + check_string = IO.read(TESTFILES + '/ms/mzml/mspire_simulated.MSn.check.mzML') - - it 'writes 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 + [IO.read(tmpfile), as_string].each do |st| + sanitize_version(check_string).should == sanitize_version(st) 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) + File.unlink(tmpfile) if File.exist?(tmpfile) end end end