waters_connect support in Skyline and pwiz

pwiz.vcxproj

@@ -465,6 +465,9 @@
     <ClCompile Include="pwiz\data\vendor_readers\UIMF\Reader_UIMF_Test.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UIMF\SpectrumList_UIMF.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\ChromatogramList_UNIFI.cpp" />
+    <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\ParallelDownloadQueue.cpp">
+      <CompileAsManaged Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">true</CompileAsManaged>
+    </ClCompile>
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI_Test.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI_Detail.cpp" />
@@ -613,6 +616,8 @@
       <CompileAsManaged Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">true</CompileAsManaged>
       <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|Win32'">PWIZ_READER_THERMO;PWIZ_READER_AGILENT;PWIZ_READER_BRUKER;PWIZ_READER_WATERS;PWIZ_READER_ABI;PWIZ_READER_ABI_T2D;WIN32;USE_RAW_PTR;PWIZ_BINDINGS_CLI_COMBINED;%(PreprocessorDefinitions)</PreprocessorDefinitions>
       <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">PWIZ_READER_THERMO;PWIZ_READER_AGILENT;PWIZ_READER_BRUKER;PWIZ_READER_WATERS;PWIZ_READER_ABI;PWIZ_READER_ABI_T2D;WIN32;USE_RAW_PTR;PWIZ_BINDINGS_CLI_COMBINED;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <AdditionalUsingDirectories Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">$(SolutionDir)build-nt-x86\msvc-release-x86_64;$(SolutionDir)build-nt-x86\pwiz\utility\bindings\CLI\msvc-14.3\rls\adrs-mdl-64\thrd-mlt\us-clr-tr</AdditionalUsingDirectories>
+      <ForcedUsingFiles Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">pwiz_bindings_cli.dll</ForcedUsingFiles>
     </ClCompile>
     <ClCompile Include="pwiz\utility\bindings\CLI\msdata\Reader.cpp">
       <CompileAsManaged Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|Win32'">true</CompileAsManaged>
@@ -866,8 +871,10 @@
     <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UIMF\UIMFReaderTest.cpp" />
     <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\UnifiData.cpp">
       <ExternalWarningLevel Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">Level1</ExternalWarningLevel>
+      <CompileAsManaged Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">true</CompileAsManaged>
     </ClCompile>
     <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\UnifiDataTest.cpp" />
+    <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\WatersConnectData.ipp" />
     <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\Waters\RawData.cpp" />
     <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\Waters\RawDataTest.cpp" />
     <ClCompile Include="pwiz_tools\BiblioSpec\src\BuildParser.cpp" />
@@ -992,6 +999,7 @@
     <ClInclude Include="pwiz\data\vendor_readers\UIMF\Reader_UIMF.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UIMF\SpectrumList_UIMF.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\ChromatogramList_UNIFI.hpp" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\ParallelDownloadQueue.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI_Detail.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\SpectrumList_UNIFI.hpp" />
@@ -1359,6 +1367,7 @@
     <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\thermo\ScanFilter.h" />
     <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\UIMF\UIMFReader.hpp" />
     <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\UnifiData.hpp" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\WatersConnectProtobuf.hpp" />
     <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Waters\MassLynxRaw.hpp" />
     <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Waters\MassLynxRawChromatogramReader.h" />
     <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Waters\MassLynxRawDataFile.h" />

pwiz.vcxproj.filters

@@ -592,6 +592,8 @@
     <ClCompile Include="libraries\SQLite\sqlite3pp.cpp" />
     <ClCompile Include="pwiz\data\msdata\mzmlb\Connection_mzMLb.cpp" />
     <ClCompile Include="pwiz\analysis\spectrum_processing\MzShiftFilter.cpp" />
+    <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\WatersConnectData.ipp" />
+    <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\ParallelDownloadQueue.cpp" />
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="libraries\boost_aux\boost\nowide\args.hpp" />
@@ -1067,6 +1069,8 @@
     <ClInclude Include="libraries\SQLite\sqlite3pp.h" />
     <ClInclude Include="pwiz\data\msdata\mzmlb\Connection_mzMLb.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\MzShiftFilter.hpp" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\WatersConnectProtobuf.hpp" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\UNIFI\ParallelDownloadQueue.hpp" />
   </ItemGroup>
   <ItemGroup>
     <None Include="Jamroot.jam" />

pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.cpp

@@ -41,6 +41,8 @@
 #include "pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.hpp"
 #include "pwiz/data/vendor_readers/Waters/Reader_Waters.hpp"
 #include "pwiz/data/vendor_readers/Waters/SpectrumList_Waters.hpp"
+#include "pwiz/data/vendor_readers/UNIFI/Reader_UNIFI.hpp"
+#include "pwiz/data/vendor_readers/UNIFI/SpectrumList_UNIFI.hpp"
 #include "SpectrumList_LockmassRefiner.hpp"
 
 
@@ -113,6 +115,12 @@ SpectrumList_PeakPicker::SpectrumList_PeakPicker(
         {
             mode_ = 8;
         }
+
+        detail::SpectrumList_UNIFI* waters_connect = dynamic_cast<detail::SpectrumList_UNIFI*>(&*inner);
+        if (waters_connect && waters_connect->isWatersConnect())
+        {
+            mode_ = 9;
+        }
     }
 
     // add processing methods to the copy of the inner SpectrumList's data processing
@@ -137,6 +145,8 @@ SpectrumList_PeakPicker::SpectrumList_PeakPicker(
         method.userParams.push_back(UserParam("Waters/MassLynx peak picking"));
     else if (mode_ == 7)
         method.userParams.push_back(UserParam("Shimadzu peak picking"));
+    else if (mode_ == 9)
+        method.userParams.push_back(UserParam("waters_connect peak picking"));
     else if (algorithm != NULL)
         method.userParams.emplace_back(algorithm->name());
 
@@ -161,7 +171,8 @@ PWIZ_API_DECL bool SpectrumList_PeakPicker::supportsVendorPeakPicking(const std:
                                                + ReaderPtr(new Reader_Bruker_TSF)
                                                + ReaderPtr(new Reader_Shimadzu)
                                                + ReaderPtr(new Reader_Thermo)
-                                               + ReaderPtr(new Reader_Waters);
+                                               + ReaderPtr(new Reader_Waters)
+                                               + ReaderPtr(new Reader_UNIFI);
     return !peakPickingVendorReaders.identify(rawpath).empty();
 }
 
@@ -218,6 +229,10 @@ PWIZ_API_DECL SpectrumPtr SpectrumList_PeakPicker::spectrum(size_t index, Detail
             s = dynamic_cast<SpectrumList_LockmassRefiner*>(&*inner_)->spectrum(index, detailLevel, msLevelsToPeakPick_);
             break;
 
+        case 9:
+            s = dynamic_cast<detail::SpectrumList_UNIFI*>(&*inner_)->spectrum(index, detailLevel, msLevelsToPeakPick_);
+            break;
+
         case 0:
         default:
             s = inner_->spectrum(index, true); // TODO you'd think this would be "detailLevel" instead of "true" but that breaks SpectrumListFactoryTest

pwiz/data/msdata/Reader.cpp

@@ -79,7 +79,7 @@ Reader::Config::Config(const Config& rhs)
 void Reader::Config::instrumentMetadataError(const std::string& msg) const
 {
     if (unknownInstrumentIsError)
-        throw runtime_error(msg + string("; if want to convert the file anyway, use the ignoreUnknownInstrumentError flag"));
+        throw runtime_error(msg + string("; if you want to convert the file anyway, use the ignoreUnknownInstrumentError flag"));
     cerr << msg << endl;
 }
 

pwiz/data/vendor_readers/UNIFI/ChromatogramList_UNIFI.cpp

@@ -95,12 +95,12 @@ PWIZ_API_DECL void ChromatogramList_UNIFI::makeFullFileChromatogram(pwiz::msdata
 
     for (const auto& info : unifiData_->chromatogramInfo())
     {
-        if (!bal::contains(info.id, chromatogramTag) || bal::contains(info.id, "Integrated"))
+        if (!bal::contains(info.name, chromatogramTag) || bal::contains(info.name, "Integrated"))
             continue;
 
-        if (!bxp::regex_match(info.id, what, functionNumberRegex))
+        if (!bxp::regex_match(info.name, what, functionNumberRegex))
         {
-            warn_once(("unable to parse function number from chromatogram name: " + info.id).c_str());
+            warn_once(("unable to parse function number from chromatogram name: " + info.name).c_str());
             continue;
         }
 
@@ -161,33 +161,49 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_UNIFI::chromatogram(size_t index,
     result->id = ie.id;
     result->set(ie.chromatogramType);
 
+    if (detailLevel < DetailLevel_FullMetadata)
+        return result;
+
     bool getBinaryData = detailLevel == DetailLevel_FullData;
 
     switch (ie.chromatogramType)
     {
         case MS_TIC_chromatogram:
         {
-            if (detailLevel < DetailLevel_FullMetadata)
-                return result;
-
             makeFullFileChromatogram(result, "(TIC)", getBinaryData);
         }
         break;
 
         case MS_basepeak_chromatogram:
         {
-            if (detailLevel < DetailLevel_FullMetadata)
-                return result;
-
             makeFullFileChromatogram(result, "(BPC)", getBinaryData);
         }
         break;
 
-        case MS_emission_chromatogram:
+        case MS_SRM_chromatogram:
         {
-            if (detailLevel < DetailLevel_FullMetadata)
-                return result;
+            result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, MS_number_of_detector_counts);
+
+            UnifiChromatogram chromatogram;
+            unifiData_->getChromatogram(ie.chromatogramInfoIndex, chromatogram, getBinaryData);
+            result->defaultArrayLength = chromatogram.arrayLength;
+            result->set(translate(chromatogram.polarity));
+
+            result->precursor.isolationWindow.set(MS_isolation_window_target_m_z, chromatogram.Q1, MS_m_z);
+            //result->precursor.activation.set(MS_collision_energy, );
+
+            result->product.isolationWindow.set(MS_isolation_window_target_m_z, chromatogram.Q3, MS_m_z);
 
+            if (getBinaryData)
+            {
+                swap(chromatogram.timeArray, result->getTimeArray()->data);
+                swap(chromatogram.intensityArray, result->getIntensityArray()->data);
+            }
+        }
+        break;
+
+        case MS_emission_chromatogram:
+        {
             result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, MS_number_of_detector_counts);
 
             UnifiChromatogram chromatogram;
@@ -204,9 +220,6 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_UNIFI::chromatogram(size_t index,
 
         case MS_absorption_chromatogram:
         {
-            if (detailLevel < DetailLevel_FullMetadata)
-                return result;
-
             result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, UO_absorbance_unit);
 
             UnifiChromatogram chromatogram;
@@ -220,6 +233,9 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_UNIFI::chromatogram(size_t index,
             }
         }
         break;
+
+        default:
+            throw std::runtime_error("unhandled chromatogram type");
     }
 
     return result;
@@ -231,12 +247,12 @@ PWIZ_API_DECL void ChromatogramList_UNIFI::createIndex() const
     for (size_t i=0; i < unifiData_->chromatogramInfo().size(); ++i)
     {
         const auto& chromatogramInfo = unifiData_->chromatogramInfo()[i];
-        switch (chromatogramInfo.detectorType)
+        switch (chromatogramInfo.type)
         {
-            case DetectorType::MS:
+            case UnifiChromatogramInfo::TIC:
             {
                 // we only make 1 TIC and BPI chromatogram, not one per function like UNIFI provides
-                if (!hasTIC && bal::contains(chromatogramInfo.id, "(TIC)"))
+                if (!hasTIC && bal::contains(chromatogramInfo.name, "(TIC)"))
                 {
                     hasTIC = true;
                     index_.push_back(IndexEntry());
@@ -256,21 +272,31 @@ PWIZ_API_DECL void ChromatogramList_UNIFI::createIndex() const
             }
             break;
 
-            case DetectorType::FLR:
+            case UnifiChromatogramInfo::MRM:
+            {
+            index_.push_back(IndexEntry());
+            IndexEntry& ie = index_.back();
+            ie.id = "SRM SIC " + chromatogramInfo.name;
+            ie.chromatogramInfoIndex = i;
+            ie.chromatogramType = MS_SRM_chromatogram;
+            }
+            break;
+
+            case UnifiChromatogramInfo::FLR:
             {
                 index_.push_back(IndexEntry());
                 IndexEntry& ie = index_.back();
-                ie.id = chromatogramInfo.id;
+                ie.id = chromatogramInfo.name;
                 ie.chromatogramInfoIndex = i;
                 ie.chromatogramType = MS_emission_chromatogram;
             }
             break;
 
-            case DetectorType::UV:
+            case UnifiChromatogramInfo::UV:
             {
                 index_.push_back(IndexEntry());
                 IndexEntry& ie = index_.back();
-                ie.id = chromatogramInfo.id;
+                ie.id = chromatogramInfo.name;
                 ie.chromatogramInfoIndex = i;
                 ie.chromatogramType = MS_absorption_chromatogram;
             }

pwiz/data/vendor_readers/UNIFI/Reader_UNIFI.cpp

@@ -29,13 +29,18 @@
 #include "pwiz/utility/misc/Std.hpp"
 #include "pwiz/data/msdata/Version.hpp"
 #include <boost/foreach_field.hpp>
+#include <boost/range/algorithm/find_if.hpp>
 
 
 PWIZ_API_DECL std::string pwiz::msdata::Reader_UNIFI::identify(const std::string& filename, const std::string& head) const
 {
     std::string result;
-    if ((bal::istarts_with(filename, "http://") || bal::istarts_with(filename, "https://")) && bal::icontains(filename, "/sampleresults"))
+    if (!bal::istarts_with(filename, "http://") && !bal::istarts_with(filename, "https://"))
+        return result;
+    if (bal::icontains(filename, "/sampleresults"))
         result = getType();
+    else if (bal::icontains(filename, "sampleSetId=") || bal::icontains(filename, "injectionId=")) // both are required but reader will handle the error message
+        result = "waters_connect";
     return result;
 }
 
@@ -73,10 +78,15 @@ void fillInMetadata(const string& sampleResultUrl, MSData& msd, const UnifiDataP
         else
             msd.fileDescription.fileContent.set(MS_SRM_chromatogram);
     }*/
+
+    string apiName = "UNIFI";
+    if (unifiData->getRemoteApiType() == UnifiData::RemoteApi::Waters_Connect)
+        apiName = "waters_connect";
+
     auto queryStrBegin = sampleResultUrl.rfind(")?");
     SourceFilePtr sourceFile(new SourceFile);
     bfs::path p(sampleResultUrl);
-    sourceFile->id = "UNIFI";
+    sourceFile->id = apiName;
     sourceFile->location = sampleResultUrl.substr(0, (queryStrBegin != string::npos ? queryStrBegin + 1 : sampleResultUrl.length()));
     //sourceFile->set(MS_WIFF_nativeID_format);
     //sourceFile->set(MS_UNIFI_WIFF_format);
@@ -97,8 +107,11 @@ void fillInMetadata(const string& sampleResultUrl, MSData& msd, const UnifiDataP
     sourceFile->name = msd.id;
 
     SoftwarePtr acquisitionSoftware(new Software);
-    acquisitionSoftware->id = "UNIFI";
-    acquisitionSoftware->set(MS_UNIFY);
+    if (unifiData->getRemoteApiType() == UnifiData::RemoteApi::Unifi)
+        acquisitionSoftware->set(MS_UNIFY);
+    else
+        acquisitionSoftware->set(MS_waters_connect);
+    acquisitionSoftware->id = apiName;
     acquisitionSoftware->version = "1.0";
     msd.softwarePtrs.push_back(acquisitionSoftware);
 
@@ -120,8 +133,16 @@ void fillInMetadata(const string& sampleResultUrl, MSData& msd, const UnifiDataP
     if (sl) sl->setDataProcessingPtr(dpPwiz);
     if (cl) cl->setDataProcessingPtr(dpPwiz);
 
-    msd.fileDescription.fileContent.set(MS_MS1_spectrum);
-    msd.fileDescription.fileContent.set(MS_MSn_spectrum);
+    if (unifiData->numberOfSpectra() > 0)
+    {
+        msd.fileDescription.fileContent.set(MS_MS1_spectrum);
+        msd.fileDescription.fileContent.set(MS_MSn_spectrum);
+    }
+
+    const auto& ci = unifiData->chromatogramInfo();
+    bool hasMrm = ci.end() != boost::range::find_if(ci, [](const UnifiChromatogramInfo& info) { return info.type == UnifiChromatogramInfo::MRM; });
+    if (hasMrm)
+        msd.fileDescription.fileContent.set(MS_SRM_chromatogram);
 
     InstrumentConfigurationPtr ic(new InstrumentConfiguration("IC1"));
     ic->set(MS_Waters_instrument_model);

pwiz/data/vendor_readers/UNIFI/Reader_UNIFI_Detail.cpp

@@ -149,8 +149,9 @@ PWIZ_API_DECL CVID translate(Polarity polarity)
         case Polarity::Negative:
             return MS_negative_scan;
         case Polarity::Unknown:
-        default:
             return CVID_Unknown;
+        default:
+            throw std::runtime_error("invalid polarity value");
     }
 }