[ADD] FileConverter FeatureXML to OMS

src/openms/include/OpenMS/FORMAT/OMSFile.h

@@ -90,6 +90,7 @@ namespace OpenMS
 
   protected:
 
+    // qint64 as key for unique_id, due to sqlite restriction to signed integers.
     using Key = qint64;
 
     LogType log_type_;

src/openms/source/FORMAT/OMSFile.cpp

@@ -297,9 +297,9 @@ namespace OpenMS
       "parent_id INTEGER NOT NULL, "                            \
       "name TEXT NOT NULL, "                                    \
       "data_value_id INTEGER NOT NULL, "                        \
+      "UNIQUE (parent_id, name), "                              \
       "FOREIGN KEY (parent_id) REFERENCES " + parent_ref + ", " \
-      "FOREIGN KEY (data_value_id) REFERENCES DataValue (id), " \
-      "UNIQUE (parent_id, name)");
+      "FOREIGN KEY (data_value_id) REFERENCES DataValue (id)");
   }
 
 
@@ -1478,9 +1478,9 @@ namespace OpenMS
   void OMSFile::OMSFileStore::storeMapMetaData_(const FeatureMap& features)
   {
     createTable_("FEAT_MapMetaData",
-                 "unique_id INTEGER, "          \
-                 "identifier TEXT, "            \
-                 "file_path TEXT, "             \
+                 "unique_id INTEGER UNIQUE NOT NULL, " \
+                 "identifier TEXT, "                   \
+                 "file_path TEXT, "                    \
                  "file_type TEXT");
     QSqlQuery query(QSqlDatabase::database(db_name_));
     // @TODO: worth using a prepared query for just one insert?

src/topp/FileConverter.cpp

@@ -48,13 +48,17 @@
 #include <OpenMS/FORMAT/IBSpectraFile.h>
 #include <OpenMS/FORMAT/SqMassFile.h>
 #include <OpenMS/FORMAT/CachedMzML.h>
+#include <OpenMS/FORMAT/OMSFile.h>
 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
 #include <OpenMS/APPLICATIONS/TOPPBase.h>
 #include <OpenMS/KERNEL/ConversionHelper.h>
 #include <OpenMS/KERNEL/ChromatogramTools.h>
 
 #include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
 #include <OpenMS/FORMAT/DATAACCESS/MSDataCachedConsumer.h>
+#include <OpenMS/METADATA/ID/IdentificationDataConverter.h>
+
+
 
 
 using namespace OpenMS;
@@ -125,6 +129,7 @@ using namespace std;
   @ref OpenMS::KroenikFile "kroenik"
   @ref OpenMS::EDTAFile "edta"
   @ref OpenMS::SqMassFile "sqmass"
+  @ref OpenMS::OMSFile "oms"
 
   @note See @ref TOPP_IDFileConverter for similar functionality for protein/peptide identification file formats.
 
@@ -338,7 +343,7 @@ class TOPPFileConverter :
     String method("none,ensure,reassign");
     setValidStrings_("UID_postprocessing", ListUtils::create<String>(method));
 
-    vector<String> output_formats = {"mzML", "mzXML", "cachedMzML", "mgf", "featureXML", "consensusXML", "edta", "mzData", "dta2d", "csv", "sqmass"};
+    vector<String> output_formats = {"mzML", "mzXML", "cachedMzML", "mgf", "featureXML", "consensusXML", "edta", "mzData", "dta2d", "csv", "sqmass","oms"};
     registerOutputFile_("out", "<file>", "", "Output file");
     setValidFormats_("out", output_formats);
     registerStringOption_("out_type", "<type>", "", "Output file type -- default: determined from file extension or content\nNote: that not all conversion paths work or make sense.", false, true);
@@ -429,14 +434,9 @@ class TOPPFileConverter :
     //-------------------------------------------------------------
     // reading input
     //-------------------------------------------------------------
-    typedef PeakMap MSExperimentType;
-    MSExperimentType exp;
-
-    typedef MSExperimentType::SpectrumType SpectrumType;
-
-    typedef FeatureMap FeatureMapType;
-
-    FeatureMapType fm;
+    typedef MSExperiment::SpectrumType SpectrumType;
+    MSExperiment exp;
+    FeatureMap fm;
     ConsensusMap cm;
 
     writeDebug_(String("Loading input file"), 1);
@@ -504,7 +504,8 @@ class TOPPFileConverter :
       fh.loadFeatures(in, fm, in_type);
       fm.sortByPosition();
       if ((out_type != FileTypes::FEATUREXML) &&
-          (out_type != FileTypes::CONSENSUSXML))
+          (out_type != FileTypes::CONSENSUSXML) &&
+          (out_type != FileTypes::OMS))
       {
         // You will lose information and waste memory. Enough reasons to issue a warning!
         writeLog_("Warning: Converting features to peaks. You will lose information! Mass traces are added, if present as 'num_of_masstraces' and 'masstrace_intensity' (X>=0) meta values.");
@@ -710,7 +711,7 @@ class TOPPFileConverter :
                                                  CONVERSION_MZDATA));
       MzDataFile f;
       f.setLogType(log_type_);
-      ChromatogramTools().convertChromatogramsToSpectra<MSExperimentType>(exp);
+      ChromatogramTools().convertChromatogramsToSpectra<MSExperiment>(exp);
       f.store(out, exp);
     }
     else if (out_type == FileTypes::MZXML)
@@ -722,7 +723,7 @@ class TOPPFileConverter :
       f.setLogType(log_type_);
       f.getOptions().setForceMQCompatability(force_MaxQuant_compatibility);
       f.getOptions().setWriteIndex(write_scan_index);
-      //ChromatogramTools().convertChromatogramsToSpectra<MSExperimentType>(exp);
+      //ChromatogramTools().convertChromatogramsToSpectra<MSExperiment>(exp);
       f.store(out, exp);
     }
     else if (out_type == FileTypes::DTA2D)
@@ -732,7 +733,7 @@ class TOPPFileConverter :
                                                  FORMAT_CONVERSION));
       DTA2DFile f;
       f.setLogType(log_type_);
-      ChromatogramTools().convertChromatogramsToSpectra<MSExperimentType>(exp);
+      ChromatogramTools().convertChromatogramsToSpectra<MSExperiment>(exp);
       if (TIC_DTA2D)
       {
         // store the total ion chromatogram (TIC)
@@ -773,6 +774,11 @@ class TOPPFileConverter :
       {
         MapConversion::convert(cm, true, fm);
       }
+      else if (in_type == FileTypes::OMS)
+      {
+        OMSFile().load(in, fm);
+        IdentificationDataConverter::exportFeatureIDs(fm);
+      }
       else // not loaded as feature map or consensus map
       {
         // The feature specific information is only defaulted. Enough reasons to issue a warning!
@@ -783,7 +789,7 @@ class TOPPFileConverter :
         feature.setQuality(0, 1); // override default
         feature.setQuality(1, 1); // override default
         feature.setOverallQuality(1); // override default
-        for (MSExperimentType::ConstIterator spec_iter = exp.begin();
+        for (MSExperiment::ConstIterator spec_iter = exp.begin();
              spec_iter != exp.end();
              ++spec_iter
              )
@@ -880,6 +886,16 @@ class TOPPFileConverter :
       SqMassFile sqm;
       sqm.store(out, exp);
     }
+    else if (out_type == FileTypes::OMS)
+    {
+      if (in_type != FileTypes::FEATUREXML)
+      {
+        OPENMS_LOG_ERROR << "Incompatible input data: FileConverter can only convert featureXML files to oms format.";
+        return INCOMPATIBLE_INPUT_DATA;
+      }
+      IdentificationDataConverter::importFeatureIDs(fm);
+      OMSFile().store(out, fm);
+    }
     else
     {
       writeLog_("Unknown output file type given. Aborting!");