Merge pull request #405 from sbmlteam/add-infer-reaction-converter

Add basic converter for inferring reactions

examples/c++/CMakeLists.txt

@@ -53,6 +53,7 @@ foreach(example
     createExampleSBML
     echoSBML
     inferUnits
+    inferReactions
     inlineFunctionDefintions
     convertReactions
     getAllElementsWithNotes
@@ -147,6 +148,11 @@ add_test(NAME test_cxx_echoSBML
          ${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
          echoSBML.out.xml
 )
+add_test(NAME test_cxx_inferReactions
+         COMMAND "$<TARGET_FILE:example_cpp_inferReactions>"
+         ${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
+         inferReactions.out.xml
+)
 add_test(NAME test_cxx_inferUnits
          COMMAND "$<TARGET_FILE:example_cpp_inferUnits>"
          ${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml

examples/c++/inferReactions.cpp

@@ -0,0 +1,109 @@
+/**
+ * @file    inferReactions.cpp
+ * @brief   Loads an SBML File and converts ODEs to Reactions
+ * @author  Sarah Keating
+ * @author  Frank T. Bergmann
+ *
+ * <!--------------------------------------------------------------------------
+ * This sample program is distributed under a different license than the rest
+ * of libSBML.  This program uses the open-source MIT license, as follows:
+ *
+ * Copyright (c) 2013-2018 by the California Institute of Technology
+ * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
+ * and the University of Heidelberg (Germany), with support from the National
+ * Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a
+ * copy of this software and associated documentation files (the "Software"),
+ * to deal in the Software without restriction, including without limitation
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ * and/or sell copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ * DEALINGS IN THE SOFTWARE.
+ *
+ * Neither the name of the California Institute of Technology (Caltech), nor
+ * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
+ * of Heidelberg, nor the names of any contributors, may be used to endorse
+ * or promote products derived from this software without specific prior
+ * written permission.
+ * ------------------------------------------------------------------------ -->
+ */
+
+
+#include <iostream>
+#include <sbml/SBMLTypes.h>
+#include <sbml/conversion/ConversionProperties.h>
+
+using namespace std;
+LIBSBML_CPP_NAMESPACE_USE
+
+int
+main (int argc, char *argv[])
+{
+
+  if (argc != 3)
+  {
+    cout 
+	     << endl
+	     << "Usage: inferReactions input-filename output-filename" << endl
+	     << endl
+	     << "This program will attempt to convert all ODEs" << endl
+	     << "contained in the source model, and write a new SBML file."
+	     << endl
+	     << endl;
+    return 1;
+  }
+
+  const char* inputFile   = argv[1];
+  const char* outputFile  = argv[2];
+
+  // read document 
+  SBMLDocument* document  = readSBML(inputFile);
+  unsigned int  errors    = document->getNumErrors(LIBSBML_SEV_ERROR);
+
+  // stop in case of errors
+  if (errors > 0)
+  {
+    cerr << "Encountered the following SBML errors:" << endl;
+    document->printErrors(cerr);
+    cerr << "Conversion skipped.  Please correct the problems above first."
+	 << endl;
+    return errors;
+  }
+
+  // create conversion object that identifies the function definition converter
+  ConversionProperties props;
+  props.addOption("inferReactions", true,
+                  "Infer reactions from rateRules in the model");
+
+  // convert
+  int success = document->convert(props);
+
+  if (success != LIBSBML_OPERATION_SUCCESS)
+  {
+    cerr << "Unable to perform conversion due to the following:" << endl;
+    document->printErrors(cerr);
+    return errors;
+  }   
+  else
+  {
+    cout << "Conversion completed." << endl;
+    writeSBML(document, outputFile);
+  }
+
+  delete document;
+
+  return 0;
+}
+
+