- add cross ref element as discussed in HARMONY 2019

- the Content element has a list of crossReft element
sbmlteam · Mar 27, 2019 · ac32a7a · ac32a7a
1 parent 8902b68
commit ac32a7a
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Showing 92 changed files with 13,103 additions and 745 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,9 @@
 doc
 *.bak
 *.user
-.idea/
+.idea/
+.vs
+.vscode
+build
+temp_deviser_file.xml
+.DS_Store
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.2.2
+0.2.3
diff --git a/dev/combine-archive.xml b/dev/combine-archive.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package name="Combine" fullname="Combine Archive" version="1" required="false">
-  <language name="OMEX" baseClass="CaBase" documentClass="OmexManifest" prefix="Ca" libraryName="libCombine" isPackage="false">
+  <language name="OMEX" baseClass="CaBase" documentClass="OmexManifest" prefix="Ca" libraryName="libCombine" isPackage="false" uses_ASTNode="true" uses_XMLNode="true">
     <library_version major="1" minor="0" revision="0"/>
-    <versions>
-      <version namespace="http://identifiers.org/combine.specifications/omex-manifest"/>
-    </versions>
+    <language_versions>
+      <version level="1" version="1" namespace="http://identifiers.org/combine.specifications/omex-manifest"/>
+    </language_versions>
   </language>
   <versions>
     <pkgVersion level="3" version="1" pkg_version="1">
@@ -14,13 +14,19 @@
             <attribute name="location" required="true" type="string" abstract="false"/>
             <attribute name="format" required="true" type="string" abstract="false"/>
             <attribute name="master" required="false" type="bool" abstract="false"/>
+            <attribute name="crossRef" required="false" type="inline_lo_element" element="CrossRef" abstract="false"/>
           </attributes>
         </element>
         <element name="OmexManifest" typeCode="LIB_COMBINE_OMEXMANIFEST" hasListOf="false" hasChildren="false" hasMath="false" childrenOverwriteElementName="false" abstract="false">
           <attributes>
             <attribute name="content" required="false" type="inline_lo_element" element="Content" abstract="false"/>
           </attributes>
         </element>
+        <element name="CrossRef" typeCode="LIB_COMBINE_CROSSREF" hasListOf="true" hasChildren="false" hasMath="false" childrenOverwriteElementName="false" minNumListOfChildren="0" maxNumListOfChildren="0" abstract="false" elementName="crossRef">
+          <attributes>
+            <attribute name="location" required="true" type="string" abstract="false"/>
+          </attributes>
+        </element>
       </elements>
     </pkgVersion>
   </versions>

diff --git a/dev/generated/CMakeLists.txt b/dev/generated/CMakeLists.txt
@@ -40,7 +40,7 @@ if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt")
 endif()
 
 MATH(EXPR LIBCOMBINE_VERSION_NUMERIC "${LIBCOMBINE_VERSION_MAJOR} * 10000 + ${LIBCOMBINE_VERSION_MINOR} * 100 + ${LIBCOMBINE_VERSION_PATCH}" )
-set(LIBCOMBINE_VERSION "${LIBCOMBINE_VERSION_MAJOR}.${LIBCOMBINE_VERSION_MINOR}.${LIBCOMBINE_VERSION_PATCH}${LIBCOMBINE_VERSION_RELEASE}")
+set(PACKAGE_VERSION "${LIBCOMBINE_VERSION_MAJOR}.${LIBCOMBINE_VERSION_MINOR}.${LIBCOMBINE_VERSION_PATCH}${LIBCOMBINE_VERSION_RELEASE}")
 set(PACKAGE_NAME "libCombine")
 
 # add make dist and make check target as they are already familiar for
@@ -69,16 +69,19 @@ set(CPACK_RPM_PACKAGE_LICENSE "BSD")
 set(CPACK_RPM_PACKAGE_GROUP "Libraries/Development")
 set(CPACK_DEBIAN_PACKAGE_SECTION "Libraries")
 
-set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR};/.svn/;/.libs/;/.deps/;/.bzr/;.*.o$;.*.lo$;.*.la$;/.git/;${CPACK_SOURCE_IGNORE_FILES};/.DS_Store;/.svnignore;blib;libsbml-dist;*.txt.user")
+set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR};/out/;/.git/;/.svn/;/.libs/;/.deps/;/.bzr/;.*.pyc$;.*.o$;.*.lo$;.*.la$;${CPACK_SOURCE_IGNORE_FILES};/.DS_Store;/.svnignore;blib;libcombine-dist")
+
+if(UNIX)
+    set(CPACK_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+    set(CPACK_SET_DESTDIR "ON")
+endif()
 
-set(ADDITIONAL_LIB_DIRS)
 if(CMAKE_SIZEOF_VOID_P EQUAL 4)
     set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "i386")
     set(CPACK_RPM_PACKAGE_ARCHITECTURE "i386")
 else()
     set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
     set(CPACK_RPM_PACKAGE_ARCHITECTURE "x86_64")
-    set(ADDITIONAL_LIB_DIRS "/usr/lib64" "/usr/lib/x86_64-linux-gnu/")
 endif()
 
 include(CPack)
@@ -173,8 +176,6 @@ if("${LIBCOMBINE_DEPENDENCY_DIR}" STREQUAL "")
   "Directory containing libraries that libCombine depends upon. (Particularly important on Windows.)" FORCE)
 endif()
 
-set(LIBCOMBINE_ROOT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
-set(LIBCOMBINE_ROOT_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR})
 
 ###############################################################################
 #
@@ -191,6 +192,9 @@ if(WITH_SWIG)
     find_program(SWIG_EXECUTABLE
       NAMES swig
       PATHS
+        c:/swigwin-3.0.12
+        c:/swigwin-3.0.10
+        c:/swigwin-3.0.8
         c:/swigwin-3.0.5
         c:/swigwin-3.0.2
         c:/swigwin-3.0.0
@@ -385,13 +389,13 @@ if(UNIX OR CYGWIN)
     set(PATH_SEP "/")
     set(FILE_SEP ":")
     set( MISC_PREFIX "share/libcombine/" )
-    set(LIBCOMBINE_LIBRARY omex)
+    set(LIBCOMBINE_LIBRARY combine)
 else()
     set( MISC_PREFIX "" )
     set(PATH_SEP "\\")
     set(FILE_SEP ";")
     if(MINGW)
-        set(LIBCOMBINE_LIBRARY omex)
+        set(LIBCOMBINE_LIBRARY combine)
     else()
         set(LIBCOMBINE_LIBRARY libcombine)
     endif()
@@ -474,11 +478,11 @@ if(UNIX)
         set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DLINUX")
     endif(APPLE)
 
-    add_definitions( -DPACKAGE_VERSION=\"${LIBCOMBINE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
-    set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DPACKAGE_VERSION=\"${LIBCOMBINE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\"")
+    add_definitions( -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
+    set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\"")
 
 else(UNIX)
-    add_definitions(-DPACKAGE_VERSION=\"${LIBCOMBINE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
+    add_definitions(-DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
 
     add_definitions(-DWIN32)
     set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DWIN32")
@@ -576,7 +580,7 @@ endif()
 
 ###############################################################################
 #
-# Initialize OMEX sources
+# Initialize LIBCOMBINE sources
 #
 set(LIBCOMBINE_SOURCES)
 
@@ -665,6 +669,7 @@ add_subdirectory(src/bindings)
 
 
 
+
 ###############################################################################
 #
 # Build examples if specified
@@ -708,16 +713,14 @@ endif()
 
 message(STATUS "
 ----------------------------------------------------------------------
-libCombine version ${LIBCOMBINE_VERSION}
+libCombine version ${PACKAGE_VERSION}
 ----------------------------------------------------------------------
 
    More information and the latest version are available online at
-   https://github.com/fbergmann/libCombine/
 
    Please report problems using the issue tracker at
-   https://github.com/fbergmann/libCombine/issues
 
-   To contact the developers directly, email fbergman@caltech.edu
+   To contact the developers directly, email sbml-team@caltech.edu
 
    Configured on host '${HOSTNAME}'
      host type                     = ${CMAKE_SYSTEM_NAME}

diff --git a/dev/generated/src/CMakeLists.txt b/dev/generated/src/CMakeLists.txt
@@ -84,7 +84,7 @@ configure_file(
     ${CMAKE_CURRENT_BINARY_DIR}/omex/common/libcombine-config-common.h
 )
 
-# Replace: @LIBCOMBINE_VERSION@ and @LIBCOMBINE_VERSION_NUMERIC@
+# Replace: @PACKAGE_VERSION@ and @LIBCOMBINE_VERSION_NUMERIC@
 configure_file (
   "${CMAKE_CURRENT_SOURCE_DIR}/omex/common/libcombine-version.h.cmake"
   "${CMAKE_CURRENT_BINARY_DIR}/omex/common/libcombine-version.h"
@@ -95,10 +95,6 @@ configure_file (
   "${CMAKE_CURRENT_BINARY_DIR}/omex/common/libcombine-namespace.h"
 )
 
-configure_file (
-  "${CMAKE_CURRENT_SOURCE_DIR}/omex/common/libcombine-package.h.cmake"
-  "${CMAKE_CURRENT_BINARY_DIR}/omex/common/libcombine-package.h"
-)
 
 ###############################################################################
 #

diff --git a/dev/generated/src/bindings/csharp/AssemblyInfo.cs.in b/dev/generated/src/bindings/csharp/AssemblyInfo.cs.in
@@ -2,12 +2,12 @@ using System.Reflection;
 using System.Runtime.CompilerServices;
 using System.Runtime.InteropServices;
 
-[assembly: AssemblyTitle("libCombine C# Binding Proxy Class DLL")]
+[assembly: AssemblyTitle("libSEDML C# Binding Proxy Class DLL")]
 [assembly: AssemblyDescription("")]
 [assembly: AssemblyConfiguration("")]
-[assembly: AssemblyCompany("The SBML Team")]
-[assembly: AssemblyProduct("libcombinecsP.dll")]
-[assembly: AssemblyCopyright("Copyright (C) 2016 SBML Team")]
+[assembly: AssemblyCompany("The SEDML Team")]
+[assembly: AssemblyProduct("libsedmlcsP.dll")]
+[assembly: AssemblyCopyright("Copyright (C) Frank T. Bergmann 2013")]
 [assembly: AssemblyTrademark("")]
 [assembly: AssemblyCulture("")]
 

diff --git a/dev/generated/src/bindings/csharp/compile-native-files.cmake b/dev/generated/src/bindings/csharp/compile-native-files.cmake
@@ -7,7 +7,11 @@
  # This file is part of libSBML. Please visit http://sbml.org for more
  # information about SBML, and the latest version of libSBML.
  #
- # Copyright (C) 2013-2016 jointly by the following organizations:
+ # Copyright (C) 2019 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2013-2018 jointly by the following organizations:
  # 1. California Institute of Technology, Pasadena, CA, USA
  # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
  # 3. University of Heidelberg, Heidelberg, Germany

diff --git a/dev/generated/src/bindings/csharp/libcombine.i b/dev/generated/src/bindings/csharp/libcombine.i
@@ -7,7 +7,11 @@
  * This file is part of libSBML. Please visit http://sbml.org for more
  * information about SBML, and the latest version of libSBML.
  *
- * Copyright (C) 2013-2016 jointly by the following organizations:
+ * Copyright (C) 2019 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
  * 1. California Institute of Technology, Pasadena, CA, USA
  * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
  * 3. University of Heidelberg, Heidelberg, Germany

diff --git a/dev/generated/src/bindings/csharp/local.cpp b/dev/generated/src/bindings/csharp/local.cpp
@@ -7,7 +7,11 @@
  * This file is part of libSBML. Please visit http://sbml.org for more
  * information about SBML, and the latest version of libSBML.
  *
- * Copyright (C) 2013-2016 jointly by the following organizations:
+ * Copyright (C) 2019 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
  * 1. California Institute of Technology, Pasadena, CA, USA
  * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
  * 3. University of Heidelberg, Heidelberg, Germany

diff --git a/dev/generated/src/bindings/csharp/local.i b/dev/generated/src/bindings/csharp/local.i
@@ -7,7 +7,11 @@
  * This file is part of libSBML. Please visit http://sbml.org for more
  * information about SBML, and the latest version of libSBML.
  *
- * Copyright (C) 2013-2016 jointly by the following organizations:
+ * Copyright (C) 2019 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
  * 1. California Institute of Technology, Pasadena, CA, USA
  * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
  * 3. University of Heidelberg, Heidelberg, Germany
@@ -201,6 +205,9 @@ SWIGCSHARP_IMTYPE_WSTRING(const char*)
     case (int) libcombine.LIB_COMBINE_CONTENT:
       return new CaContent(cPtr, owner);
 
+    case (int) libcombine.OMEX_COMBINE_CROSSREF:
+      return new CaCrossRef(cPtr, owner);
+
     case (int) libcombine.OMEX_LIST_OF:
       String name = sb.getElementName();
       if(name == "listOf")
@@ -211,6 +218,10 @@ SWIGCSHARP_IMTYPE_WSTRING(const char*)
       {
          return new CaListOfContents(cPtr, owner);
       }
+      else if (name == "listOfCrossRefs")
+      {
+         return new CaListOfCrossRefs(cPtr, owner);
+      }
 
       return new CaListOf(cPtr, owner);        
 
@@ -551,7 +562,9 @@ COVARIANT_RTYPE_CLONE(CaConstructorException)
 COVARIANT_RTYPE_CLONE(CaNamespaces)
 COVARIANT_RTYPE_CLONE(CaContent)
 COVARIANT_RTYPE_CLONE(CaOmexManifest)
+COVARIANT_RTYPE_CLONE(CaCrossRef)
 COVARIANT_RTYPE_CLONE(CaListOfContents)
+COVARIANT_RTYPE_CLONE(CaListOfCrossRefs)
 
 /**
 *
@@ -601,6 +614,7 @@ COVARIANT_RTYPE_LISTOF_GET_REMOVE(Unit)
 %csmethodmodifiers ListOfLocalParameters::remove(unsigned int n)  "public new"
 
 COVARIANT_RTYPE_LISTOF_GET_REMOVE(CaListOfContents)
+COVARIANT_RTYPE_LISTOF_GET_REMOVE(CaListOfCrossRefs)
 
 %define COVARIANT_GETID(_CNAME_)
 %typemap(cstype) string   _CNAME_ ## ::getId  "_CNAME_"
@@ -733,7 +747,9 @@ COVARIANT_RTYPE_LISTOF_GET_REMOVE(CaListOfContents)
 
 SEDMLCONSTRUCTOR_EXCEPTION(CaContent)
 SEDMLCONSTRUCTOR_EXCEPTION(CaOmexManifest)
+SEDMLCONSTRUCTOR_EXCEPTION(CaCrossRef)
 SEDMLCONSTRUCTOR_EXCEPTION(CaListOfContents)
+SEDMLCONSTRUCTOR_EXCEPTION(CaListOfCrossRefs)
 
 %define XMLCONSTRUCTOR_EXCEPTION(SBASE_CLASS_NAME)
 %exception SBASE_CLASS_NAME