Merge pull request #144 from fbergmann/set-kisao-name-automatically

When the KiSAO ID is set, automatically set the corresponding name.

CMakeLists.txt

@@ -38,9 +38,13 @@
 #
 ###############################################################################
 
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 2.8.12)
 project (libsedml)
 
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED YES)
+set(CMAKE_CXX_EXTENSIONS NO)
+
 SET (CONAN_PATHS ${CMAKE_BINARY_DIR}/../conan_paths.cmake)
 if (NOT EXISTS ${CONAN_PATHS})
 SET (CONAN_PATHS ${CMAKE_BINARY_DIR}/conan_paths.cmake)
@@ -445,12 +449,8 @@ endif(WITH_CSHARP)
 # or make test
 #
 
-# we do use tests, that require 2.8.4
-cmake_minimum_required(VERSION 2.8.4)
-
 enable_testing()
 
-
 # On some Linux  (64bit) systems (64bit) the libraries should be installed into lib64 rather
 # than lib. It will default to 'lib' but can be overwritten.
 

src/kisao/transform_kisao.py

@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jun 21 12:05:03 2021
+
+@author: Lucian
+"""
+
+import csv
+
+kcpp = open("../sedml/kisaomap.cpp", "w")
+kcpp.write("""
+/**
+ * \\file    kisao.cpp
+ * \\brief   KiSAO map
+ * \\author  Lucian Smith
+ * 
+ * <!--------------------------------------------------------------------------
+ * 
+ * This file is part of libSEDML.  Please visit http://sed-ml.org for more
+ * information about SED-ML. The latest version of libSEDML can be found on 
+ * github: https://github.com/fbergmann/libSEDML/
+ * 
+ * 
+ * Copyright (c) 2013-2021, Frank T. Bergmann  
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met: 
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer. 
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution. 
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ * 
+ * ---------------------------------------------------------------------- -->
+ * 
+ */
+ 
+#include <map>
+#include <string>
+
+std::map<int, std::string> g_kisaomap = {
+""")
+
+with open('KISAO.csv', newline='') as csvfile:
+    reader = csv.reader(csvfile)
+    for row in reader:
+        if "Class ID" in row:
+            continue
+        k_id = int(row[0].split("_")[-1])
+        k_name = row[1]
+        kcpp.write('   {' + str(k_id) + ', "' + k_name + '"},\n')
+        print(k_id, k_name)
+
+kcpp.write("};\n")
+kcpp.close()

src/sedml/SedAlgorithm.cpp

@@ -34,13 +34,16 @@
 #include <sedml/SedAlgorithm.h>
 #include <sbml/xml/XMLInputStream.h>
 
+#include <map>
+
 
 using namespace std;
 
 
 
 LIBSEDML_CPP_NAMESPACE_BEGIN
 
+extern map<int, string> g_kisaomap;
 
 
 
@@ -150,6 +153,12 @@ int
 SedAlgorithm::setKisaoID(const std::string& kisaoID)
 {
   mKisaoID = kisaoID;
+  if (!isSetName()) {
+      int knum = getKisaoIDasInt();
+      if (g_kisaomap.find(knum) != g_kisaomap.end()) {
+          setName(g_kisaomap[knum]);
+      }
+  }
   return LIBSEDML_OPERATION_SUCCESS;
 }
 
@@ -976,6 +985,9 @@ SedAlgorithm::setKisaoID(int kisaoID)
       << std::setw(7)
       << kisaoID; 
   mKisaoID = str.str();
+  if (!isSetName() && g_kisaomap.find(kisaoID) != g_kisaomap.end()) {
+      setName(g_kisaomap[kisaoID]);
+  }
   return LIBSEDML_OPERATION_SUCCESS;
 }
 

src/sedml/SedAlgorithmParameter.cpp

@@ -34,14 +34,15 @@
 #include <sedml/SedAlgorithmParameter.h>
 #include <sedml/SedListOfAlgorithmParameters.h>
 #include <sbml/xml/XMLInputStream.h>
-
+#include <map>
 
 using namespace std;
 
 
 
 LIBSEDML_CPP_NAMESPACE_BEGIN
 
+extern map<int, string> g_kisaomap;
 
 
 
@@ -194,6 +195,12 @@ int
 SedAlgorithmParameter::setKisaoID(const std::string& kisaoID)
 {
   mKisaoID = kisaoID;
+  if (!isSetName()) {
+      int knum = getKisaoIDasInt();
+      if (g_kisaomap.find(knum) != g_kisaomap.end()) {
+          setName(g_kisaomap[knum]);
+      }
+  }
   return LIBSEDML_OPERATION_SUCCESS;
 }
 
@@ -1128,6 +1135,9 @@ SedAlgorithmParameter::setKisaoID(int kisaoID)
       << std::setw(7)
       << kisaoID; 
   mKisaoID = str.str();
+  if (!isSetName() && g_kisaomap.find(kisaoID) != g_kisaomap.end()) {
+      setName(g_kisaomap[kisaoID]);
+  }
   return LIBSEDML_OPERATION_SUCCESS;
 }
 

src/sedml/SedBase.cpp

@@ -2831,7 +2831,7 @@ void
 SedBase::writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream) const
 {
   string sedmlPrefix    = getSedPrefix();
-  if (!mId.empty() && (mIdAllowedPreV4 || getVersion()>=4) || getLevel()>1)
+  if (!mId.empty() && (mIdAllowedPreV4 || getVersion()>=4 || getLevel()>1))
   {
       stream.writeAttribute("id", sedmlPrefix, mId);
   }