36 #include "CellMLToSharedLibraryConverter.hpp"
45 #include <boost/foreach.hpp>
49 #include "Warnings.hpp"
52 #include "DynamicModelLoaderRegistry.hpp"
53 #include "GetCurrentWorkingDirectory.hpp"
55 #define IGNORE_EXCEPTIONS(code) \
70 std::string component)
71 : mPreserveGeneratedSources(preserveGeneratedSources),
72 mComponentName(component)
79 DynamicCellModelLoaderPtr p_loader;
82 size_t dot_position = absolute_path.find_last_of(
".");
83 if (dot_position == std::string::npos || absolute_path[dot_position+1] ==
'/')
86 EXCEPTION(
"File does not have an extension: " + absolute_path);
88 std::string extension = absolute_path.substr(dot_position+1);
93 if (extension ==
"so")
95 WARN_ONCE_ONLY(
"CellMLToSharedLibraryConverter asked to load a \".so\" file. On this architecture it should be \".dylib\"");
97 absolute_path.replace(dot_position+1, 5, extension);
102 if (!file_path_copy.
Exists())
104 EXCEPTION(
"Dynamically loadable cell model '" + absolute_path +
"' does not exist.");
106 if (extension ==
"cellml")
109 size_t slash_position = absolute_path.find_last_of(
"/\\");
110 assert(slash_position != std::string::npos);
111 std::string folder = absolute_path.substr(0, slash_position+1);
112 std::string leaf = absolute_path.substr(slash_position+1, dot_position-slash_position);
113 std::string so_path = folder +
"lib" + leaf +
msSoSuffix;
120 EXCEPTION(
"Unable to convert .cellml to .so unless called collectively, due to possible race conditions.");
135 EXCEPTION(
"Unsupported extension '." + extension +
"' of file '" + absolute_path +
"'; must be .so, .dylib or .cellml");
142 const std::string& rCellmlFolder)
147 std::string old_cwd = GetCurrentWorkingDirectory();
151 if (!chaste_root.
IsDir())
154 <<
"' - you need the source to use CellML models directly in Chaste.");
157 if (!component_dir.
IsDir())
169 std::stringstream folder_name;
170 folder_name <<
"dynamic/tmp_" << getpid() <<
"_" << time(NULL);
191 std::vector<FileFinder> cellml_files = cellml_folder.
FindMatches(cellml_leaf_name +
"*");
193 BOOST_FOREACH(
const FileFinder& r_cellml_file, cellml_files)
195 r_cellml_file.
CopyTo(tmp_folder);
199 std::string cmake_lists_filename = tmp_folder.
GetAbsolutePath() +
"/CMakeLists.txt";
200 std::ofstream cmake_lists_filestream(cmake_lists_filename.c_str());
201 cmake_lists_filestream <<
"cmake_minimum_required(VERSION 2.8.12)\n" <<
202 "add_compile_options(-std=c++11)\n" <<
204 "chaste_do_cellml(sources " << cellml_file.
GetAbsolutePath() <<
" " <<
"ON)\n" <<
205 "set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})\n" <<
206 "include_directories(${Chaste_THIRD_PARTY_INCLUDE_DIRS} ${Chaste_INCLUDE_DIRS})\n" <<
207 "add_library(" << cellml_leaf_name <<
" SHARED " <<
"${sources})\n" <<
208 "if (${CMAKE_SYSTEM_NAME} MATCHES \"Darwin\")\n" <<
209 " target_link_libraries(" << cellml_leaf_name <<
" \"-Wl,-undefined,dynamic_lookup\")\n" <<
213 cmake_lists_filestream.close();
214 std::string cmake_args =
" -DCMAKE_PREFIX_PATH=" + chaste_root.
GetAbsolutePath() +
216 " -DChaste_ENABLE_TESTING=OFF" +
217 " -DBUILD_SHARED_LIBS=ON";
219 EXPECT0(system,
"cmake" + cmake_args +
" .");
232 std::vector<FileFinder> generated_files = build_folder.
FindMatches(
"*.?pp");
233 BOOST_FOREACH(
const FileFinder& r_generated_file, generated_files)
235 r_generated_file.
CopyTo(destination_folder_for_sources);
247 so_file.CopyTo(destination_folder);
270 EXCEPTION(
"Conversion of CellML to Chaste shared object failed. Error was: " + e.
GetMessage());
278 const std::string& rModelName,
279 const std::vector<std::string>& rArgs,
280 const std::string& rExtraXml)
284 out_stream p_optfile = rHandler.
OpenOutputFile(rModelName +
"-conf.xml");
285 (*p_optfile) <<
"<?xml version='1.0'?>" << std::endl
286 <<
"<pycml_config>" << std::endl;
289 (*p_optfile) <<
"<command_line_args>" << std::endl;
290 for (
unsigned i=0; i<rArgs.size(); i++)
292 (*p_optfile) <<
"<arg>" << rArgs[i] <<
"</arg>" << std::endl;
294 (*p_optfile) <<
"</command_line_args>" << std::endl;
296 (*p_optfile) << rExtraXml <<
"</pycml_config>" << std::endl;
void DangerousRemove() const
static DynamicModelLoaderRegistry * Instance()
std::string ChasteBuildType()
std::string GetAbsolutePath() const
#define EXCEPTION(message)
FileFinder CopyTo(const FileFinder &rDest) const
#define EXPECT0(cmd, arg)
std::string ChasteBuildDirName()
DynamicCellModelLoaderPtr Convert(const FileFinder &rFilePath, bool isCollective=true)
out_stream OpenOutputFile(const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
std::string GetMessage() const
CellMLToSharedLibraryConverter(bool preserveGeneratedSources=false, std::string component="heart")
DynamicCellModelLoaderPtr GetLoader(const std::string &rPath)
#define EXCEPT_IF_NOT(test)
std::vector< FileFinder > FindMatches(const std::string &rPattern) const
static const std::string msSoSuffix
bool mPreserveGeneratedSources
FileFinder GetParent() const
std::string GetLeafNameNoExtension() const
static void CreateOptionsFile(const OutputFileHandler &rHandler, const std::string &rModelName, const std::vector< std::string > &rArgs, const std::string &rExtraXml="")
void ConvertCellmlToSo(const std::string &rCellmlFullPath, const std::string &rCellmlFolder)
virtual void SetPath(const std::string &rPath, RelativeTo::Value relativeTo)
#define IGNORE_RET(cmd, arg)
std::string mComponentName
bool IsNewerThan(const FileFinder &rOtherEntity) const