Citations.cpp

/*
 
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This file is part of Chaste.
 
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modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * 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.
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
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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 HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
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*/
 
#include "Citations.hpp"
#include "FilesystemPermissions.hpp"
#include "PetscTools.hpp"
 
// Initialise 'member' variables
std::vector<const char*> Citations::mCitations;
bool Citations::mUseChasteImplementation = false;
 
void Citations::Register(const char pCitation[], PetscBool* pSet)
{
    // Figure out if we can use PETSc's implementation.
    // Note that the effect of this if() is to ensure we don't switch implementation if PETSc is initialised after the first citation is registered.
    // (If PETSc is finalised after the first citation is registered we will probably switch implementation, but there's no way to avoid that.)
    if (!mUseChasteImplementation)
    {
#if ((PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 5) || PETSC_VERSION_MAJOR > 3)
        mUseChasteImplementation = !PetscTools::IsInitialised();
#else
        mUseChasteImplementation = true;
#endif
    }
 
    if (!mUseChasteImplementation)
    {
#if ((PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 5) || PETSC_VERSION_MAJOR > 3)
        PetscCitationsRegister(pCitation, pSet);
#endif
    }
    else if (!(*pSet))
    {
        // Not yet added this one
        mCitations.push_back(pCitation);
        *pSet = PETSC_TRUE;
    }
}
 
void Citations::Print()
{
    if (mUseChasteImplementation)
    {
        if (PetscTools::AmMaster() && CommandLineArguments::Instance()->OptionExists("-citations"))
        {
            std::ostream* p_output = &(std::cout);
            bool writing_to_file = false;
 
            if (CommandLineArguments::Instance()->GetNumberOfArgumentsForOption("-citations") > 0)
            {
                // We've got a file to write to - assume the user has given us something sensible!
                writing_to_file = true;
                std::string out_file_path = CommandLineArguments::Instance()->GetStringCorrespondingToOption("-citations");
                p_output = new std::ofstream(out_file_path.c_str(), std::ios::out);
                EXCEPT_IF_NOT(p_output->good());
                FilesystemPermissions::SetFilePermissions(out_file_path);
            }
 
            /* Write header */
            (*p_output) << "If you publish results based on this computation please cite the following:" << std::endl;
            (*p_output) << "===========================================================================" << std::endl;
            /* Write citations */
            for (unsigned i = 0; i < mCitations.size(); ++i)
            {
                (*p_output) << mCitations[i];
            }
            /* Write footer */
            (*p_output) << "===========================================================================" << std::endl;
 
            if (writing_to_file)
            {
                delete p_output;
            }
        }
    }
}