LookupTableLoader.cpp

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#include <boost/archive/archive_exception.hpp>
#include <sys/stat.h> // For system commands to download and unpack Lookup Table file.

// Chaste source includes
#include "CheckpointArchiveTypes.hpp" // Should be included first in Chaste related files.

#include "CommandLineArguments.hpp"
#include "FileFinder.hpp"

// ApPredict includes
#include "LookupTableGenerator.hpp"
#include "LookupTableLoader.hpp"

const std::string LookupTableLoader::mRemoteURL = "https://cardiac.nottingham.ac.uk/lookup_tables/";

LookupTableLoader::LookupTableLoader(const std::string& rModelName, const double& rHertz)
        : mModelName(rModelName),
          mHertz(rHertz),
          mIdealLookupTable(""),
          mBestAvailableLookupTable("")
{
    // Here we will attempt to use any lookup table associated with this model and
    // pacing rate.
    std::stringstream lookup_table_archive_name;
    lookup_table_archive_name << mModelName;

    // We will parse the command line arguments and work out minimal set of channels that are involved.
    // N.B. this vector should agree with the ordering in the tuple at the top of
    // TestMakeALookupTable to get the correct orderings in the filenames.
    // first -- channel name
    // second -- whether it is needed for a lookup table.
    mIdealChannelsInvolved = std::vector<std::pair<std::string, bool> >{
        std::pair<std::string, bool>{ "hERG", false },
        std::pair<std::string, bool>{ "IKs", false },
        std::pair<std::string, bool>{ "INa", false },
        std::pair<std::string, bool>{ "ICaL", false },
        std::pair<std::string, bool>{ "Ito", false },
        std::pair<std::string, bool>{ "INaL", false },
        std::pair<std::string, bool>{ "IK1", false }
    };

    // This modifies #mIdealChannelsInvolved to match command line args.
    DecideIdealTable();
    std::cout << "My ideal lookup table would be " << mIdealLookupTable << std::endl;

    LoadTableFromLocalBoostArchive(mIdealLookupTable);

    // Only continue with the logic if the local ideal table wasn't loaded.
    if (mpLookupTable == nullptr)
    {
        // Get lists of available files
        std::vector<std::string> website_list = GetManifestOfTablesOnGarysWebsite();
        std::vector<std::string> local_list = GetManifestOfLocalTablesInCwd();

        // Get all plausible combos that might actually work.
        std::vector<std::string> possible_list = GenerateAllCompatibleTables();
        for (unsigned i = 0; i < possible_list.size(); i++)
        {
            //std::cout << "Possible: " << possible_list[i] << std::endl;

            // See if it appears in any local files?
            if (std::find(local_list.begin(), local_list.end(), possible_list[i]) != local_list.end())
            {
                std::cout << "Local lookup table found for " << possible_list[i] << std::endl;
                mBestAvailableLookupTable = possible_list[i];
                break;
            }

            // Or web files?
            if (std::find(website_list.begin(), website_list.end(), possible_list[i]) != website_list.end())
            {
                std::cout << "Web lookup table found for " << possible_list[i] << std::endl;
                mBestAvailableLookupTable = possible_list[i];
                // Download and unpack it
                DownloadAndUnpack(mBestAvailableLookupTable);
                break;
            }
        }

        if (mBestAvailableLookupTable != "")
        {
            LoadTableFromLocalBoostArchive(mBestAvailableLookupTable);
        }
        else
        {
            WARNING("No lookup table is available, please run without --credible-intervals.");
        }
    }
}

void LookupTableLoader::DecideIdealTable()
{
    // Parse the inputs
    CommandLineArguments* p_args = CommandLineArguments::Instance();
    unsigned ideal_dimension = 0u;

    // can't read from ApPredictMethods' mShortNames since they are in a different order, for historical reasons!!
    // so redefined here (not ideal).
    std::vector<std::string> command_line_names{ "herg", "iks", "na", "cal", "ito", "nal", "ik1" };

    // Got through command line args in order that we want them in the file name
    std::string ideal_lookup_table;
    for (unsigned i = 0; i < command_line_names.size(); i++)
    {
        if (p_args->OptionExists("--ic50-" + command_line_names[i])
            || p_args->OptionExists("--pic50-" + command_line_names[i])
            || p_args->OptionExists("--ic50-drug-two-" + command_line_names[i])
            || p_args->OptionExists("--pic50-drug-two-" + command_line_names[i]))
        {
            mIdealChannelsInvolved[i].second = true;
            ideal_lookup_table += "_" + mIdealChannelsInvolved[i].first;
            ideal_dimension++;
        }
    }

    // Add suffix
    std::stringstream hertz;
    hertz << mHertz;
    mIdealLookupTable = mModelName + "_" + std::to_string(ideal_dimension) + "d" + ideal_lookup_table + "_" + hertz.str() + "Hz_generator";
}

void LookupTableLoader::LoadTableFromLocalBoostArchive(const std::string& rLookupTableBaseName)
{
    // See if there is a table available in current working directory.
    FileFinder ascii_archive_file(rLookupTableBaseName + ".arch", RelativeTo::AbsoluteOrCwd);
    FileFinder binary_archive_file(rLookupTableBaseName + "_BINARY.arch", RelativeTo::AbsoluteOrCwd);

    if (!ascii_archive_file.IsFile() && !binary_archive_file.IsFile())
    {
        // Neither local ascii nor binary are present.
        return;
    }

    // First we try loading the binary version of the archive, if it exists.
    if (binary_archive_file.IsFile())
    {
        std::cout << "Loading lookup table from binary archive into memory, this "
                     "can take a few seconds..."
                  << std::flush;
        Timer::Reset();

        // Create a pointer to the input archive
        std::ifstream ifs((binary_archive_file.GetAbsolutePath()).c_str(),
                          std::ios::binary);
        boost::archive::binary_iarchive input_arch(ifs);

        // Restore from the archive
        AbstractUntemplatedLookupTableGenerator* p_generator;
        input_arch >> p_generator;
        mpLookupTable.reset(p_generator);

        std::cout << " loaded in " << Timer::GetElapsedTime()
                  << " secs.\nLookup table is available for generation of credible "
                     "intervals.\n";

        // Since loading the binary archive works, we can try and get rid of the
        // ascii one to clean up.
        if (ascii_archive_file.IsFile())
        {
            try
            {
                // The ascii file is not in a testoutput folder so we need to over-ride
                // our usual safety checks.
                ascii_archive_file.DangerousRemove();
                std::cout << "Ascii lookup table archive file removed to tidy up, will "
                             "use the binary one in future."
                          << std::endl;
            }
            catch (Exception& e)
            {
                WARNING("Could not remove ascii lookup table archive, error was: "
                        << e.GetMessage() << "\nSimulations continued anyway.");
            }
        }

        // We have finished and loaded the generator.
        return;
    }

    // If there is no binary archive, then try loading the ascii version and
    // creating a binary one for next time.
    if (ascii_archive_file.IsFile())
    {
        std::cout << "Loading lookup table from file into memory, this can take a "
                     "few seconds..."
                  << std::flush;
        Timer::Reset();

        // Create a pointer to the input archive
        std::ifstream ifs((ascii_archive_file.GetAbsolutePath()).c_str(),
                          std::ios::binary);

        // restore from the archive
        AbstractUntemplatedLookupTableGenerator* p_generator;
        try
        {
            boost::archive::text_iarchive input_arch(ifs);
            input_arch >> p_generator;
        }
        catch (boost::archive::archive_exception& e)
        {
            if (std::string(e.what()) == "unsupported version")
            {
                EXCEPTION(
                    "The lookup table archive was created on a newer version of boost, "
                    "please upgrade your boost to the latest supported by this version "
                    "of Chaste.");
            }
            else
            {
                EXCEPTION("Error in loading Lookup Table from boost archive: '"
                          << e.what() << "'.");
            }
        }
        mpLookupTable.reset(p_generator);

        std::cout << " loaded in " << Timer::GetElapsedTime() << " secs."
                                                                 "\nLookup table is available for generation of credible intervals.\n";

        try
        {
            std::cout << "Saving a binary version of the archive for faster loading next time..." << std::flush;

            // Save a binary version to speed things up next time round.
            AbstractUntemplatedLookupTableGenerator* const p_arch_generator = mpLookupTable.get();

            std::ofstream binary_ofs(binary_archive_file.GetAbsolutePath().c_str(),
                                     std::ios::binary);
            boost::archive::binary_oarchive output_arch(binary_ofs);

            output_arch << p_arch_generator;

            std::cout << "done!\n";
        }
        catch (Exception& e)
        {
            WARNING("Did not manage to create binary lookup table archive. Error was: "
                    << e.GetMessage() << "\nContinuing to use ascii archive.");
        }
    }
}

std::vector<std::string> LookupTableLoader::GetManifestOfTablesOnGarysWebsite()
{
    const std::string manifest_filename = "appredict_lookup_table_manifest.txt";
    std::vector<std::string> available_tables;

    // If no archive exists, try to download and unpack one.
    std::string mainfest_URL = mRemoteURL + manifest_filename;
    FileFinder manifest(manifest_filename, RelativeTo::AbsoluteOrCwd);

    // First check to see whether the remote manifest is accessible
    // The "--server-response" argument prints the server status and the "--spider" means don't download anything.
    std::string command = "wget --server-response --spider " + mainfest_URL;
    int return_code = system(command.c_str());
    if (return_code != 0)
    {
        std::cout << "Could not find the remote manifest of available Lookup Tables on the web, "
                     "we either don't have web access or the lookup table host server is down..."
                  << std::endl;
        return available_tables;
    }

    try
    {
        if (manifest.IsFile())
        {
            std::cout << "\n\nAttempting to overwrite local lookup table manifest with the latest from:\n"
                      << mainfest_URL << "\n\n";
        }
        else
        {
            std::cout << "\n\nAttempting to download lookup table manifest from:\n"
                      << mainfest_URL << "\n\n";
        }

        EXPECT0(system, "wget --dns-timeout=10 --connect-timeout=10 -O " + manifest_filename + " " + mainfest_URL);

        std::cout << "Download succeeded.\n";
    }
    catch (Exception& e)
    {
        std::cout << "Could not download and unpack the Lookup Table manifest, "
                     "we either don't have web access or the lookup table host server is down..."
                  << std::endl;
        return available_tables;
    }

    EXCEPT_IF_NOT(manifest.IsFile());

    std::ifstream manifest_stream(manifest_filename);
    std::string filename;

    // Check for suitable Hertz
    std::stringstream hertz;
    hertz << mHertz;
    std::string hertz_string = hertz.str();

    while (manifest_stream >> filename)
    {
        // If the manifest file starts with the model name
        if (filename.compare(0, mModelName.length(), mModelName) == 0)
        {
            // Look for 'XHz_generator'
            size_t hertz_pos = filename.find(hertz_string + "Hz_generator");
            if (hertz_pos != std::string::npos)
            {
                // Take off .arch.tgz
                size_t extension_pos = filename.find(".arch.tgz");
                available_tables.push_back(filename.substr(0, extension_pos));
            }
        }
    }
    return available_tables;
}

std::vector<std::string> LookupTableLoader::GetManifestOfLocalTablesInCwd()
{
    FileFinder cwd("", RelativeTo::AbsoluteOrCwd);

    std::vector<FileFinder> matching_files = cwd.FindMatches("*.arch");

    const std::string binary_ending = "_BINARY";

    // Check for suitable Hertz
    std::stringstream hertz;
    hertz << mHertz;
    std::string hertz_string = hertz.str();

    std::vector<std::string> available_tables;
    for (unsigned i = 0; i < matching_files.size(); i++)
    {
        std::string base_file_name = matching_files[i].GetLeafNameNoExtension();

        // If matching file ends in _BINARY
        if (0 == base_file_name.compare(base_file_name.length() - binary_ending.length(), binary_ending.length(), binary_ending))
        {
            // Strip off the "_BINARY" extension
            base_file_name = base_file_name.substr(0, base_file_name.length() - binary_ending.length());
        }

        // If the manifest file starts with the model name
        if (base_file_name.compare(0, mModelName.length(), mModelName) == 0)
        {
            // Look for 'XHz_generator'
            size_t hertz_pos = base_file_name.find(hertz_string + "Hz_generator");
            if (hertz_pos != std::string::npos)
            {
                // Only add if it isn't already present
                if (std::find(available_tables.begin(), available_tables.end(), base_file_name) == available_tables.end())
                {
                    available_tables.push_back(base_file_name);
                }
            }
        }
    }
    return available_tables;
}

std::vector<std::string> LookupTableLoader::GenerateAllCompatibleTables()
{

    // Work out how many we start with, ideal number
    unsigned ideal_num = 0;
    std::vector<bool> ideal(7, false);
    for (unsigned i = 0; i < mIdealChannelsInvolved.size(); i++)
    {
        if (mIdealChannelsInvolved[i].second == true)
        {
            ideal_num++;
            ideal[i] = true;
        }
    }

    unsigned max_num_to_add = mIdealChannelsInvolved.size() - ideal_num;

    /*
     * Now follows some fairly horrible logic to do combinations that would work.
     *
     * Probably a far simpler way to do this, but it works!
     */
    std::vector<std::vector<bool> > compatible_channels;
    compatible_channels.push_back(ideal);
    std::vector<std::vector<bool> > compatible_channels_added_this_dim;
    std::vector<std::vector<bool> > start_points_this_dimension;

    start_points_this_dimension.push_back(ideal);
    // Loop over the dimensions (add 1,2,3,4...)
    for (unsigned dim = 0; dim < max_num_to_add; dim++)
    {
        compatible_channels_added_this_dim.clear();
        for (unsigned s = 0; s < start_points_this_dimension.size(); s++)
        {
            std::vector<bool> start_point = start_points_this_dimension[s];
            // Look over the channels
            for (unsigned i = 0; i < mIdealChannelsInvolved.size(); i++)
            {
                if (mIdealChannelsInvolved[i].second == false)
                {
                    std::vector<bool> possible = start_point;
                    possible[i] = true;
                    if (std::find(compatible_channels.begin(), compatible_channels.end(), possible) == compatible_channels.end())
                    {
                        compatible_channels.push_back(possible);
                        compatible_channels_added_this_dim.push_back(possible);
                    }
                }
            }
        }
        start_points_this_dimension.clear();
        start_points_this_dimension = compatible_channels_added_this_dim;
    }

    // Convert bools to filenames
    std::vector<std::string> compatible_tables;
    for (unsigned i = 0; i < compatible_channels.size(); i++)
    {
        std::vector<bool> channels_this_combo = compatible_channels[i];
        std::string channels_text;
        unsigned dimension = 0;
        for (unsigned j = 0; j < mIdealChannelsInvolved.size(); j++)
        {
            if (channels_this_combo[j])
            {
                channels_text += "_" + mIdealChannelsInvolved[j].first;
                dimension++;
            }
        }

        std::stringstream name;
        name << mModelName << "_" << dimension << "d" << channels_text << "_" << mHertz << "Hz_generator";
        compatible_tables.push_back(name.str());
    }
    return compatible_tables;
}

void LookupTableLoader::DownloadAndUnpack(const std::string& rArchiveFileBaseName)
{
    std::string lookup_table_URL = mRemoteURL + rArchiveFileBaseName + ".arch.tgz";
    try
    {
        std::cout << "\n\nAttempting to download an action potential lookup table from:\n"
                  << lookup_table_URL << "\n\n";

        EXPECT0(system, "wget --dns-timeout=10 --connect-timeout=10 " + lookup_table_URL);

        std::cout << "Download succeeded, unpacking...\n";

        EXPECT0(system, "tar xzf " + rArchiveFileBaseName + ".arch.tgz");

        std::cout << "Unpacking succeeded, removing .tgz file...\n";

        EXPECT0(system, "rm -f " + rArchiveFileBaseName + ".arch.tgz");
    }
    catch (Exception& e)
    {
        std::cout << "Could not download and unpack the Lookup Table archive, continuing without it..." << std::endl;
    }
}

bool LookupTableLoader::IsLookupTableAvailable()
{
    return (mpLookupTable != nullptr);
}

boost::shared_ptr<AbstractUntemplatedLookupTableGenerator> LookupTableLoader::GetLookupTable()
{
    if (mpLookupTable == nullptr)
    {
        EXCEPTION("A lookup table could not be loaded.");
    }

    return mpLookupTable;
}


std::string LookupTableLoader::GetIdealTable()
{
    return mIdealLookupTable;
}

std::string LookupTableLoader::GetBestAvailableTable()
{
    return mBestAvailableLookupTable;
}