file.cpp

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/*-
 * SPDX-License-Identifier: BSD-2-Clause
 *
 * Copyright (c) 2022 NKI/AVL, Netherlands Cancer Institute
 *
 * 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 "cif++/file.hpp"
#include "cif++/gzio.hpp"

namespace cif
{

// --------------------------------------------------------------------
void file::set_validator(const validator *v)
{
    m_validator = v;
    for (auto &db : *this)
        db.set_validator(v);
}

bool file::is_valid() const
{
    if (m_validator == nullptr)
        std::runtime_error("No validator loaded explicitly, cannot continue");

    bool result = true;
    for (auto &d : *this)
        result = d.is_valid() and result;

    if (result)
        result = validate_links();

    return result;
}

bool file::is_valid()
{
    if (m_validator == nullptr)
    {
        if (VERBOSE > 0)
            std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;

        load_dictionary();
    }

    bool result = not empty();

    for (auto &d : *this)
        result = d.is_valid() and result;

    if (result)
        result = validate_links();

    return result;
}

bool file::validate_links() const
{
    if (m_validator == nullptr)
        std::runtime_error("No validator loaded explicitly, cannot continue");
    
    bool result = true;

    for (auto &db : *this)
        result = db.validate_links() and result;
    
    return result;
}

void file::load_dictionary()
{
    if (not empty())
    {
        auto *audit_conform = front().get("audit_conform");
        if (audit_conform and not audit_conform->empty())
        {
            std::string name = audit_conform->front().get<std::string>("dict_name");

            if (name == "mmcif_pdbx_v50")
                name = "mmcif_pdbx.dic";    // we had a bug here in libcifpp... 

            if (not name.empty())
            {
                try
                {
                    load_dictionary(name);
                }
                catch (const std::exception &ex)
                {
                    if (VERBOSE)
                        std::cerr << "Failed to load dictionary " << std::quoted(name) << ": " << ex.what() << std::endl;
                }
            }
        }
    }

    // if (not m_validator)
    //  load_dictionary("mmcif_pdbx.dic");  // TODO: maybe incorrect? Perhaps improve?
}

void file::load_dictionary(std::string_view name)
{
    set_validator(&validator_factory::instance()[name]);
}

bool file::contains(std::string_view name) const
{
    return std::find_if(begin(), end(), [name](const datablock &db) { return iequals(db.name(), name); }) != end();
}

datablock &file::operator[](std::string_view name)
{
    auto i = std::find_if(begin(), end(), [name](const datablock &c)
        { return iequals(c.name(), name); });

    if (i != end())
        return *i;

    emplace_back(name);
    return back();
}

const datablock &file::operator[](std::string_view name) const
{
    static const datablock s_empty;
    auto i = std::find_if(begin(), end(), [name](const datablock &c)
        { return iequals(c.name(), name); });
    return i == end() ? s_empty : *i;
}

std::tuple<file::iterator, bool> file::emplace(std::string_view name)
{
    bool is_new = true;

    auto i = begin();
    while (i != end())
    {
        if (iequals(name, i->name()))
        {
            is_new = false;

            if (i != begin())
            {
                auto n = std::next(i);
                splice(begin(), *this, i, n);
            }

            break;
        }

        ++i;
    }

    if (is_new)
    {
        auto &db = emplace_front(name);
        db.set_validator(m_validator);
    }

    return std::make_tuple(begin(), is_new);
}

void file::load(const std::filesystem::path &p)
{
    try
    {
        gzio::ifstream in(p);
        if (not in.is_open())
            throw std::runtime_error("Could not open file " + p.string());

        load(in);
    }
    catch (const std::exception &)
    {
        throw_with_nested(std::runtime_error("Error reading file " + p.string()));
    }
}

void file::load(std::istream &is)
{
    auto saved = m_validator;
    set_validator(nullptr);

    parser p(is, *this);
    p.parse_file();

    if (saved != nullptr)
        set_validator(saved);
    else
        load_dictionary();
}

void file::save(const std::filesystem::path &p) const
{
    gzio::ofstream outFile(p);
    save(outFile);
}

void file::save(std::ostream &os) const
{
    // if (not is_valid())
    //  std::cout << "File is not valid!" << std::endl;

    for (auto &db : *this)
        db.write(os);
}

} // namespace cif