datablock.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++/datablock.hpp"

namespace cif
{

datablock::datablock(const datablock &db)
    : std::list<category>(db)
    , m_name(db.m_name)
    , m_validator(db.m_validator)
{
    for (auto &cat : *this)
        cat.update_links(*this);
}

datablock &datablock::operator=(const datablock &db)
{
    if (this != &db)
    {
        std::list<category>::operator=(db);
        m_name = db.m_name;
        m_validator = db.m_validator;

        for (auto &cat : *this)
            cat.update_links(*this);
    }

    return *this;
}

void datablock::set_validator(const validator *v)
{
    m_validator = v;

    try
    {
        for (auto &cat : *this)
            cat.set_validator(v, *this);
    }
    catch (const std::exception &)
    {
        throw_with_nested(std::runtime_error("Error while setting validator in datablock " + m_name));
    }
}

const validator *datablock::get_validator() const
{
    return m_validator;
}

bool datablock::is_valid() const
{
    if (m_validator == nullptr)
        throw std::runtime_error("Validator not specified");

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

    return result;
}

bool datablock::validate_links() const
{
    bool result = true;

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

// --------------------------------------------------------------------

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

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

    auto &cat = emplace_back(name);

    if (m_validator)
        cat.set_validator(m_validator, *this);

    return back();
}

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

category *datablock::get(std::string_view name)
{
    auto i = std::find_if(begin(), end(), [name](const category &c)
        { return iequals(c.name(), name); });
    return i == end() ? nullptr : &*i;
}

const category *datablock::get(std::string_view name) const
{
    return const_cast<datablock *>(this)->get(name);
}

std::tuple<datablock::iterator, bool> datablock::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 &c = emplace_front(name);
        c.set_validator(m_validator, *this);
    }

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

std::vector<std::string> datablock::get_tag_order() const
{
    std::vector<std::string> result;

    // for entry and audit_conform on top

    auto ci = find_if(begin(), end(), [](const category &cat) { return cat.name() == "entry"; });
    if (ci != end())
    {
        auto cto = ci->get_tag_order();
        result.insert(result.end(), cto.begin(), cto.end());
    }

    ci = find_if(begin(), end(), [](const category &cat) { return cat.name() == "audit_conform"; });
    if (ci != end())
    {
        auto cto = ci->get_tag_order();
        result.insert(result.end(), cto.begin(), cto.end());
    }

    for (auto &cat : *this)
    {
        if (cat.name() == "entry" or cat.name() == "audit_conform")
            continue;
        auto cto = cat.get_tag_order();
        result.insert(result.end(), cto.begin(), cto.end());
    }

    return result;
}

void datablock::write(std::ostream &os) const
{
    os << "data_" << m_name << std::endl
       << "# " << std::endl;

    // mmcif support, sort of. First write the 'entry' Category
    // and if it exists, _AND_ we have a Validator, write out the
    // audit_conform record.

    for (auto &cat : *this)
    {
        if (cat.name() != "entry")
            continue;

        cat.write(os);

        break;
    }

    // If the dictionary declares an audit_conform category, put it in,
    // but only if it does not exist already!
    if (get("audit_conform"))
        get("audit_conform")->write(os);
    else if (m_validator != nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
    {
        category auditConform("audit_conform");
        auditConform.emplace({
            {"dict_name", m_validator->name()},
            {"dict_version", m_validator->version()}});
        auditConform.write(os);
    }

    for (auto &cat : *this)
    {
        if (cat.name() != "entry" and cat.name() != "audit_conform")
            cat.write(os);
    }
}

void datablock::write(std::ostream &os, const std::vector<std::string> &tag_order)
{
    os << "data_" << m_name << std::endl
       << "# " << std::endl;

    std::vector<std::string> cat_order;
    for (auto &o : tag_order)
    {
        std::string cat_name, item_name;
        std::tie(cat_name, item_name) = split_tag_name(o);
        if (find_if(cat_order.rbegin(), cat_order.rend(), [cat_name](const std::string &s) -> bool
                { return iequals(cat_name, s); }) == cat_order.rend())
            cat_order.push_back(cat_name);
    }

    for (auto &c : cat_order)
    {
        auto cat = get(c);
        if (cat == nullptr)
            continue;

        std::vector<std::string> items;
        for (auto &o : tag_order)
        {
            std::string cat_name, item_name;
            std::tie(cat_name, item_name) = split_tag_name(o);

            if (cat_name == c)
                items.push_back(item_name);
        }

        cat->write(os, items);
    }

    // for any Category we missed in the catOrder
    for (auto &cat : *this)
    {
        if (find_if(cat_order.begin(), cat_order.end(), [&](const std::string &s) -> bool
                { return iequals(cat.name(), s); }) != cat_order.end())
            continue;

        cat.write(os);
    }
}

bool datablock::operator==(const datablock &rhs) const
{
    auto &dbA = *this;
    auto &dbB = rhs;

    std::vector<std::string> catA, catB;

    for (auto &cat : dbA)
    {
        if (not cat.empty())
            catA.push_back(cat.name());
    }
    std::sort(catA.begin(), catA.end());

    for (auto &cat : dbB)
    {
        if (not cat.empty())
            catB.push_back(cat.name());
    }
    std::sort(catB.begin(), catB.end());

    // loop over categories twice, to group output
    // First iteration is to list missing categories.

    std::vector<std::string> missingA, missingB;

    auto catA_i = catA.begin(), catB_i = catB.begin();

    while (catA_i != catA.end() and catB_i != catB.end())
    {
        if (not iequals(*catA_i, *catB_i))
            return false;

        ++catA_i, ++catB_i;
    }

    if (catA_i != catA.end() or catB_i != catB.end())
        return false;

    // Second loop, now compare category values
    catA_i = catA.begin(), catB_i = catB.begin();

    while (catA_i != catA.end() and catB_i != catB.end())
    {
        std::string nA = *catA_i;
        to_lower(nA);

        std::string nB = *catB_i;
        to_lower(nB);

        int d = nA.compare(nB);
        if (d > 0)
            ++catB_i;
        else if (d < 0)
            ++catA_i;
        else
        {
            if (not (*dbA.get(*catA_i) == *dbB.get(*catB_i)))
                return false;
            ++catA_i;
            ++catB_i;
        }
    }

    return true;
}

} // namespace cif::cif