Program Listing for File parser.hpp

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/*-
 * SPDX-License-Identifier: BSD-2-Clause
 *
 * Copyright (c) 2020 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.
 */

#pragma once

#include "cif++/row.hpp"

#include <map>

namespace cif
{

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

class parse_error : public std::runtime_error
{
  public:
    parse_error(uint32_t line_nr, const std::string &message)
        : std::runtime_error("parse error at line " + std::to_string(line_nr) + ": " + message)
    {
    }
};

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

// TODO: Need to implement support for transformed long lines

class sac_parser
{
  public:
    using datablock_index = std::map<std::string, std::size_t>;

    virtual ~sac_parser() = default;
    enum CharTraitsMask : uint8_t
    {
        kOrdinaryMask = 1 << 0,
        kNonBlankMask = 1 << 1,
        kTextLeadMask = 1 << 2,
        kAnyPrintMask = 1 << 3
    };

    static constexpr bool is_space(int ch)
    {
        return ch == ' ' or ch == '\t' or ch == '\r' or ch == '\n';
    }

    static constexpr bool is_white(int ch)
    {
        return is_space(ch) or ch == '#';
    }

    static constexpr bool is_ordinary(int ch)
    {
        return ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kOrdinaryMask) != 0;
    }

    static constexpr bool is_non_blank(int ch)
    {
        return ch > 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kNonBlankMask) != 0;
    }

    static constexpr bool is_text_lead(int ch)
    {
        return ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kTextLeadMask) != 0;
    }

    static constexpr bool is_any_print(int ch)
    {
        return ch == '\t' or
               (ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kAnyPrintMask) != 0);
    }

    static bool is_unquoted_string(std::string_view text);

  protected:
    static constexpr uint8_t kCharTraitsTable[128] = {
        //  0   1   2   3   4   5   6   7   8   9   a   b   c   d   e   f
        14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, //  2
        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, //  3
        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //  4
        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 15, 14, 15, 14, //  5
        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //  6
        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0,  //  7
    };

    enum class CIFToken
    {
        UNKNOWN,

        END_OF_FILE,

        DATA,
        LOOP,
        GLOBAL,
        SAVE_,
        SAVE_NAME,
        STOP,
        ITEM_NAME,
        VALUE
    };

    static constexpr const char *get_token_name(CIFToken token)
    {
        switch (token)
        {
            case CIFToken::UNKNOWN: return "Unknown";
            case CIFToken::END_OF_FILE: return "Eof";
            case CIFToken::DATA: return "DATA";
            case CIFToken::LOOP: return "LOOP";
            case CIFToken::GLOBAL: return "GLOBAL";
            case CIFToken::SAVE_: return "SAVE";
            case CIFToken::SAVE_NAME: return "SAVE+name";
            case CIFToken::STOP: return "STOP";
            case CIFToken::ITEM_NAME: return "Tag";
            case CIFToken::VALUE: return "Value";
            default: return "Invalid token parameter";
        }
    }

    // get_next_char takes the next character from the istream.
    // This function also does carriage/linefeed translation.
    int get_next_char();

    // Put the last read character back into the istream
    void retract();

    CIFToken get_next_token();

    void match(CIFToken token);

  public:

    bool parse_single_datablock(const std::string &datablock);

    datablock_index index_datablocks();

    bool parse_single_datablock(const std::string &datablock, const datablock_index &index);

    void parse_file();

  protected:

    sac_parser(std::istream &is, bool init = true);

    void parse_global();

    void parse_datablock();

    virtual void parse_save_frame();

    void error(const std::string &msg)
    {
        if (cif::VERBOSE > 0)
            std::cerr << "Error parsing mmCIF: " << msg << '\n';

        throw parse_error(m_line_nr, msg);
    }

    void warning(const std::string &msg)
    {
        if (cif::VERBOSE > 0)
            std::cerr << "parser warning at line " << m_line_nr << ": " << msg << '\n';
    }

    // production methods, these are pure virtual here

    virtual void produce_datablock(std::string_view name) = 0;
    virtual void produce_category(std::string_view name) = 0;
    virtual void produce_row() = 0;
    virtual void produce_item(std::string_view category, std::string_view item, std::string_view value) = 0;

  protected:

    enum class State
    {
        Start,
        White,
        Esc,
        Comment,
        QuestionMark,
        Dot,
        QuotedString,
        QuotedStringQuote,
        UnquotedString,
        ItemName,
        TextItem,
        TextItemNL,
        Reserved,
        Value
    };

    std::streambuf &m_source;

    // Parser state
    uint32_t m_line_nr;
    bool m_bol;
    CIFToken m_lookahead;

    // token buffer
    std::vector<char> m_token_buffer;
    std::string_view m_token_value;

};

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

class parser : public sac_parser
{
  public:
    parser(std::istream &is, file &file)
        : sac_parser(is)
        , m_file(file)
    {
    }

    void produce_datablock(std::string_view name) override;

    void produce_category(std::string_view name) override;

    void produce_row() override;

    void produce_item(std::string_view category, std::string_view item, std::string_view value) override;

  protected:
    file &m_file;
    datablock *m_datablock = nullptr;
    category *m_category = nullptr;
    row_handle m_row;

};

} // namespace cif