Program Listing for File validate.hpp

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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.
 */

#pragma once

#include "cif++/category.hpp"
#include "cif++/text.hpp"

#include <cassert>
#include <filesystem>
#include <list>
#include <mutex>
#include <optional>
#include <system_error>
#include <utility>

namespace cif
{

class category;
struct category_validator;

// --------------------------------------------------------------------
// New: error_code

enum class validation_error
{
    value_does_not_match_rx = 1,
    value_is_not_in_enumeration_list,
    not_a_known_primitive_type,
    undefined_category,
    unknown_item,
    incorrect_item_validator,
    missing_mandatory_items,
    missing_key_items,
    item_not_allowed_in_category,
    empty_file,
    empty_datablock,
    empty_category,
    not_valid_pdbx,
};
class validation_category_impl : public std::error_category
{
  public:
    const char *name() const noexcept override
    {
        return "cif::validation";
    }

    std::string message(int ev) const override
    {
        switch (static_cast<validation_error>(ev))
        {
            case validation_error::value_does_not_match_rx:
                return "Value in item does not match regular expression";
            case validation_error::value_is_not_in_enumeration_list:
                return "Value is not in the enumerated list of valid values";
            case validation_error::not_a_known_primitive_type:
                return "The type is not a known primitive type";
            case validation_error::undefined_category:
                return "Category has no definition in the dictionary";
            case validation_error::unknown_item:
                return "Item is not defined to be part of the category";
            case validation_error::incorrect_item_validator:
                return "Incorrectly specified validator for item";
            case validation_error::missing_mandatory_items:
                return "Missing mandatory items";
            case validation_error::missing_key_items:
                return "An index could not be constructed due to missing key items";
            case validation_error::item_not_allowed_in_category:
                return "Requested item not allowed in category according to dictionary";
            case validation_error::empty_file:
                return "The file contains no datablocks";
            case validation_error::empty_datablock:
                return "The datablock contains no categories";
            case validation_error::empty_category:
                return "The category is empty";
            case validation_error::not_valid_pdbx:
                return "The file is not a valid PDBx file";

            default:
                assert(false);
                return "unknown error code";
        }
    }

    bool equivalent(const std::error_code & /*code*/, int /*condition*/) const noexcept override
    {
        return false;
    }
};

inline std::error_category &validation_category()
{
    static validation_category_impl instance;
    return instance;
}

inline std::error_code make_error_code(validation_error e)
{
    return std::error_code(static_cast<int>(e), validation_category());
}

inline std::error_condition make_error_condition(validation_error e)
{
    return std::error_condition(static_cast<int>(e), validation_category());
}

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

class validation_exception : public std::runtime_error
{
  public:
    validation_exception(validation_error err)
        : validation_exception(make_error_code(err))
    {
    }

    validation_exception(validation_error err, std::string_view category)
        : validation_exception(make_error_code(err), category)
    {
    }

    validation_exception(validation_error err, std::string_view category, std::string_view item)
        : validation_exception(make_error_code(err), category, item)
    {
    }

    validation_exception(std::error_code ec);

    validation_exception(std::error_code ec, std::string_view category);

    validation_exception(std::error_code ec, std::string_view category, std::string_view item);
};

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

enum class DDL_PrimitiveType
{
    Char,
    UChar,
    Numb
};

DDL_PrimitiveType map_to_primitive_type(std::string_view s);

DDL_PrimitiveType map_to_primitive_type(std::string_view s, std::error_code &ec) noexcept;

struct regex_impl;

struct type_validator
{
    std::string m_name;
    DDL_PrimitiveType m_primitive_type;
    std::shared_ptr<regex_impl> m_rx;

    type_validator() = delete;

    type_validator(std::string_view name, DDL_PrimitiveType type, std::string_view rx);

    type_validator(const type_validator &tv);

    type_validator(type_validator &&rhs)
    {
        swap(*this, rhs);
    }

    type_validator &operator=(type_validator rhs)
    {
        swap(*this, rhs);
        return *this;
    }

    ~type_validator();

    friend void swap(type_validator &a, type_validator &b)
    {
        std::swap(a.m_name, b.m_name);
        std::swap(a.m_primitive_type, b.m_primitive_type);
        std::swap(a.m_rx, b.m_rx);
    }

    bool operator<(const type_validator &rhs) const
    {
        return icompare(m_name, rhs.m_name) < 0;
    }

    int compare(std::string_view a, std::string_view b) const;
};

struct item_alias
{
    item_alias(const std::string &alias_name, const std::string &dictionary, const std::string &version)
        : m_name(alias_name)
        , m_dict(dictionary)
        , m_vers(version)
    {
    }

    item_alias(const item_alias &) = default;
    item_alias &operator=(const item_alias &) = default;

    std::string m_name;
    std::string m_dict;
    std::string m_vers;
};

struct item_validator
{
    std::string m_item_name;
    bool m_mandatory;
    const type_validator *m_type;
    cif::iset m_enums;
    std::string m_default;
    std::string m_category;
    std::vector<item_alias> m_aliases;

    bool operator<(const item_validator &rhs) const
    {
        return icompare(m_item_name, rhs.m_item_name) < 0;
    }

    bool operator==(const item_validator &rhs) const
    {
        return iequals(m_item_name, rhs.m_item_name);
    }

    void operator()(std::string_view value) const;

    bool validate_value(std::string_view value, std::error_code &ec) const noexcept;
};

struct category_validator
{
    std::string m_name;
    std::vector<std::string> m_keys;
    cif::iset m_groups;
    cif::iset m_mandatory_items;
    std::set<item_validator> m_item_validators;

    bool operator<(const category_validator &rhs) const
    {
        return icompare(m_name, rhs.m_name) < 0;
    }

    void add_item_validator(item_validator &&v);

    const item_validator *get_validator_for_item(std::string_view item_name) const;

    const item_validator *get_validator_for_aliased_item(std::string_view item_name) const;
};

struct link_validator
{
    int m_link_group_id;
    std::string m_parent_category;
    std::vector<std::string> m_parent_keys;
    std::string m_child_category;
    std::vector<std::string> m_child_keys;
    std::string m_link_group_label;
};

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

class validator
{
  public:
    validator()
        : m_audit_conform("audit_conform")
    {
    }

    validator(std::istream &is)
        : m_audit_conform("audit_conform")
    {
        parse(is);
    }

    ~validator() = default;

    validator(const validator &rhs);

    validator(validator &&rhs)
    {
        swap(*this, rhs);
    }

    validator &operator=(validator rhs)
    {
        swap(*this, rhs);
        return *this;
    }

    friend void swap(validator &a, validator &b) noexcept;

    friend class dictionary_parser;
    friend class validator_factory;

    void parse(std::istream &is);

    void add_type_validator(type_validator &&v);

    const type_validator *get_validator_for_type(std::string_view type_code) const;

    void add_category_validator(category_validator &&v);

    const category_validator *get_validator_for_category(std::string_view category) const;

    void add_link_validator(link_validator &&v);

    std::vector<const link_validator *> get_links_for_parent(std::string_view category) const;

    std::vector<const link_validator *> get_links_for_child(std::string_view category) const;

    void report_error(validation_error err, bool fatal = true) const
    {
        report_error(make_error_code(err), fatal);
    }

    void report_error(std::error_code ec, bool fatal = true) const;

    void report_error(validation_error err, std::string_view category,
        std::string_view item, bool fatal = true) const
    {
        report_error(make_error_code(err), category, item, fatal);
    }

    void report_error(std::error_code ec, std::string_view category,
        std::string_view item, bool fatal = true) const;

    void fill_audit_conform(category &audit_conform) const;

    bool matches_audit_conform(const category &audit_conform) const;

    void append_audit_conform(const std::string &name, const std::optional<std::string> &version);

  private:
    // name is fully qualified here:
    item_validator *get_validator_for_item(std::string_view name) const;

    category m_audit_conform;

    bool m_strict = false;
    std::set<type_validator> m_type_validators;
    std::set<category_validator> m_category_validators;
    std::vector<link_validator> m_link_validators;
};

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

class validator_factory
{
  public:
    static validator_factory &instance();

    const validator &get(const category &audit_conform);

    const validator &get(std::string_view dictionary_name);

    static bool check_version(std::string_view name, std::string_view expected, std::string_view found);

    const validator &add(validator &&v)
    {
        std::unique_lock lock(m_mutex);
        return m_validators.emplace_back(std::move(v));
    }

  private:
    validator_factory() = default;

    validator construct_validator(std::string_view name, std::optional<std::string> version);

    std::mutex m_mutex;
    std::list<validator> m_validators;
};

} // namespace cif