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libcifpp
Commit 30a2ebdb by Maarten L. Hekkelman
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Merge remote-tracking branch 'github/develop-cif2fasta' into develop

parents 13ab1caf a5d43998
Showing with 1107 additions and 761 deletions
include/cif++/category.hpp
......@@ -71,7 +71,7 @@ class duplicate_key_error : public std::runtime_error
};
/// @brief A missing_key_error is thrown when an attempt is made
/// to create an index when one of the key fields is missing.
/// to create an index when one of the key items is missing.
class missing_key_error : public std::runtime_error
{
public:
......@@ -156,8 +156,16 @@ class category
// --------------------------------------------------------------------
const std::string &name() const { return m_name; } ///< Returns the name of the category
iset key_fields() const; ///< Returns the cif::iset of key field names. Retrieved from the @ref category_validator for this category
std::set<uint16_t> key_field_indices() const; ///< Returns a set of indices for the key fields.
[[deprecated("use key_items instead")]]
iset key_fields() const; ///< Returns the cif::iset of key item names. Retrieved from the @ref category_validator for this category
iset key_items() const; ///< Returns the cif::iset of key item names. Retrieved from the @ref category_validator for this category
[[deprecated("use key_item_indices instead")]]
std::set<uint16_t> key_field_indices() const; ///< Returns a set of indices for the key items.
std::set<uint16_t> key_item_indices() const; ///< Returns a set of indices for the key items.
/// @brief Set the validator for this category to @a v
/// @param v The category_validator to assign. A nullptr value is allowed.
......@@ -301,12 +309,12 @@ class category
using key_type = row_initializer;
/// @brief Return a row_handle for the row specified by \a key
/// @param key The value for the key, fields specified in the dictionary should have a value
/// @param key The value for the key, items specified in the dictionary should have a value
/// @return The row found in the index, or an undefined row_handle
row_handle operator[](const key_type &key);
/// @brief Return a const row_handle for the row specified by \a key
/// @param key The value for the key, fields specified in the dictionary should have a value
/// @param key The value for the key, items specified in the dictionary should have a value
/// @return The row found in the index, or an undefined row_handle
const row_handle operator[](const key_type &key) const
{
......@@ -323,13 +331,13 @@ class category
/// std::cout << name << ": " << value << '\n';
/// @endcode
///
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
/// @tparam Ts The types for the items requested
/// @param names The names for the items requested
template <typename... Ts, typename... Ns>
iterator_proxy<const category, Ts...> rows(Ns... names) const
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
return iterator_proxy<const category, Ts...>(*this, begin(), { names... });
}
......@@ -340,19 +348,19 @@ class category
/// for (const auto &[name, value] : cat.rows<std::string,int>("item_name", "item_value"))
/// std::cout << name << ": " << value << '\n';
///
/// // or in case we only need one column:
/// // or in case we only need one item:
///
/// for (int id : cat.rows<int>("id"))
/// std::cout << id << '\n';
/// @endcode
///
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
/// @tparam Ts The types for the items requested
/// @param names The names for the items requested
template <typename... Ts, typename... Ns>
iterator_proxy<category, Ts...> rows(Ns... names)
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
return iterator_proxy<category, Ts...>(*this, begin(), { names... });
}
......@@ -420,14 +428,14 @@ class category
/// @endcode
///
/// @param cond The condition for the query
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
/// @tparam Ts The types for the items requested
/// @param names The names for the items requested
/// @return A special iterator that loops over all elements that match.
template <typename... Ts, typename... Ns>
conditional_iterator_proxy<category, Ts...> find(condition &&cond, Ns... names)
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
return find<Ts...>(cbegin(), std::move(cond), std::forward<Ns>(names)...);
}
......@@ -435,14 +443,14 @@ class category
/// iterator can be used in a structured binding context.
///
/// @param cond The condition for the query
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
/// @tparam Ts The types for the items requested
/// @param names The names for the items requested
/// @return A special iterator that loops over all elements that match.
template <typename... Ts, typename... Ns>
conditional_iterator_proxy<const category, Ts...> find(condition &&cond, Ns... names) const
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
return find<Ts...>(cbegin(), std::move(cond), std::forward<Ns>(names)...);
}
......@@ -451,14 +459,14 @@ class category
///
/// @param pos Iterator pointing to the location where to start
/// @param cond The condition for the query
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
/// @tparam Ts The types for the items requested
/// @param names The names for the items requested
/// @return A special iterator that loops over all elements that match.
template <typename... Ts, typename... Ns>
conditional_iterator_proxy<category, Ts...> find(const_iterator pos, condition &&cond, Ns... names)
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
return { *this, pos, std::move(cond), std::forward<Ns>(names)... };
}
......@@ -467,14 +475,14 @@ class category
///
/// @param pos Iterator pointing to the location where to start
/// @param cond The condition for the query
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
/// @tparam Ts The types for the items requested
/// @param names The names for the items requested
/// @return A special iterator that loops over all elements that match.
template <typename... Ts, typename... Ns>
conditional_iterator_proxy<const category, Ts...> find(const_iterator pos, condition &&cond, Ns... names) const
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
return { *this, pos, std::move(cond), std::forward<Ns>(names)... };
}
......@@ -529,30 +537,30 @@ class category
return *h.begin();
}
/// @brief Return value for the column named @a column for the single row that
/// @brief Return value for the item named @a item for the single row that
/// matches @a cond. Throws @a multiple_results_error if there are is not exactly one row
/// @tparam The type to use for the result
/// @param cond The condition to search for
/// @param column The name of the column to return the value for
/// @param item The name of the item to return the value for
/// @return The value found
template <typename T>
T find1(condition &&cond, std::string_view column) const
T find1(condition &&cond, std::string_view item) const
{
return find1<T>(cbegin(), std::move(cond), column);
return find1<T>(cbegin(), std::move(cond), item);
}
/// @brief Return value for the column named @a column for the single row that
/// @brief Return value for the item named @a item for the single row that
/// matches @a cond when starting to search at @a pos.
/// Throws @a multiple_results_error if there are is not exactly one row
/// @tparam The type to use for the result
/// @param pos The location to start the search
/// @param cond The condition to search for
/// @param column The name of the column to return the value for
/// @param item The name of the item to return the value for
/// @return The value found
template <typename T, std::enable_if_t<not is_optional_v<T>, int> = 0>
T find1(const_iterator pos, condition &&cond, std::string_view column) const
T find1(const_iterator pos, condition &&cond, std::string_view item) const
{
auto h = find<T>(pos, std::move(cond), column);
auto h = find<T>(pos, std::move(cond), item);
if (h.size() != 1)
throw multiple_results_error();
......@@ -560,18 +568,18 @@ class category
return *h.begin();
}
/// @brief Return a value of type std::optional<T> for the column named @a column for the single row that
/// @brief Return a value of type std::optional<T> for the item named @a item for the single row that
/// matches @a cond when starting to search at @a pos.
/// If the row was not found, an empty value is returned.
/// @tparam The type to use for the result
/// @param pos The location to start the search
/// @param cond The condition to search for
/// @param column The name of the column to return the value for
/// @param item The name of the item to return the value for
/// @return The value found, can be empty if no row matches the condition
template <typename T, std::enable_if_t<is_optional_v<T>, int> = 0>
T find1(const_iterator pos, condition &&cond, std::string_view column) const
T find1(const_iterator pos, condition &&cond, std::string_view item) const
{
auto h = find<typename T::value_type>(pos, std::move(cond), column);
auto h = find<typename T::value_type>(pos, std::move(cond), item);
if (h.size() > 1)
throw multiple_results_error();
......@@ -582,34 +590,34 @@ class category
return *h.begin();
}
/// @brief Return a std::tuple for the values for the columns named in @a columns
/// @brief Return a std::tuple for the values for the items named in @a items
/// for the single row that matches @a cond
/// Throws @a multiple_results_error if there are is not exactly one row
/// @tparam The types to use for the resulting tuple
/// @param cond The condition to search for
/// @param columns The names of the columns to return the value for
/// @param items The names of the items to return the value for
/// @return The values found as a single tuple of type std::tuple<Ts...>
template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
std::tuple<Ts...> find1(condition &&cond, Cs... columns) const
std::tuple<Ts...> find1(condition &&cond, Cs... items) const
{
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
// static_assert(std::is_same_v<Cs, const char*>..., "The column names should be const char");
return find1<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(columns)...);
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
// static_assert(std::is_same_v<Cs, const char*>..., "The item names should be const char");
return find1<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(items)...);
}
/// @brief Return a std::tuple for the values for the columns named in @a columns
/// @brief Return a std::tuple for the values for the items named in @a items
/// for the single row that matches @a cond when starting to search at @a pos
/// Throws @a multiple_results_error if there are is not exactly one row
/// @tparam The types to use for the resulting tuple
/// @param pos The location to start the search
/// @param cond The condition to search for
/// @param columns The names of the columns to return the value for
/// @param items The names of the items to return the value for
/// @return The values found as a single tuple of type std::tuple<Ts...>
template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
std::tuple<Ts...> find1(const_iterator pos, condition &&cond, Cs... columns) const
std::tuple<Ts...> find1(const_iterator pos, condition &&cond, Cs... items) const
{
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(columns)...);
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(items)...);
if (h.size() != 1)
throw multiple_results_error();
......@@ -658,74 +666,74 @@ class category
return h.empty() ? row_handle{} : *h.begin();
}
/// @brief Return the value for column @a column for the first row that matches condition @a cond
/// @brief Return the value for item @a item for the first row that matches condition @a cond
/// @tparam The type of the value to return
/// @param cond The condition to search for
/// @param column The column for which the value should be returned
/// @param item The item for which the value should be returned
/// @return The value found or a default constructed value if not found
template <typename T>
T find_first(condition &&cond, std::string_view column) const
T find_first(condition &&cond, std::string_view item) const
{
return find_first<T>(cbegin(), std::move(cond), column);
return find_first<T>(cbegin(), std::move(cond), item);
}
/// @brief Return the value for column @a column for the first row that matches condition @a cond
/// @brief Return the value for item @a item for the first row that matches condition @a cond
/// when starting the search at @a pos
/// @tparam The type of the value to return
/// @param pos The location to start searching
/// @param cond The condition to search for
/// @param column The column for which the value should be returned
/// @param item The item for which the value should be returned
/// @return The value found or a default constructed value if not found
template <typename T>
T find_first(const_iterator pos, condition &&cond, std::string_view column) const
T find_first(const_iterator pos, condition &&cond, std::string_view item) const
{
auto h = find<T>(pos, std::move(cond), column);
auto h = find<T>(pos, std::move(cond), item);
return h.empty() ? T{} : *h.begin();
}
/// @brief Return a tuple containing the values for the columns @a columns for the first row that matches condition @a cond
/// @brief Return a tuple containing the values for the items @a items for the first row that matches condition @a cond
/// @tparam The types of the values to return
/// @param cond The condition to search for
/// @param columns The columns for which the values should be returned
/// @param items The items for which the values should be returned
/// @return The values found or default constructed values if not found
template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
std::tuple<Ts...> find_first(condition &&cond, Cs... columns) const
std::tuple<Ts...> find_first(condition &&cond, Cs... items) const
{
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
// static_assert(std::is_same_v<Cs, const char*>..., "The column names should be const char");
return find_first<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(columns)...);
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
// static_assert(std::is_same_v<Cs, const char*>..., "The item names should be const char");
return find_first<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(items)...);
}
/// @brief Return a tuple containing the values for the columns @a columns for the first row that matches condition @a cond
/// @brief Return a tuple containing the values for the items @a items for the first row that matches condition @a cond
/// when starting the search at @a pos
/// @tparam The types of the values to return
/// @param pos The location to start searching
/// @param cond The condition to search for
/// @param columns The columns for which the values should be returned
/// @param items The items for which the values should be returned
/// @return The values found or default constructed values if not found
template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
std::tuple<Ts...> find_first(const_iterator pos, condition &&cond, Cs... columns) const
std::tuple<Ts...> find_first(const_iterator pos, condition &&cond, Cs... items) const
{
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(columns)...);
static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(items)...);
return h.empty() ? std::tuple<Ts...>{} : *h.begin();
}
// --------------------------------------------------------------------
/// @brief Return the maximum value for column @a column for all rows that match condition @a cond
/// @brief Return the maximum value for item @a item for all rows that match condition @a cond
/// @tparam The type of the value to return
/// @param column The column to use for the value
/// @param item The item to use for the value
/// @param cond The condition to search for
/// @return The value found or the minimal value for the type
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
T find_max(std::string_view column, condition &&cond) const
T find_max(std::string_view item, condition &&cond) const
{
T result = std::numeric_limits<T>::min();
for (auto v : find<T>(std::move(cond), column))
for (auto v : find<T>(std::move(cond), item))
{
if (result < v)
result = v;
......@@ -734,27 +742,27 @@ class category
return result;
}
/// @brief Return the maximum value for column @a column for all rows
/// @brief Return the maximum value for item @a item for all rows
/// @tparam The type of the value to return
/// @param column The column to use for the value
/// @param item The item to use for the value
/// @return The value found or the minimal value for the type
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
T find_max(std::string_view column) const
T find_max(std::string_view item) const
{
return find_max<T>(column, all());
return find_max<T>(item, all());
}
/// @brief Return the minimum value for column @a column for all rows that match condition @a cond
/// @brief Return the minimum value for item @a item for all rows that match condition @a cond
/// @tparam The type of the value to return
/// @param column The column to use for the value
/// @param item The item to use for the value
/// @param cond The condition to search for
/// @return The value found or the maximum value for the type
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
T find_min(std::string_view column, condition &&cond) const
T find_min(std::string_view item, condition &&cond) const
{
T result = std::numeric_limits<T>::max();
for (auto v : find<T>(std::move(cond), column))
for (auto v : find<T>(std::move(cond), item))
{
if (result > v)
result = v;
......@@ -763,14 +771,14 @@ class category
return result;
}
/// @brief Return the maximum value for column @a column for all rows
/// @brief Return the maximum value for item @a item for all rows
/// @tparam The type of the value to return
/// @param column The column to use for the value
/// @param item The item to use for the value
/// @return The value found or the maximum value for the type
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
T find_min(std::string_view column) const
T find_min(std::string_view item) const
{
return find_min<T>(column, all());
return find_min<T>(item, all());
}
/// @brief Return whether a row exists that matches condition @a cond
......@@ -918,7 +926,7 @@ class category
for (auto i = b; i != e; ++i)
{
// item_value *new_item = this->create_item(*i);
r->append(add_column(i->name()), { i->value() });
r->append(add_item(i->name()), { i->value() });
}
}
catch (...)
......@@ -949,111 +957,172 @@ class category
{ return prefix + std::to_string(nr + 1); });
}
/// @brief Generate a new, unique value for a item named @a tag
/// @param tag The name of the item
/// @brief Generate a new, unique value for a item named @a item_name
/// @param item_name The name of the item
/// @return a new unique value
std::string get_unique_value(std::string_view tag);
std::string get_unique_value(std::string_view item_name);
// --------------------------------------------------------------------
/// \brief Update a single column named @a tag in the rows that match \a cond to value \a value
/// \brief Update a single item named @a item_name in the rows that match \a cond to value \a value
/// making sure the linked categories are updated according to the link.
/// That means, child categories are updated if the links are absolute
/// and unique. If they are not, the child category rows are split.
void update_value(condition &&cond, std::string_view tag, std::string_view value)
void update_value(condition &&cond, std::string_view item_name, std::string_view value)
{
auto rs = find(std::move(cond));
std::vector<row_handle> rows;
std::copy(rs.begin(), rs.end(), std::back_inserter(rows));
update_value(rows, tag, value);
update_value(rows, item_name, value);
}
/// \brief Update a single column named @a tag in @a rows to value \a value
/// \brief Update a single item named @a item_name in @a rows to value \a value
/// making sure the linked categories are updated according to the link.
/// That means, child categories are updated if the links are absolute
/// and unique. If they are not, the child category rows are split.
void update_value(const std::vector<row_handle> &rows, std::string_view tag, std::string_view value);
void update_value(const std::vector<row_handle> &rows, std::string_view item_name, std::string_view value);
// --------------------------------------------------------------------
/// \brief Return the index number for \a column_name
// Naming used to be very inconsistent. For backward compatibility,
// the old function names are here as deprecated variants.
/// \brief Return the index number for \a column_name
[[deprecated("Use get_item_ix instead")]]
uint16_t get_column_ix(std::string_view column_name) const
{
return get_item_ix(column_name);
}
/// @brief Return the name for column with index @a ix
/// @param ix The index number
/// @return The name of the column
[[deprecated("use get_item_name instead")]]
std::string_view get_column_name(uint16_t ix) const
{
return get_item_name(ix);
}
/// @brief Make sure a item with name @a item_name is known and return its index number
/// @param item_name The name of the item
/// @return The index number of the item
[[deprecated("use add_item instead")]]
uint16_t add_column(std::string_view item_name)
{
return add_item(item_name);
}
/** @brief Remove column name @a colum_name
* @param column_name The column to be removed
*/
[[deprecated("use remove_item instead")]]
void remove_column(std::string_view column_name)
{
remove_item(column_name);
}
/** @brief Rename column @a from_name to @a to_name */
[[deprecated("use rename_item instead")]]
void rename_column(std::string_view from_name, std::string_view to_name)
{
rename_item(from_name, to_name);
}
/// @brief Return whether a column with name @a name exists in this category
/// @param name The name of the column
/// @return True if the column exists
[[deprecated("use has_item instead")]]
bool has_column(std::string_view name) const
{
return has_item(name);
}
/// @brief Return the cif::iset of columns in this category
[[deprecated("use get_items instead")]]
iset get_columns() const
{
return get_items();
}
// --------------------------------------------------------------------
/// \brief Return the index number for \a item_name
uint16_t get_item_ix(std::string_view item_name) const
{
uint16_t result;
for (result = 0; result < m_columns.size(); ++result)
for (result = 0; result < m_items.size(); ++result)
{
if (iequals(column_name, m_columns[result].m_name))
if (iequals(item_name, m_items[result].m_name))
break;
}
if (VERBOSE > 0 and result == m_columns.size() and m_cat_validator != nullptr) // validate the name, if it is known at all (since it was not found)
if (VERBOSE > 0 and result == m_items.size() and m_cat_validator != nullptr) // validate the name, if it is known at all (since it was not found)
{
auto iv = m_cat_validator->get_validator_for_item(column_name);
auto iv = m_cat_validator->get_validator_for_item(item_name);
if (iv == nullptr)
std::cerr << "Invalid name used '" << column_name << "' is not a known column in " + m_name << '\n';
std::cerr << "Invalid name used '" << item_name << "' is not a known item in " + m_name << '\n';
}
return result;
}
/// @brief Return the name for column with index @a ix
/// @brief Return the name for item with index @a ix
/// @param ix The index number
/// @return The name of the column
std::string_view get_column_name(uint16_t ix) const
/// @return The name of the item
std::string_view get_item_name(uint16_t ix) const
{
if (ix >= m_columns.size())
throw std::out_of_range("column index is out of range");
if (ix >= m_items.size())
throw std::out_of_range("item index is out of range");
return m_columns[ix].m_name;
return m_items[ix].m_name;
}
/// @brief Make sure a column with name @a column_name is known and return its index number
/// @param column_name The name of the column
/// @return The index number of the column
uint16_t add_column(std::string_view column_name)
/// @brief Make sure a item with name @a item_name is known and return its index number
/// @param item_name The name of the item
/// @return The index number of the item
uint16_t add_item(std::string_view item_name)
{
using namespace std::literals;
uint16_t result = get_column_ix(column_name);
uint16_t result = get_item_ix(item_name);
if (result == m_columns.size())
if (result == m_items.size())
{
const item_validator *item_validator = nullptr;
if (m_cat_validator != nullptr)
{
item_validator = m_cat_validator->get_validator_for_item(column_name);
item_validator = m_cat_validator->get_validator_for_item(item_name);
if (item_validator == nullptr)
m_validator->report_error("tag " + std::string(column_name) + " not allowed in category " + m_name, false);
m_validator->report_error( validation_error::item_not_allowed_in_category, m_name, item_name, false);
}
m_columns.emplace_back(column_name, item_validator);
m_items.emplace_back(item_name, item_validator);
}
return result;
}
/** @brief Remove column name @a colum_name
* @param column_name The column to be removed
/** @brief Remove item name @a colum_name
* @param item_name The item to be removed
*/
void remove_column(std::string_view column_name);
void remove_item(std::string_view item_name);
/** @brief Rename column @a from_name to @a to_name */
void rename_column(std::string_view from_name, std::string_view to_name);
/** @brief Rename item @a from_name to @a to_name */
void rename_item(std::string_view from_name, std::string_view to_name);
/// @brief Return whether a column with name @a name exists in this category
/// @param name The name of the column
/// @return True if the column exists
bool has_column(std::string_view name) const
/// @brief Return whether a item with name @a name exists in this category
/// @param name The name of the item
/// @return True if the item exists
bool has_item(std::string_view name) const
{
return get_column_ix(name) < m_columns.size();
return get_item_ix(name) < m_items.size();
}
/// @brief Return the cif::iset of columns in this category
iset get_columns() const;
/// @brief Return the cif::iset of items in this category
iset get_items() const;
// --------------------------------------------------------------------
......@@ -1069,23 +1138,31 @@ class category
// --------------------------------------------------------------------
/// This function returns effectively the list of fully qualified column
/// names, that is category_name + '.' + column_name for each column
std::vector<std::string> get_tag_order() const;
/// This function returns effectively the list of fully qualified item
/// names, that is category_name + '.' + item_name for each item
[[deprecated("use get_item_order instead")]]
std::vector<std::string> get_tag_order() const
{
return get_item_order();
}
/// This function returns effectively the list of fully qualified item
/// names, that is category_name + '.' + item_name for each item
std::vector<std::string> get_item_order() const;
/// Write the contents of the category to the std::ostream @a os
void write(std::ostream &os) const;
/// @brief Write the contents of the category to the std::ostream @a os and
/// use @a order as the order of the columns. If @a addMissingColumns is
/// false, columns that do not contain any value will be suppressed
/// use @a order as the order of the items. If @a addMissingItems is
/// false, items that do not contain any value will be suppressed
/// @param os The std::ostream to write to
/// @param order The order in which the columns should appear
/// @param addMissingColumns When false, empty columns are suppressed from the output
void write(std::ostream &os, const std::vector<std::string> &order, bool addMissingColumns = true);
/// @param order The order in which the items should appear
/// @param addMissingItems When false, empty items are suppressed from the output
void write(std::ostream &os, const std::vector<std::string> &order, bool addMissingItems = true);
private:
void write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyColumns) const;
void write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyItems) const;
public:
/// friend function to make it possible to do:
......@@ -1099,7 +1176,7 @@ class category
}
private:
void update_value(row *row, uint16_t column, std::string_view value, bool updateLinked, bool validate = true);
void update_value(row *row, uint16_t item, std::string_view value, bool updateLinked, bool validate = true);
void erase_orphans(condition &&cond, category &parent);
......@@ -1136,12 +1213,12 @@ class category
row_handle create_copy(row_handle r);
struct item_column
struct item_entry
{
std::string m_name;
const item_validator *m_validator;
item_column(std::string_view name, const item_validator *validator)
item_entry(std::string_view name, const item_validator *validator)
: m_name(name)
, m_validator(validator)
{
......@@ -1171,12 +1248,12 @@ class category
// --------------------------------------------------------------------
void swap_item(uint16_t column_ix, row_handle &a, row_handle &b);
void swap_item(uint16_t item_ix, row_handle &a, row_handle &b);
// --------------------------------------------------------------------
std::string m_name;
std::vector<item_column> m_columns;
std::vector<item_entry> m_items;
const validator *m_validator = nullptr;
const category_validator *m_cat_validator = nullptr;
std::vector<link> m_parent_links, m_child_links;
......
include/cif++/condition.hpp
......@@ -39,17 +39,17 @@
* query you can use to find rows in a @ref cif::category
*
* Conditions are created as standard C++ expressions. That means
* you can use the standard comparison operators to compare field
* you can use the standard comparison operators to compare item
* contents with a value and boolean operators to chain everything
* together.
*
* To create a query that simply compares one field with one value:
* To create a query that simply compares one item with one value:
*
* @code {.cpp}
* cif::condition c = cif::key("id") == 1;
* @endcode
*
* That will find rows where the ID field contains the number 1. If
* That will find rows where the ID item contains the number 1. If
* using cif::key is a bit too much typing, you can also write:
*
* @code{.cpp}
......@@ -64,7 +64,7 @@
* auto c3 = "id"_key == 1 or "id"_key == 2;
* @endcode
*
* There are some special values you can use. To find rows with field that
* There are some special values you can use. To find rows with item that
* do not have a value:
*
* @code{.cpp}
......@@ -83,7 +83,7 @@
* auto c6 = cif::all;
* @endcode
*
* And when you want to search for any column containing the value 'foo':
* And when you want to search for any item containing the value 'foo':
*
* @code{.cpp}
* auto c7 = cif::any == "foo";
......@@ -104,31 +104,40 @@ namespace cif
/// we declare a function to access its contents
/**
* @brief Get the fields that can be used as key in conditions for a category
* @brief Get the items that can be used as key in conditions for a category
*
* @param cat The category whose fields to return
* @return iset The set of key field names
* @param cat The category whose items to return
* @return iset The set of key item names
*/
[[deprecated("use get_category_items instead")]]
iset get_category_fields(const category &cat);
/**
* @brief Get the column index for column @a col in category @a cat
* @brief Get the items that can be used as key in conditions for a category
*
* @param cat The category whose items to return
* @return iset The set of key field names
*/
iset get_category_items(const category &cat);
/**
* @brief Get the item index for item @a col in category @a cat
*
* @param cat The category
* @param col The name of the column
* @param col The name of the item
* @return uint16_t The index
*/
uint16_t get_column_ix(const category &cat, std::string_view col);
uint16_t get_item_ix(const category &cat, std::string_view col);
/**
* @brief Return whether the column @a col in category @a cat has a primitive type of *uchar*
* @brief Return whether the item @a col in category @a cat has a primitive type of *uchar*
*
* @param cat The category
* @param col The column name
* @param col The item name
* @return true If the primitive type is of type *uchar*
* @return false If the primitive type is not of type *uchar*
*/
bool is_column_type_uchar(const category &cat, std::string_view col);
bool is_item_type_uchar(const category &cat, std::string_view col);
// --------------------------------------------------------------------
// some more templates to be able to do querying
......@@ -219,7 +228,7 @@ class condition
/**
* @brief Prepare the condition to be used on category @a c. This will
* take care of setting the correct indices for fields e.g.
* take care of setting the correct indices for items e.g.
*
* @param c The category this query should act upon
*/
......@@ -305,14 +314,14 @@ namespace detail
{
struct key_is_empty_condition_impl : public condition_impl
{
key_is_empty_condition_impl(const std::string &item_tag)
: m_item_tag(item_tag)
key_is_empty_condition_impl(const std::string &item_name)
: m_item_name(item_name)
{
}
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_item_ix = get_item_ix(c, m_item_name);
return this;
}
......@@ -323,23 +332,23 @@ namespace detail
void str(std::ostream &os) const override
{
os << m_item_tag << " IS NULL";
os << m_item_name << " IS NULL";
}
std::string m_item_tag;
std::string m_item_name;
uint16_t m_item_ix = 0;
};
struct key_is_not_empty_condition_impl : public condition_impl
{
key_is_not_empty_condition_impl(const std::string &item_tag)
: m_item_tag(item_tag)
key_is_not_empty_condition_impl(const std::string &item_name)
: m_item_name(item_name)
{
}
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_item_ix = get_item_ix(c, m_item_name);
return this;
}
......@@ -350,17 +359,17 @@ namespace detail
void str(std::ostream &os) const override
{
os << m_item_tag << " IS NOT NULL";
os << m_item_name << " IS NOT NULL";
}
std::string m_item_tag;
std::string m_item_name;
uint16_t m_item_ix = 0;
};
struct key_equals_condition_impl : public condition_impl
{
key_equals_condition_impl(item &&i)
: m_item_tag(i.name())
: m_item_name(i.name())
, m_value(i.value())
{
}
......@@ -374,7 +383,7 @@ namespace detail
void str(std::ostream &os) const override
{
os << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value;
os << m_item_name << (m_icase ? "^ " : " ") << " == " << m_value;
}
virtual std::optional<row_handle> single() const override
......@@ -390,13 +399,13 @@ namespace detail
if (m_single_hit.has_value() or ri->m_single_hit.has_value())
return m_single_hit == ri->m_single_hit;
else
// watch out, both m_item_ix might be the same while tags might be diffent (in case they both do not exist in the category)
return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_tag == ri->m_item_tag;
// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_name == ri->m_item_name;
}
return this == rhs;
}
std::string m_item_tag;
std::string m_item_name;
uint16_t m_item_ix = 0;
bool m_icase = false;
std::string m_value;
......@@ -406,7 +415,7 @@ namespace detail
struct key_equals_or_empty_condition_impl : public condition_impl
{
key_equals_or_empty_condition_impl(key_equals_condition_impl *equals)
: m_item_tag(equals->m_item_tag)
: m_item_name(equals->m_item_name)
, m_value(equals->m_value)
, m_icase(equals->m_icase)
, m_single_hit(equals->m_single_hit)
......@@ -415,8 +424,8 @@ namespace detail
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
m_item_ix = get_item_ix(c, m_item_name);
m_icase = is_item_type_uchar(c, m_item_name);
return this;
}
......@@ -432,7 +441,7 @@ namespace detail
void str(std::ostream &os) const override
{
os << '(' << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value << " OR " << m_item_tag << " IS NULL)";
os << '(' << m_item_name << (m_icase ? "^ " : " ") << " == " << m_value << " OR " << m_item_name << " IS NULL)";
}
virtual std::optional<row_handle> single() const override
......@@ -448,13 +457,13 @@ namespace detail
if (m_single_hit.has_value() or ri->m_single_hit.has_value())
return m_single_hit == ri->m_single_hit;
else
// watch out, both m_item_ix might be the same while tags might be diffent (in case they both do not exist in the category)
return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_tag == ri->m_item_tag;
// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_name == ri->m_item_name;
}
return this == rhs;
}
std::string m_item_tag;
std::string m_item_name;
uint16_t m_item_ix = 0;
std::string m_value;
bool m_icase = false;
......@@ -464,8 +473,8 @@ namespace detail
struct key_compare_condition_impl : public condition_impl
{
template <typename COMP>
key_compare_condition_impl(const std::string &item_tag, COMP &&comp, const std::string &s)
: m_item_tag(item_tag)
key_compare_condition_impl(const std::string &item_name, COMP &&comp, const std::string &s)
: m_item_name(item_name)
, m_compare(std::move(comp))
, m_str(s)
{
......@@ -473,8 +482,8 @@ namespace detail
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
m_item_ix = get_item_ix(c, m_item_name);
m_icase = is_item_type_uchar(c, m_item_name);
return this;
}
......@@ -485,10 +494,10 @@ namespace detail
void str(std::ostream &os) const override
{
os << m_item_tag << (m_icase ? "^ " : " ") << m_str;
os << m_item_name << (m_icase ? "^ " : " ") << m_str;
}
std::string m_item_tag;
std::string m_item_name;
uint16_t m_item_ix = 0;
bool m_icase = false;
std::function<bool(row_handle, bool)> m_compare;
......@@ -497,8 +506,8 @@ namespace detail
struct key_matches_condition_impl : public condition_impl
{
key_matches_condition_impl(const std::string &item_tag, const std::regex &rx)
: m_item_tag(item_tag)
key_matches_condition_impl(const std::string &item_name, const std::regex &rx)
: m_item_name(item_name)
, m_item_ix(0)
, mRx(rx)
{
......@@ -506,7 +515,7 @@ namespace detail
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_item_ix = get_item_ix(c, m_item_name);
return this;
}
......@@ -518,10 +527,10 @@ namespace detail
void str(std::ostream &os) const override
{
os << m_item_tag << " =~ expression";
os << m_item_name << " =~ expression";
}
std::string m_item_tag;
std::string m_item_name;
uint16_t m_item_ix;
std::regex mRx;
};
......@@ -541,7 +550,7 @@ namespace detail
auto &c = r.get_category();
bool result = false;
for (auto &f : get_category_fields(c))
for (auto &f : get_category_items(c))
{
try
{
......@@ -579,7 +588,7 @@ namespace detail
auto &c = r.get_category();
bool result = false;
for (auto &f : get_category_fields(c))
for (auto &f : get_category_items(c))
{
try
{
......@@ -864,7 +873,7 @@ inline condition operator or(condition &&a, condition &&b)
auto ci = static_cast<detail::key_equals_condition_impl *>(a.m_impl);
auto ce = static_cast<detail::key_is_empty_condition_impl *>(b.m_impl);
if (ci->m_item_tag == ce->m_item_tag)
if (ci->m_item_name == ce->m_item_name)
return condition(new detail::key_equals_or_empty_condition_impl(ci));
}
else if (typeid(*b.m_impl) == typeid(detail::key_equals_condition_impl) and
......@@ -873,7 +882,7 @@ inline condition operator or(condition &&a, condition &&b)
auto ci = static_cast<detail::key_equals_condition_impl *>(b.m_impl);
auto ce = static_cast<detail::key_is_empty_condition_impl *>(a.m_impl);
if (ci->m_item_tag == ce->m_item_tag)
if (ci->m_item_name == ce->m_item_name)
return condition(new detail::key_equals_or_empty_condition_impl(ci));
}
......@@ -887,7 +896,7 @@ inline condition operator or(condition &&a, condition &&b)
}
/**
* @brief A helper class to make it possible to search for empty fields (NULL)
* @brief A helper class to make it possible to search for empty items (NULL)
*
* @code{.cpp}
* "id"_key == cif::empty_type();
......@@ -909,45 +918,45 @@ struct empty_type
inline constexpr empty_type null = empty_type();
/**
* @brief Class to use in creating conditions, creates a reference to a field or column
* @brief Class to use in creating conditions, creates a reference to a item or item
*
*/
struct key
{
/**
* @brief Construct a new key object using @a itemTag as name
* @brief Construct a new key object using @a item_name as name
*
* @param itemTag
* @param item_name
*/
explicit key(const std::string &itemTag)
: m_item_tag(itemTag)
explicit key(const std::string &item_name)
: m_item_name(item_name)
{
}
/**
* @brief Construct a new key object using @a itemTag as name
* @brief Construct a new key object using @a item_name as name
*
* @param itemTag
* @param item_name
*/
explicit key(const char *itemTag)
: m_item_tag(itemTag)
explicit key(const char *item_name)
: m_item_name(item_name)
{
}
/**
* @brief Construct a new key object using @a itemTag as name
* @brief Construct a new key object using @a item_name as name
*
* @param itemTag
* @param item_name
*/
explicit key(std::string_view itemTag)
: m_item_tag(itemTag)
explicit key(std::string_view item_name)
: m_item_name(item_name)
{
}
key(const key &) = delete;
key &operator=(const key &) = delete;
std::string m_item_tag; ///< The column name
std::string m_item_name; ///< The item name
};
/**
......@@ -956,7 +965,7 @@ struct key
template <typename T>
condition operator==(const key &key, const T &v)
{
return condition(new detail::key_equals_condition_impl({ key.m_item_tag, v }));
return condition(new detail::key_equals_condition_impl({ key.m_item_name, v }));
}
/**
......@@ -965,9 +974,9 @@ condition operator==(const key &key, const T &v)
inline condition operator==(const key &key, std::string_view value)
{
if (not value.empty())
return condition(new detail::key_equals_condition_impl({ key.m_item_tag, value }));
return condition(new detail::key_equals_condition_impl({ key.m_item_name, value }));
else
return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
}
/**
......@@ -997,8 +1006,8 @@ condition operator>(const key &key, const T &v)
s << " > " << v;
return condition(new detail::key_compare_condition_impl(
key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
{ return r[tag].template compare<T>(v, icase) > 0; },
key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
{ return r[item_name].template compare<T>(v, icase) > 0; },
s.str()));
}
......@@ -1012,8 +1021,8 @@ condition operator>=(const key &key, const T &v)
s << " >= " << v;
return condition(new detail::key_compare_condition_impl(
key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
{ return r[tag].template compare<T>(v, icase) >= 0; },
key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
{ return r[item_name].template compare<T>(v, icase) >= 0; },
s.str()));
}
......@@ -1027,8 +1036,8 @@ condition operator<(const key &key, const T &v)
s << " < " << v;
return condition(new detail::key_compare_condition_impl(
key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
{ return r[tag].template compare<T>(v, icase) < 0; },
key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
{ return r[item_name].template compare<T>(v, icase) < 0; },
s.str()));
}
......@@ -1042,8 +1051,8 @@ condition operator<=(const key &key, const T &v)
s << " <= " << v;
return condition(new detail::key_compare_condition_impl(
key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
{ return r[tag].template compare<T>(v, icase) <= 0; },
key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
{ return r[item_name].template compare<T>(v, icase) <= 0; },
s.str()));
}
......@@ -1052,7 +1061,7 @@ condition operator<=(const key &key, const T &v)
*/
inline condition operator==(const key &key, const std::regex &rx)
{
return condition(new detail::key_matches_condition_impl(key.m_item_tag, rx));
return condition(new detail::key_matches_condition_impl(key.m_item_name, rx));
}
/**
......@@ -1060,7 +1069,7 @@ inline condition operator==(const key &key, const std::regex &rx)
*/
inline condition operator==(const key &key, const empty_type &)
{
return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
}
/**
......@@ -1068,20 +1077,20 @@ inline condition operator==(const key &key, const empty_type &)
*/
inline condition operator!=(const key &key, const empty_type &)
{
return condition(new detail::key_is_not_empty_condition_impl(key.m_item_tag));
return condition(new detail::key_is_not_empty_condition_impl(key.m_item_name));
}
/**
* @brief Create a condition to search any column for a value @a v if @a v contains a value
* @brief Create a condition to search any item for a value @a v if @a v contains a value
* compare to null if not.
*/
template <typename T>
condition operator==(const key &key, const std::optional<T> &v)
{
if (v.has_value())
return condition(new detail::key_equals_condition_impl({ key.m_item_tag, *v }));
return condition(new detail::key_equals_condition_impl({ key.m_item_name, *v }));
else
return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
}
/**
......@@ -1099,12 +1108,12 @@ struct any_type
/** @endcond */
/**
* @brief A helper for any field constructs
* @brief A helper for any item constructs
*/
inline constexpr any_type any = any_type{};
/**
* @brief Create a condition to search any column for a value @a v
* @brief Create a condition to search any item for a value @a v
*/
template <typename T>
condition operator==(const any_type &, const T &v)
......@@ -1113,7 +1122,7 @@ condition operator==(const any_type &, const T &v)
}
/**
* @brief Create a condition to search any column for a regular expression @a rx
* @brief Create a condition to search any item for a regular expression @a rx
*/
inline condition operator==(const any_type &, const std::regex &rx)
{
......@@ -1131,9 +1140,9 @@ inline condition all()
namespace literals
{
/**
* @brief Return a cif::key for the column name @a text
* @brief Return a cif::key for the item name @a text
*
* @param text The name of the column
* @param text The name of the item
* @param length The length of @a text
* @return key The cif::key created
*/
......
include/cif++/datablock.hpp
......@@ -169,7 +169,16 @@ class datablock : public std::list<category>
/**
* @brief Get the preferred order of the categories when writing them
*/
std::vector<std::string> get_tag_order() const;
[[deprecated("use get_item_order instead")]]
std::vector<std::string> get_tag_order() const
{
return get_item_order();
}
/**
* @brief Get the preferred order of the categories when writing them
*/
std::vector<std::string> get_item_order() const;
/**
* @brief Write out the contents to @a os
......@@ -177,9 +186,9 @@ class datablock : public std::list<category>
void write(std::ostream &os) const;
/**
* @brief Write out the contents to @a os using the order defined in @a tag_order
* @brief Write out the contents to @a os using the order defined in @a item_name_order
*/
void write(std::ostream &os, const std::vector<std::string> &tag_order);
void write(std::ostream &os, const std::vector<std::string> &item_name_order);
/**
* @brief Friend operator<< to write datablock @a db to std::ostream @a os
......
include/cif++/item.hpp
......@@ -44,7 +44,7 @@
/** \file item.hpp
*
* This file contains the declaration of item but also the item_value and item_handle
* These handle the storage of and access to the data for a single data field.
* These handle the storage of and access to the data for a single data item.
*/
namespace cif
......@@ -227,10 +227,10 @@ class item
/// \brief empty means either null or unknown
bool empty() const { return m_value.empty(); }
/// \brief returns true if the field contains '.'
/// \brief returns true if the item contains '.'
bool is_null() const { return m_value == "."; }
/// \brief returns true if the field contains '?'
/// \brief returns true if the item contains '?'
bool is_unknown() const { return m_value == "?"; }
/// \brief the length of the value string
......@@ -464,14 +464,14 @@ struct item_handle
/** Easy way to test for an empty item */
explicit operator bool() const { return not empty(); }
/// is_null return true if the field contains '.'
/// is_null return true if the item contains '.'
bool is_null() const
{
auto txt = text();
return txt.length() == 1 and txt.front() == '.';
}
/// is_unknown returns true if the field contains '?'
/// is_unknown returns true if the item contains '?'
bool is_unknown() const
{
auto txt = text();
......@@ -484,11 +484,11 @@ struct item_handle
/**
* @brief Construct a new item handle object
*
* @param column Column index
* @param item Item index
* @param row Reference to the row
*/
item_handle(uint16_t column, row_handle &row)
: m_column(column)
item_handle(uint16_t item, row_handle &row)
: m_item_ix(item)
, m_row_handle(row)
{
}
......@@ -505,7 +505,7 @@ struct item_handle
private:
item_handle();
uint16_t m_column;
uint16_t m_item_ix;
row_handle &m_row_handle;
void assign_value(const item &value);
......
include/cif++/iterator.hpp
......@@ -90,7 +90,7 @@ class iterator_impl
: m_category(rhs.m_category)
, m_current(rhs.m_current)
, m_value(rhs.m_value)
, m_column_ix(rhs.m_column_ix)
, m_item_ix(rhs.m_item_ix)
{
}
......@@ -99,7 +99,7 @@ class iterator_impl
: m_category(rhs.m_category)
, m_current(const_cast<row_type *>(rhs.m_current))
, m_value(rhs.m_value)
, m_column_ix(rhs.m_column_ix)
, m_item_ix(rhs.m_item_ix)
{
m_value = get(std::make_index_sequence<N>());
}
......@@ -108,7 +108,7 @@ class iterator_impl
iterator_impl(const iterator_impl<IRowType> &rhs, const std::array<uint16_t, N> &cix)
: m_category(rhs.m_category)
, m_current(rhs.m_current)
, m_column_ix(cix)
, m_item_ix(cix)
{
m_value = get(std::make_index_sequence<N>());
}
......@@ -117,7 +117,7 @@ class iterator_impl
{
m_category = i.m_category;
m_current = i.m_current;
m_column_ix = i.m_column_ix;
m_item_ix = i.m_item_ix;
m_value = i.m_value;
return *this;
}
......@@ -185,7 +185,7 @@ class iterator_impl
if (m_current != nullptr)
{
row_handle rh{ *m_category, *m_current };
return tuple_type{ rh[m_column_ix[Is]].template as<Ts>()... };
return tuple_type{ rh[m_item_ix[Is]].template as<Ts>()... };
}
return {};
......@@ -194,7 +194,7 @@ class iterator_impl
category_type *m_category = nullptr;
row_type *m_current = nullptr;
value_type m_value;
std::array<uint16_t, N> m_column_ix;
std::array<uint16_t, N> m_item_ix;
};
/**
......@@ -348,7 +348,7 @@ class iterator_impl<Category, T>
: m_category(rhs.m_category)
, m_current(rhs.m_current)
, m_value(rhs.m_value)
, m_column_ix(rhs.m_column_ix)
, m_item_ix(rhs.m_item_ix)
{
}
......@@ -357,7 +357,7 @@ class iterator_impl<Category, T>
: m_category(rhs.m_category)
, m_current(const_cast<row_type *>(rhs.m_current))
, m_value(rhs.m_value)
, m_column_ix(rhs.m_column_ix)
, m_item_ix(rhs.m_item_ix)
{
m_value = get(m_current);
}
......@@ -366,7 +366,7 @@ class iterator_impl<Category, T>
iterator_impl(const iterator_impl<IRowType> &rhs, const std::array<uint16_t, 1> &cix)
: m_category(rhs.m_category)
, m_current(rhs.m_current)
, m_column_ix(cix[0])
, m_item_ix(cix[0])
{
m_value = get();
}
......@@ -375,7 +375,7 @@ class iterator_impl<Category, T>
{
m_category = i.m_category;
m_current = i.m_current;
m_column_ix = i.m_column_ix;
m_item_ix = i.m_item_ix;
m_value = i.m_value;
return *this;
}
......@@ -442,7 +442,7 @@ class iterator_impl<Category, T>
if (m_current != nullptr)
{
row_handle rh{ *m_category, *m_current };
return rh[m_column_ix].template as<T>();
return rh[m_item_ix].template as<T>();
}
return {};
......@@ -451,7 +451,7 @@ class iterator_impl<Category, T>
category_type *m_category = nullptr;
row_type *m_current = nullptr;
value_type m_value;
uint16_t m_column_ix;
uint16_t m_item_ix;
};
// --------------------------------------------------------------------
......@@ -482,8 +482,8 @@ class iterator_proxy
using iterator = iterator_impl<category_type, Ts...>;
using row_iterator = iterator_impl<category_type>;
iterator_proxy(category_type &cat, row_iterator pos, char const *const columns[N]);
iterator_proxy(category_type &cat, row_iterator pos, std::initializer_list<char const *> columns);
iterator_proxy(category_type &cat, row_iterator pos, char const *const items[N]);
iterator_proxy(category_type &cat, row_iterator pos, std::initializer_list<char const *> items);
iterator_proxy(iterator_proxy &&p);
iterator_proxy &operator=(iterator_proxy &&p);
......@@ -492,8 +492,8 @@ class iterator_proxy
iterator_proxy &operator=(const iterator_proxy &) = delete;
/** @endcond */
iterator begin() const { return iterator(m_begin, m_column_ix); } ///< Return the iterator pointing to the first row
iterator end() const { return iterator(m_end, m_column_ix); } ///< Return the iterator pointing past the last row
iterator begin() const { return iterator(m_begin, m_item_ix); } ///< Return the iterator pointing to the first row
iterator end() const { return iterator(m_end, m_item_ix); } ///< Return the iterator pointing past the last row
bool empty() const { return m_begin == m_end; } ///< Return true if the range is empty
explicit operator bool() const { return not empty(); } ///< Easy way to detect if the range is empty
......@@ -510,13 +510,13 @@ class iterator_proxy
std::swap(m_category, rhs.m_category);
std::swap(m_begin, rhs.m_begin);
std::swap(m_end, rhs.m_end);
std::swap(m_column_ix, rhs.m_column_ix);
std::swap(m_item_ix, rhs.m_item_ix);
}
private:
category_type *m_category;
row_iterator m_begin, m_end;
std::array<uint16_t, N> m_column_ix;
std::array<uint16_t, N> m_item_ix;
};
// --------------------------------------------------------------------
......@@ -651,26 +651,26 @@ class conditional_iterator_proxy
/** @cond */
template <typename Category, typename... Ts>
iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, char const *const columns[N])
iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, char const *const items[N])
: m_category(&cat)
, m_begin(pos)
, m_end(cat.end())
{
for (uint16_t i = 0; i < N; ++i)
m_column_ix[i] = m_category->get_column_ix(columns[i]);
m_item_ix[i] = m_category->get_item_ix(items[i]);
}
template <typename Category, typename... Ts>
iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, std::initializer_list<char const *> columns)
iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, std::initializer_list<char const *> items)
: m_category(&cat)
, m_begin(pos)
, m_end(cat.end())
{
// static_assert(columns.size() == N, "The list of column names should be exactly the same as the list of requested columns");
// static_assert(items.size() == N, "The list of item names should be exactly the same as the list of requested items");
std::uint16_t i = 0;
for (auto column : columns)
m_column_ix[i++] = m_category->get_column_ix(column);
for (auto item : items)
m_item_ix[i++] = m_category->get_item_ix(item);
}
// --------------------------------------------------------------------
......@@ -707,7 +707,7 @@ conditional_iterator_proxy<Category, Ts...>::conditional_iterator_proxy(Category
, mCBegin(pos)
, mCEnd(cat.end())
{
static_assert(sizeof...(Ts) == sizeof...(Ns), "Number of column names should be equal to number of requested value types");
static_assert(sizeof...(Ts) == sizeof...(Ns), "Number of item names should be equal to number of requested value types");
if (m_condition)
{
......@@ -720,7 +720,7 @@ conditional_iterator_proxy<Category, Ts...>::conditional_iterator_proxy(Category
mCBegin = mCEnd;
uint16_t i = 0;
((mCix[i++] = m_cat->get_column_ix(names)), ...);
((mCix[i++] = m_cat->get_item_ix(names)), ...);
}
template <typename Category, typename... Ts>
......
include/cif++/model.hpp
......@@ -72,7 +72,7 @@ class structure;
*
* The class atom is a kind of flyweight class. It can be copied
* with low overhead. All data is stored in the underlying mmCIF
* categories but some very often used fields are cached in the
* categories but some very often used items are cached in the
* impl.
*
* It is also possible to have symmetry copies of atoms. They
......@@ -207,7 +207,7 @@ class atom
/// \brief Copy assignement operator
atom &operator=(const atom &rhs) = default;
/// \brief Return the field named @a name in the _atom_site category for this atom
/// \brief Return the item named @a name in the _atom_site category for this atom
std::string get_property(std::string_view name) const
{
if (not m_impl)
......@@ -215,7 +215,7 @@ class atom
return m_impl->get_property(name);
}
/// \brief Return the field named @a name in the _atom_site category for this atom cast to an int
/// \brief Return the item named @a name in the _atom_site category for this atom cast to an int
int get_property_int(std::string_view name) const
{
if (not m_impl)
......@@ -223,7 +223,7 @@ class atom
return m_impl->get_property_int(name);
}
/// \brief Return the field named @a name in the _atom_site category for this atom cast to a float
/// \brief Return the item named @a name in the _atom_site category for this atom cast to a float
float get_property_float(std::string_view name) const
{
if (not m_impl)
......@@ -231,7 +231,7 @@ class atom
return m_impl->get_property_float(name);
}
/// \brief Set value for the field named @a name in the _atom_site category to @a value
/// \brief Set value for the item named @a name in the _atom_site category to @a value
void set_property(const std::string_view name, const std::string &value)
{
if (not m_impl)
......@@ -239,7 +239,7 @@ class atom
m_impl->set_property(name, value);
}
/// \brief Set value for the field named @a name in the _atom_site category to @a value
/// \brief Set value for the item named @a name in the _atom_site category to @a value
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
void set_property(const std::string_view name, const T &value)
{
......@@ -730,7 +730,7 @@ class sugar : public residue
/**
* @brief Return the sugar number in the glycosylation tree
*
* To store the sugar number, the auth_seq_id field has been overloaded
* To store the sugar number, the auth_seq_id item has been overloaded
* in the specification. But since a sugar number should be, ehm, a number
* and auth_seq_id is specified to contain a string, we do a check here
* to see if it really is a number.
......
include/cif++/parser.hpp
......@@ -143,9 +143,9 @@ class sac_parser
enum class CIFToken
{
Unknown,
UNKNOWN,
Eof,
END_OF_FILE,
DATA,
LOOP,
......@@ -153,24 +153,24 @@ class sac_parser
SAVE_,
SAVE_NAME,
STOP,
Tag,
Value
ITEM_NAME,
VALUE
};
static constexpr const char *get_token_name(CIFToken token)
{
switch (token)
{
case CIFToken::Unknown: return "Unknown";
case CIFToken::Eof: return "Eof";
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::Tag: return "Tag";
case CIFToken::Value: return "Value";
case CIFToken::ITEM_NAME: return "Tag";
case CIFToken::VALUE: return "Value";
default: return "Invalid token parameter";
}
}
......@@ -267,9 +267,9 @@ class sac_parser
QuotedString,
QuotedStringQuote,
UnquotedString,
Tag,
TextField,
TextFieldNL,
ItemName,
TextItem,
TextItemNL,
Reserved,
Value
};
......
include/cif++/pdb.hpp
......@@ -28,6 +28,8 @@
#include "cif++/file.hpp"
#include <system_error>
/**
* @file pdb.hpp
*
......@@ -119,6 +121,8 @@ void reconstruct_pdbx(file &pdbx_file, std::string_view dictionary = "mmcif_pdbx
* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
*
* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
*
* This function throws a std::system_error in case of an error
*
* \param file The input file
* \param dictionary The mmcif dictionary to use
......@@ -127,6 +131,43 @@ void reconstruct_pdbx(file &pdbx_file, std::string_view dictionary = "mmcif_pdbx
bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary = "mmcif_pdbx");
/** \brief This is an extension to cif::validator, use the logic in common
* PDBx files to see if the file is internally consistent.
*
* This function for now checks if the following categories are consistent:
*
* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
*
* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
*
* The dictionary is assumed to be specified in the file or to be the
* default mmcif_pdbx.dic dictionary.
*
* \param file The input file
* \param ec The error_code in case something was wrong
* \result Returns true if the file was valid and consistent
*/
bool is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec);
/** \brief This is an extension to cif::validator, use the logic in common
* PDBx files to see if the file is internally consistent.
*
* This function for now checks if the following categories are consistent:
*
* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
*
* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
*
* \param file The input file
* \param dictionary The dictionary to use
* \param ec The error_code in case something was wrong
* \result Returns true if the file was valid and consistent
*/
bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary,
std::error_code &ec);
// --------------------------------------------------------------------
// Other I/O related routines
......
include/cif++/row.hpp
......@@ -51,7 +51,7 @@
* std::string name = rh["label_atom_id"].as<std::string>();
*
* // by index:
* uint16_t ix = atom_site.get_column_ix("label_atom_id");
* uint16_t ix = atom_site.get_item_ix("label_atom_id");
* assert(rh[ix].as<std::string() == name);
* @endcode
*
......@@ -87,15 +87,15 @@ namespace detail
{
static constexpr size_t N = sizeof...(C);
get_row_result(const row_handle &r, std::array<uint16_t, N> &&columns)
get_row_result(const row_handle &r, std::array<uint16_t, N> &&items)
: m_row(r)
, m_columns(std::move(columns))
, m_items(std::move(items))
{
}
const item_handle operator[](uint16_t ix) const
{
return m_row[m_columns[ix]];
return m_row[m_items[ix]];
}
template <typename... Ts, std::enable_if_t<N == sizeof...(Ts), int> = 0>
......@@ -107,11 +107,11 @@ namespace detail
template <typename... Ts, size_t... Is>
std::tuple<Ts...> get(std::index_sequence<Is...>) const
{
return std::tuple<Ts...>{ m_row[m_columns[Is]].template as<Ts>()... };
return std::tuple<Ts...>{ m_row[m_items[Is]].template as<Ts>()... };
}
const row_handle &m_row;
std::array<uint16_t, N> m_columns;
std::array<uint16_t, N> m_items;
};
// we want to be able to tie some variables to a get_row_result, for this we use tiewraps
......@@ -244,70 +244,70 @@ class row_handle
return not empty();
}
/// \brief return a cif::item_handle to the item in column @a column_ix
item_handle operator[](uint16_t column_ix)
/// \brief return a cif::item_handle to the item in item @a item_ix
item_handle operator[](uint16_t item_ix)
{
return empty() ? item_handle::s_null_item : item_handle(column_ix, *this);
return empty() ? item_handle::s_null_item : item_handle(item_ix, *this);
}
/// \brief return a const cif::item_handle to the item in column @a column_ix
const item_handle operator[](uint16_t column_ix) const
/// \brief return a const cif::item_handle to the item in item @a item_ix
const item_handle operator[](uint16_t item_ix) const
{
return empty() ? item_handle::s_null_item : item_handle(column_ix, const_cast<row_handle &>(*this));
return empty() ? item_handle::s_null_item : item_handle(item_ix, const_cast<row_handle &>(*this));
}
/// \brief return a cif::item_handle to the item in the column named @a column_name
item_handle operator[](std::string_view column_name)
/// \brief return a cif::item_handle to the item in the item named @a item_name
item_handle operator[](std::string_view item_name)
{
return empty() ? item_handle::s_null_item : item_handle(add_column(column_name), *this);
return empty() ? item_handle::s_null_item : item_handle(add_item(item_name), *this);
}
/// \brief return a const cif::item_handle to the item in the column named @a column_name
const item_handle operator[](std::string_view column_name) const
/// \brief return a const cif::item_handle to the item in the item named @a item_name
const item_handle operator[](std::string_view item_name) const
{
return empty() ? item_handle::s_null_item : item_handle(get_column_ix(column_name), const_cast<row_handle &>(*this));
return empty() ? item_handle::s_null_item : item_handle(get_item_ix(item_name), const_cast<row_handle &>(*this));
}
/// \brief Return an object that can be used in combination with cif::tie
/// to assign the values for the columns @a columns
/// to assign the values for the items @a items
template <typename... C>
auto get(C... columns) const
auto get(C... items) const
{
return detail::get_row_result<C...>(*this, { get_column_ix(columns)... });
return detail::get_row_result<C...>(*this, { get_item_ix(items)... });
}
/// \brief Return a tuple of values of types @a Ts for the columns @a columns
/// \brief Return a tuple of values of types @a Ts for the items @a items
template <typename... Ts, typename... C, std::enable_if_t<sizeof...(Ts) == sizeof...(C) and sizeof...(C) != 1, int> = 0>
std::tuple<Ts...> get(C... columns) const
std::tuple<Ts...> get(C... items) const
{
return detail::get_row_result<Ts...>(*this, { get_column_ix(columns)... });
return detail::get_row_result<Ts...>(*this, { get_item_ix(items)... });
}
/// \brief Get the value of column @a column cast to type @a T
/// \brief Get the value of item @a item cast to type @a T
template <typename T>
T get(const char *column) const
T get(const char *item) const
{
return operator[](get_column_ix(column)).template as<T>();
return operator[](get_item_ix(item)).template as<T>();
}
/// \brief Get the value of column @a column cast to type @a T
/// \brief Get the value of item @a item cast to type @a T
template <typename T>
T get(std::string_view column) const
T get(std::string_view item) const
{
return operator[](get_column_ix(column)).template as<T>();
return operator[](get_item_ix(item)).template as<T>();
}
/// \brief assign each of the columns named in @a values to their respective value
/// \brief assign each of the items named in @a values to their respective value
void assign(const std::vector<item> &values)
{
for (auto &value : values)
assign(value, true);
}
/** \brief assign the value @a value to the column named @a name
/** \brief assign the value @a value to the item named @a name
*
* If updateLinked it true, linked records are updated as well.
* That means that if column @a name is part of the link definition
* That means that if item @a name is part of the link definition
* and the link results in a linked record in another category
* this record in the linked category is updated as well.
*
......@@ -317,13 +317,13 @@ class row_handle
void assign(std::string_view name, std::string_view value, bool updateLinked, bool validate = true)
{
assign(add_column(name), value, updateLinked, validate);
assign(add_item(name), value, updateLinked, validate);
}
/** \brief assign the value @a value to column at index @a column
/** \brief assign the value @a value to item at index @a item
*
* If updateLinked it true, linked records are updated as well.
* That means that if column @a column is part of the link definition
* That means that if item @a item is part of the link definition
* and the link results in a linked record in another category
* this record in the linked category is updated as well.
*
......@@ -331,7 +331,7 @@ class row_handle
* checked to see if it conforms to the rules defined in the dictionary
*/
void assign(uint16_t column, std::string_view value, bool updateLinked, bool validate = true);
void assign(uint16_t item, std::string_view value, bool updateLinked, bool validate = true);
/// \brief compare two rows
bool operator==(const row_handle &rhs) const { return m_category == rhs.m_category and m_row == rhs.m_row; }
......@@ -340,10 +340,10 @@ class row_handle
bool operator!=(const row_handle &rhs) const { return m_category != rhs.m_category or m_row != rhs.m_row; }
private:
uint16_t get_column_ix(std::string_view name) const;
std::string_view get_column_name(uint16_t ix) const;
uint16_t get_item_ix(std::string_view name) const;
std::string_view get_item_name(uint16_t ix) const;
uint16_t add_column(std::string_view name);
uint16_t add_item(std::string_view name);
row *get_row()
{
......@@ -360,7 +360,7 @@ class row_handle
assign(i.name(), i.value(), updateLinked);
}
void swap(uint16_t column, row_handle &r);
void swap(uint16_t item, row_handle &r);
category *m_category = nullptr;
row *m_row = nullptr;
......
include/cif++/text.hpp
......@@ -317,7 +317,7 @@ inline char tolower(int ch)
// --------------------------------------------------------------------
/** \brief return a tuple consisting of the category and item name for @a tag
/** \brief return a tuple consisting of the category and item name for @a item_name
*
* The category name is stripped of its leading underscore character.
*
......@@ -325,7 +325,19 @@ inline char tolower(int ch)
* cif 1.0 formatted data.
*/
std::tuple<std::string, std::string> split_tag_name(std::string_view tag);
[[deprecated("use split_item_name instead")]]
std::tuple<std::string, std::string> split_tag_name(std::string_view item_name);
/** \brief return a tuple consisting of the category and item name for @a item_name
*
* The category name is stripped of its leading underscore character.
*
* If no dot character was found, the category name is empty. That's for
* cif 1.0 formatted data.
*/
std::tuple<std::string, std::string> split_item_name(std::string_view item_name);
// --------------------------------------------------------------------
......
include/cif++/validate.hpp
......@@ -28,9 +28,11 @@
#include "cif++/text.hpp"
#include <cassert>
#include <filesystem>
#include <list>
#include <mutex>
#include <system_error>
#include <utility>
/**
......@@ -49,29 +51,123 @@ namespace cif
struct category_validator;
// --------------------------------------------------------------------
// New: error_code
/**
* @brief The exception thrown when a validation error occurs
* @enum validation_error
*
* @brief A stronly typed class containing the error codes reported by @ref cif::validator and friends
*/
class validation_error : public std::exception
enum class validation_error
{
value_does_not_match_rx = 1, /**< The value of an item does not conform to the regular expression specified for it */
value_is_not_in_enumeration_list, /**< The value of an item is not in the list of values allowed */
not_a_known_primitive_type, /**< The type is not a known primitive type */
undefined_category, /**< Category has no definition in the dictionary */
unknown_item, /**< The item is not defined to be part of the category */
incorrect_item_validator, /**< Incorrectly specified validator for item */
missing_mandatory_items, /**< Missing mandatory items */
missing_key_items, /**< An index could not be constructed due to missing key items */
item_not_allowed_in_category, /**< Requested item allowed in category according to dictionary */
empty_file, /**< The file contains no datablocks */
empty_datablock, /**< The datablock contains no categories */
empty_category, /**< The category is empty */
not_valid_pdbx, /**< The file is not a valid PDBx file */
};
/**
* @brief The implementation for @ref validation_category error messages
*
*/
class validation_category_impl : public std::error_category
{
public:
/// @brief Constructor
validation_error(const std::string &msg);
/**
* @brief User friendly name
*
* @return const char*
*/
/// @brief Constructor
validation_error(const std::string &cat, const std::string &item,
const std::string &msg);
const char *name() const noexcept override
{
return "cif::validation";
}
/// @brief The description of the error
const char *what() const noexcept { return m_msg.c_str(); }
/**
* @brief Provide the error message as a string for the error code @a ev
*
* @param ev The error code
* @return std::string
*/
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 "The 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 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";
}
}
/// @cond
std::string m_msg;
/// @endcond
/**
* @brief Return whether two error codes are equivalent, always false in this case
*
*/
bool equivalent(const std::error_code & /*code*/, int /*condition*/) const noexcept override
{
return false;
}
};
/**
* @brief Return the implementation for the validation_category
*
* @return std::error_category&
*/
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());
}
// --------------------------------------------------------------------
/** @brief the primitive types known */
......@@ -85,6 +181,9 @@ enum class DDL_PrimitiveType
/// @brief Return the DDL_PrimitiveType encoded in @a s
DDL_PrimitiveType map_to_primitive_type(std::string_view s);
/// @brief Return the DDL_PrimitiveType encoded in @a s, error reporting variant
DDL_PrimitiveType map_to_primitive_type(std::string_view s, std::error_code &ec) noexcept;
struct regex_impl;
/**
......@@ -177,7 +276,7 @@ struct item_alias
*/
struct item_validator
{
std::string m_tag; ///< The item name
std::string m_item_name; ///< The item name
bool m_mandatory; ///< Flag indicating this item is mandatory
const type_validator *m_type; ///< The type for this item
cif::iset m_enums; ///< If filled, the set of allowed values
......@@ -188,18 +287,21 @@ struct item_validator
/// @brief Compare based on the name
bool operator<(const item_validator &rhs) const
{
return icompare(m_tag, rhs.m_tag) < 0;
return icompare(m_item_name, rhs.m_item_name) < 0;
}
/// @brief Compare based on the name
bool operator==(const item_validator &rhs) const
{
return iequals(m_tag, rhs.m_tag);
return iequals(m_item_name, rhs.m_item_name);
}
/// @brief Validate the value in @a value for this item
/// Will throw a validation_error exception if it fails
/// Will throw a std::system_error exception if it fails
void operator()(std::string_view value) const;
/// @brief A more gentle version of value validation
bool validate_value(std::string_view value, std::error_code &ec) const noexcept;
};
/**
......@@ -213,7 +315,7 @@ struct category_validator
std::string m_name; ///< The name of the category
std::vector<std::string> m_keys; ///< The list of items that make up the key
cif::iset m_groups; ///< The category groups this category belongs to
cif::iset m_mandatory_fields; ///< The mandatory fields for this category
cif::iset m_mandatory_items; ///< The mandatory items for this category
std::set<item_validator> m_item_validators; ///< The item validators for the items in this category
/// @brief return true if this category sorts before @a rhs
......@@ -225,11 +327,11 @@ struct category_validator
/// @brief Add item_validator @a v to the list of item validators
void add_item_validator(item_validator &&v);
/// @brief Return the item_validator for item @a tag, may return nullptr
const item_validator *get_validator_for_item(std::string_view tag) const;
/// @brief Return the item_validator for item @a item_name, may return nullptr
const item_validator *get_validator_for_item(std::string_view item_name) const;
/// @brief Return the item_validator for an item that has as alias name @a tag, may return nullptr
const item_validator *get_validator_for_aliased_item(std::string_view tag) const;
/// @brief Return the item_validator for an item that has as alias name @a item_name, may return nullptr
const item_validator *get_validator_for_aliased_item(std::string_view item_name) const;
};
/**
......@@ -308,7 +410,24 @@ class validator
std::vector<const link_validator *> get_links_for_child(std::string_view category) const;
/// @brief Bottleneck function to report an error in validation
void report_error(const std::string &msg, bool fatal) const;
void report_error(validation_error err, bool fatal = true) const
{
report_error(make_error_code(err), fatal);
}
/// @brief Bottleneck function to report an error in validation
void report_error(std::error_code ec, bool fatal = true) const;
/// @brief Bottleneck function to report an error in validation
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);
}
/// @brief Bottleneck function to report an error in validation
void report_error(std::error_code ec, std::string_view category,
std::string_view item, bool fatal = true) const;
const std::string &name() const { return m_name; } ///< Get the name of this validator
void set_name(const std::string &name) { m_name = name; } ///< Set the name of this validator
......
src/category.cpp
......@@ -33,7 +33,7 @@
#include <stack>
// TODO: Find out what the rules are exactly for linked items, the current implementation
// is inconsistent. It all depends whether a link is satified if a field taking part in the
// is inconsistent. It all depends whether a link is satified if a item taking part in the
// set of linked items is null at one side and not null in the other.
namespace cif
......@@ -52,7 +52,7 @@ class row_comparator
for (auto &k : cv->m_keys)
{
uint16_t ix = cat.add_column(k);
uint16_t ix = cat.add_item(k);
auto iv = cv->get_validator_for_item(k);
if (iv == nullptr)
......@@ -300,7 +300,7 @@ class category_index
return h;
}
// Fix m_next fields for rows in order of this index
// Fix m_next items for rows in order of this index
entry *reorder(entry *e)
{
auto result = e;
......@@ -356,9 +356,9 @@ row *category_index::find_by_value(const category &cat, row_initializer k) const
// sort the values in k first
row_initializer k2;
for (auto &f : cat.key_field_indices())
for (auto &f : cat.key_item_indices())
{
auto fld = cat.get_column_name(f);
auto fld = cat.get_item_name(f);
auto ki = find_if(k.begin(), k.end(), [&fld](auto &i)
{ return i.name() == fld; });
......@@ -404,7 +404,7 @@ category_index::entry *category_index::insert(category &cat, entry *h, row *v)
row_handle rh(cat, *v);
std::ostringstream os;
for (auto col : cat.key_fields())
for (auto col : cat.key_items())
{
if (rh[col])
os << col << ": " << std::quoted(rh[col].text()) << "; ";
......@@ -508,7 +508,7 @@ category::category(std::string_view name)
category::category(const category &rhs)
: m_name(rhs.m_name)
, m_columns(rhs.m_columns)
, m_items(rhs.m_items)
, m_cascade(rhs.m_cascade)
{
for (auto r = rhs.m_head; r != nullptr; r = r->m_next)
......@@ -523,7 +523,7 @@ category::category(const category &rhs)
category::category(category &&rhs)
: m_name(std::move(rhs.m_name))
, m_columns(std::move(rhs.m_columns))
, m_items(std::move(rhs.m_items))
, m_validator(rhs.m_validator)
, m_cat_validator(rhs.m_cat_validator)
, m_parent_links(std::move(rhs.m_parent_links))
......@@ -546,7 +546,7 @@ category &category::operator=(const category &rhs)
clear();
m_name = rhs.m_name;
m_columns = rhs.m_columns;
m_items = rhs.m_items;
m_cascade = rhs.m_cascade;
m_validator = nullptr;
......@@ -573,7 +573,7 @@ category &category::operator=(category &&rhs)
if (this != &rhs)
{
m_name = std::move(rhs.m_name);
m_columns = std::move(rhs.m_columns);
m_items = std::move(rhs.m_items);
m_cascade = rhs.m_cascade;
m_validator = rhs.m_validator;
m_cat_validator = rhs.m_cat_validator;
......@@ -595,11 +595,11 @@ category::~category()
// --------------------------------------------------------------------
void category::remove_column(std::string_view column_name)
void category::remove_item(std::string_view item_name)
{
for (size_t ix = 0; ix < m_columns.size(); ++ix)
for (size_t ix = 0; ix < m_items.size(); ++ix)
{
if (not iequals(column_name, m_columns[ix].m_name))
if (not iequals(item_name, m_items[ix].m_name))
continue;
for (row *r = m_head; r != nullptr; r = r->m_next)
......@@ -608,62 +608,62 @@ void category::remove_column(std::string_view column_name)
r->erase(r->begin() + ix);
}
m_columns.erase(m_columns.begin() + ix);
m_items.erase(m_items.begin() + ix);
break;
}
}
void category::rename_column(std::string_view from_name, std::string_view to_name)
void category::rename_item(std::string_view from_name, std::string_view to_name)
{
for (size_t ix = 0; ix < m_columns.size(); ++ix)
for (size_t ix = 0; ix < m_items.size(); ++ix)
{
if (not iequals(from_name, m_columns[ix].m_name))
if (not iequals(from_name, m_items[ix].m_name))
continue;
m_columns[ix].m_name = to_name;
m_columns[ix].m_validator = m_cat_validator ? m_cat_validator->get_validator_for_item(to_name) : nullptr;
m_items[ix].m_name = to_name;
m_items[ix].m_validator = m_cat_validator ? m_cat_validator->get_validator_for_item(to_name) : nullptr;
break;
}
}
iset category::get_columns() const
iset category::get_items() const
{
iset result;
for (auto &col : m_columns)
for (auto &col : m_items)
result.insert(col.m_name);
return result;
}
iset category::key_fields() const
iset category::key_items() const
{
if (m_validator == nullptr)
throw std::runtime_error("No Validator specified");
if (m_cat_validator == nullptr)
m_validator->report_error("undefined Category", true);
m_validator->report_error(validation_error::undefined_category);
iset result;
for (auto &iv : m_cat_validator->m_item_validators)
result.insert(iv.m_tag);
result.insert(iv.m_item_name);
return result;
}
std::set<uint16_t> category::key_field_indices() const
std::set<uint16_t> category::key_item_indices() const
{
if (m_validator == nullptr)
throw std::runtime_error("No Validator specified");
if (m_cat_validator == nullptr)
m_validator->report_error("undefined Category", true);
m_validator->report_error(validation_error::undefined_category);
std::set<uint16_t> result;
for (auto &k : m_cat_validator->m_keys)
result.insert(get_column_ix(k));
result.insert(get_item_ix(k));
return result;
}
......@@ -693,8 +693,8 @@ void category::set_validator(const validator *v, datablock &db)
std::vector<uint16_t> kix;
for (auto k : m_cat_validator->m_keys)
{
kix.push_back(get_column_ix(k));
if (kix.back() >= m_columns.size())
kix.push_back(get_item_ix(k));
if (kix.back() >= m_items.size())
missing.insert(k);
}
}
......@@ -704,7 +704,7 @@ void category::set_validator(const validator *v, datablock &db)
else
{
std::ostringstream msg;
msg << "Cannot construct index since the key field" << (missing.size() > 1 ? "s" : "") << " "
msg << "Cannot construct index since the key item" << (missing.size() > 1 ? "s" : "") << " "
<< cif::join(missing, ", ") << " in " << m_name << " " << (missing.size() == 1 ? "is" : "are") << " missing\n";
throw missing_key_error(msg.str(), *missing.begin());
}
......@@ -713,8 +713,8 @@ void category::set_validator(const validator *v, datablock &db)
else
m_cat_validator = nullptr;
for (auto &&[column, cv] : m_columns)
cv = m_cat_validator ? m_cat_validator->get_validator_for_item(column) : nullptr;
for (auto &&[item, cv] : m_items)
cv = m_cat_validator ? m_cat_validator->get_validator_for_item(item) : nullptr;
update_links(db);
}
......@@ -760,31 +760,31 @@ bool category::is_valid() const
if (m_cat_validator == nullptr)
{
m_validator->report_error("undefined category " + m_name, false);
m_validator->report_error(validation_error::undefined_category, m_name, {}, false);
return false;
}
auto mandatory = m_cat_validator->m_mandatory_fields;
auto mandatory = m_cat_validator->m_mandatory_items;
for (auto &col : m_columns)
for (auto &col : m_items)
{
auto iv = m_cat_validator->get_validator_for_item(col.m_name);
if (iv == nullptr)
{
m_validator->report_error("Field " + col.m_name + " is not valid in category " + m_name, false);
m_validator->report_error(validation_error::unknown_item, col.m_name, m_name, false);
result = false;
}
// col.m_validator = iv;
if (col.m_validator != iv)
m_validator->report_error("Column validator is not specified correctly", true);
m_validator->report_error(validation_error::incorrect_item_validator, true);
mandatory.erase(col.m_name);
}
if (not mandatory.empty())
{
m_validator->report_error("In category " + m_name + " the following mandatory fields are missing: " + join(mandatory, ", "), false);
m_validator->report_error(validation_error::missing_mandatory_items, m_name, join(mandatory, ", "), false);
result = false;
}
......@@ -794,44 +794,44 @@ bool category::is_valid() const
for (auto k : m_cat_validator->m_keys)
{
if (get_column_ix(k) >= m_columns.size())
if (get_item_ix(k) >= m_items.size())
missing.insert(k);
}
m_validator->report_error("In category " + m_name + " the index is missing, likely due to missing key fields: " + join(missing, ", "), false);
m_validator->report_error(validation_error::missing_key_items, m_name, join(missing, ", "), false);
result = false;
}
#if not defined(NDEBUG)
// check index?
if (m_index)
{
if (m_index->size() != size())
m_validator->report_error("size of index is not equal to size of category " + m_name, true);
// m_index->validate();
for (auto r : *this)
{
auto p = r.get_row();
if (m_index->find(*this, p) != p)
m_validator->report_error("Key not found in index for category " + m_name, true);
}
}
#endif
// #if not defined(NDEBUG)
// // check index?
// if (m_index)
// {
// if (m_index->size() != size())
// m_validator->report_error("size of index is not equal to size of category " + m_name, true);
// // m_index->validate();
// for (auto r : *this)
// {
// auto p = r.get_row();
// if (m_index->find(*this, p) != p)
// m_validator->report_error("Key not found in index for category " + m_name, true);
// }
// }
// #endif
// validate all values
mandatory = m_cat_validator->m_mandatory_fields;
mandatory = m_cat_validator->m_mandatory_items;
for (auto ri = m_head; ri != nullptr; ri = ri->m_next)
{
for (uint16_t cix = 0; cix < m_columns.size(); ++cix)
for (uint16_t cix = 0; cix < m_items.size(); ++cix)
{
bool seen = false;
auto iv = m_columns[cix].m_validator;
auto iv = m_items[cix].m_validator;
if (iv == nullptr)
{
m_validator->report_error("invalid field " + m_columns[cix].m_name + " for category " + m_name, false);
m_validator->report_error(validation_error::unknown_item, m_name, m_items[cix].m_name, false);
result = false;
continue;
}
......@@ -840,14 +840,13 @@ bool category::is_valid() const
if (vi != nullptr)
{
seen = true;
try
{
(*iv)(vi->text());
}
catch (const std::exception &e)
std::error_code ec;
iv->validate_value(vi->text(), ec);
if (ec != std::errc())
{
result = false;
m_validator->report_error("Error validating " + m_columns[cix].m_name + ": " + e.what(), false);
m_validator->report_error(ec, m_name, m_items[cix].m_name, false);
continue;
}
}
......@@ -857,7 +856,7 @@ bool category::is_valid() const
if (iv != nullptr and iv->m_mandatory)
{
m_validator->report_error("missing mandatory field " + m_columns[cix].m_name + " for category " + m_name, false);
m_validator->report_error(validation_error::missing_mandatory_items, m_name, m_items[cix].m_name, false);
result = false;
}
}
......@@ -989,10 +988,10 @@ condition category::get_children_condition(row_handle rh, const category &childC
condition result;
iset mandatoryChildFields;
iset mandatoryChildItems;
auto childCatValidator = m_validator->get_validator_for_category(childCat.name());
if (childCatValidator != nullptr)
mandatoryChildFields = childCatValidator->m_mandatory_fields;
mandatoryChildItems = childCatValidator->m_mandatory_items;
auto links = m_validator->get_links_for_parent(m_name);
links.erase(remove_if(links.begin(), links.end(), [n = childCat.m_name](auto &l)
......@@ -1014,7 +1013,7 @@ condition category::get_children_condition(row_handle rh, const category &childC
if (parentValue.empty())
cond = std::move(cond) and key(childKey) == null;
else if (link->m_parent_keys.size() > 1 and not mandatoryChildFields.contains(childKey))
else if (link->m_parent_keys.size() > 1 and not mandatoryChildItems.contains(childKey))
cond = std::move(cond) and (key(childKey) == parentValue.text() or key(childKey) == null);
else
cond = std::move(cond) and key(childKey) == parentValue.text();
......@@ -1281,17 +1280,17 @@ std::string category::get_unique_id(std::function<std::string(int)> generator)
std::string result = generator(static_cast<int>(m_last_unique_num++));
std::string id_tag = "id";
std::string id_name = "id";
if (m_cat_validator != nullptr and m_cat_validator->m_keys.size() == 1)
{
id_tag = m_cat_validator->m_keys.front();
id_name = m_cat_validator->m_keys.front();
if (m_index == nullptr and m_cat_validator != nullptr)
m_index = new category_index(*this);
for (;;)
{
if (m_index->find_by_value(*this, { { id_tag, result } }) == nullptr)
if (m_index->find_by_value(*this, { { id_name, result } }) == nullptr)
break;
result = generator(static_cast<int>(m_last_unique_num++));
}
......@@ -1300,7 +1299,7 @@ std::string category::get_unique_id(std::function<std::string(int)> generator)
{
for (;;)
{
if (not contains(key(id_tag) == result))
if (not contains(key(id_name) == result))
break;
result = generator(static_cast<int>(m_last_unique_num++));
......@@ -1310,17 +1309,17 @@ std::string category::get_unique_id(std::function<std::string(int)> generator)
return result;
}
std::string category::get_unique_value(std::string_view tag)
std::string category::get_unique_value(std::string_view item_name)
{
std::string result;
if (m_validator and m_cat_validator)
{
auto iv = m_cat_validator->get_validator_for_item(tag);
auto iv = m_cat_validator->get_validator_for_item(item_name);
if (iv and iv->m_type and iv->m_type->m_primitive_type == DDL_PrimitiveType::Numb)
{
uint64_t v = find_max<uint64_t>(tag);
uint64_t v = find_max<uint64_t>(item_name);
result = std::to_string(v + 1);
}
}
......@@ -1332,7 +1331,7 @@ std::string category::get_unique_value(std::string_view tag)
{
// result = m_name + "-" + std::to_string(ix);
result = cif_id_for_number(ix);
if (not contains(key(tag) == result))
if (not contains(key(item_name) == result))
break;
}
}
......@@ -1340,28 +1339,28 @@ std::string category::get_unique_value(std::string_view tag)
return result;
}
void category::update_value(const std::vector<row_handle> &rows, std::string_view tag, std::string_view value)
void category::update_value(const std::vector<row_handle> &rows, std::string_view item_name, std::string_view value)
{
using namespace std::literals;
if (rows.empty())
return;
auto colIx = get_column_ix(tag);
if (colIx >= m_columns.size())
throw std::runtime_error("Invalid column " + std::string{ value } + " for " + m_name);
auto colIx = get_item_ix(item_name);
if (colIx >= m_items.size())
throw std::runtime_error("Invalid item " + std::string{ value } + " for " + m_name);
auto &col = m_columns[colIx];
auto &col = m_items[colIx];
// check the value
if (col.m_validator)
(*col.m_validator)(value);
// first some sanity checks, what was the old value and is it the same for all rows?
std::string oldValue{ rows.front()[tag].text() };
std::string oldValue{ rows.front()[item_name].text() };
for (auto row : rows)
{
if (oldValue != row[tag].text())
if (oldValue != row[item_name].text())
throw std::runtime_error("Inconsistent old values in update_value");
}
......@@ -1377,20 +1376,20 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
{
for (auto &&[childCat, linked] : m_child_links)
{
if (std::find(linked->m_parent_keys.begin(), linked->m_parent_keys.end(), tag) == linked->m_parent_keys.end())
if (std::find(linked->m_parent_keys.begin(), linked->m_parent_keys.end(), item_name) == linked->m_parent_keys.end())
continue;
condition cond;
std::string childTag;
std::string childItemName;
for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
{
std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix];
if (pk == tag)
if (pk == item_name)
{
childTag = ck;
childItemName = ck;
cond = std::move(cond) && key(ck) == oldValue;
}
else
......@@ -1437,7 +1436,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix];
if (pk == tag)
if (pk == item_name)
check = std::move(check) && key(ck) == value;
else
check = std::move(check) && key(ck) == parent[pk].text();
......@@ -1459,27 +1458,27 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
// cannot update this...
if (cif::VERBOSE > 0)
std::cerr << "Cannot update child " << childCat->m_name << "." << childTag << " with value " << value << '\n';
std::cerr << "Cannot update child " << childCat->m_name << "." << childItemName << " with value " << value << '\n';
}
// finally, update the children
if (not process.empty())
childCat->update_value(process, childTag, value);
childCat->update_value(process, childItemName, value);
}
}
}
void category::update_value(row *row, uint16_t column, std::string_view value, bool updateLinked, bool validate)
void category::update_value(row *row, uint16_t item, std::string_view value, bool updateLinked, bool validate)
{
// make sure we have an index, if possible
if ((updateLinked or validate) and m_index == nullptr and m_cat_validator != nullptr)
m_index = new category_index(*this);
auto &col = m_columns[column];
auto &col = m_items[item];
std::string_view oldValue;
auto ival = row->get(column);
auto ival = row->get(item);
if (ival != nullptr)
oldValue = ival->text();
......@@ -1492,12 +1491,12 @@ void category::update_value(row *row, uint16_t column, std::string_view value, b
if (col.m_validator and validate)
col.m_validator->operator()(value);
// If the field is part of the Key for this category, remove it from the index
// If the item is part of the Key for this category, remove it from the index
// before updating
bool reinsert = false;
if (updateLinked and // an update of an Item's value
m_index != nullptr and key_field_indices().count(column))
m_index != nullptr and key_item_indices().count(item))
{
reinsert = m_index->find(*this, row);
if (reinsert)
......@@ -1506,10 +1505,10 @@ void category::update_value(row *row, uint16_t column, std::string_view value, b
// first remove old value with cix
if (ival != nullptr)
row->remove(column);
row->remove(item);
if (not value.empty())
row->append(column, { value });
row->append(item, { value });
if (reinsert and m_index != nullptr)
m_index->insert(*this, row);
......@@ -1522,22 +1521,22 @@ void category::update_value(row *row, uint16_t column, std::string_view value, b
for (auto &&[childCat, linked] : m_child_links)
{
if (std::find(linked->m_parent_keys.begin(), linked->m_parent_keys.end(), iv->m_tag) == linked->m_parent_keys.end())
if (std::find(linked->m_parent_keys.begin(), linked->m_parent_keys.end(), iv->m_item_name) == linked->m_parent_keys.end())
continue;
condition cond;
std::string childTag;
std::string childItemName;
for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
{
std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix];
// TODO: add code to *NOT* test mandatory fields for Empty
// TODO: add code to *NOT* test mandatory items for Empty
if (pk == iv->m_tag)
if (pk == iv->m_item_name)
{
childTag = ck;
childItemName = ck;
cond = std::move(cond) and key(ck) == oldStrValue;
}
else
......@@ -1570,7 +1569,7 @@ void category::update_value(row *row, uint16_t column, std::string_view value, b
std::string pk = linked->m_parent_keys[ix];
std::string ck = linked->m_child_keys[ix];
if (pk == iv->m_tag)
if (pk == iv->m_item_name)
cond_n = std::move(cond_n) and key(ck) == value;
else
{
......@@ -1592,7 +1591,7 @@ void category::update_value(row *row, uint16_t column, std::string_view value, b
}
for (auto cr : rows)
cr.assign(childTag, value, false);
cr.assign(childItemName, value, false);
}
}
}
......@@ -1640,7 +1639,7 @@ row_handle category::create_copy(row_handle r)
{
auto i = r.m_row->get(ix);
if (i != nullptr)
items.emplace_back(m_columns[ix].m_name, i->text());
items.emplace_back(m_items[ix].m_name, i->text());
}
if (m_cat_validator and m_cat_validator->m_keys.size() == 1)
......@@ -1683,12 +1682,12 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
try
{
// First, make sure all mandatory fields are supplied
// First, make sure all mandatory items are supplied
if (m_cat_validator != nullptr)
{
for (uint16_t ix = 0; ix < static_cast<uint16_t>(m_columns.size()); ++ix)
for (uint16_t ix = 0; ix < static_cast<uint16_t>(m_items.size()); ++ix)
{
const auto &[column, iv] = m_columns[ix];
const auto &[item, iv] = m_items[ix];
if (iv == nullptr)
continue;
......@@ -1703,7 +1702,7 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
}
if (not seen and iv->m_mandatory)
throw std::runtime_error("missing mandatory field " + column + " for category " + m_name);
throw std::runtime_error("missing mandatory item " + item + " for category " + m_name);
}
}
......@@ -1742,7 +1741,7 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
// #endif
}
void category::swap_item(uint16_t column_ix, row_handle &a, row_handle &b)
void category::swap_item(uint16_t item_ix, row_handle &a, row_handle &b)
{
assert(this == a.m_category);
assert(this == b.m_category);
......@@ -1750,7 +1749,7 @@ void category::swap_item(uint16_t column_ix, row_handle &a, row_handle &b)
auto &ra = *a.m_row;
auto &rb = *b.m_row;
std::swap(ra.at(column_ix), rb.at(column_ix));
std::swap(ra.at(item_ix), rb.at(item_ix));
}
void category::sort(std::function<int(row_handle, row_handle)> f)
......@@ -1790,7 +1789,7 @@ namespace detail
{
size_t write_value(std::ostream &os, std::string_view value, size_t offset, size_t width, bool right_aligned)
{
if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field
if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text item
{
if (offset > 0)
os << '\n';
......@@ -1885,36 +1884,36 @@ namespace detail
} // namespace detail
std::vector<std::string> category::get_tag_order() const
std::vector<std::string> category::get_item_order() const
{
std::vector<std::string> result;
for (auto &c : m_columns)
for (auto &c : m_items)
result.push_back("_" + m_name + "." + c.m_name);
return result;
}
void category::write(std::ostream &os) const
{
std::vector<uint16_t> order(m_columns.size());
std::vector<uint16_t> order(m_items.size());
iota(order.begin(), order.end(), static_cast<uint16_t>(0));
write(os, order, false);
}
void category::write(std::ostream &os, const std::vector<std::string> &columns, bool addMissingColumns)
void category::write(std::ostream &os, const std::vector<std::string> &items, bool addMissingItems)
{
// make sure all columns are present
for (auto &c : columns)
add_column(c);
// make sure all items are present
for (auto &c : items)
add_item(c);
std::vector<uint16_t> order;
order.reserve(m_columns.size());
order.reserve(m_items.size());
for (auto &c : columns)
order.push_back(get_column_ix(c));
for (auto &c : items)
order.push_back(get_item_ix(c));
if (addMissingColumns)
if (addMissingItems)
{
for (uint16_t i = 0; i < m_columns.size(); ++i)
for (uint16_t i = 0; i < m_items.size(); ++i)
{
if (std::find(order.begin(), order.end(), i) == order.end())
order.push_back(i);
......@@ -1924,7 +1923,7 @@ void category::write(std::ostream &os, const std::vector<std::string> &columns,
write(os, order, true);
}
void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyColumns) const
void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyItems) const
{
if (empty())
return;
......@@ -1932,13 +1931,13 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
// If the first Row has a next, we need a loop_
bool needLoop = (m_head->m_next != nullptr);
std::vector<bool> right_aligned(m_columns.size(), false);
std::vector<bool> right_aligned(m_items.size(), false);
if (m_cat_validator != nullptr)
{
for (auto cix : order)
{
auto &col = m_columns[cix];
auto &col = m_items[cix];
right_aligned[cix] = col.m_validator != nullptr and
col.m_validator->m_type != nullptr and
col.m_validator->m_type->m_primitive_type == cif::DDL_PrimitiveType::Numb;
......@@ -1949,16 +1948,16 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
{
os << "loop_\n";
std::vector<size_t> columnWidths(m_columns.size());
std::vector<size_t> itemWidths(m_items.size());
for (auto cix : order)
{
auto &col = m_columns[cix];
auto &col = m_items[cix];
os << '_';
if (not m_name.empty())
os << m_name << '.';
os << col.m_name << ' ' << '\n';
columnWidths[cix] = 2;
itemWidths[cix] = 2;
}
for (auto r = m_head; r != nullptr; r = r->m_next)
......@@ -1979,8 +1978,8 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
if (l > 132)
continue;
if (columnWidths[ix] < l + 1)
columnWidths[ix] = l + 1;
if (itemWidths[ix] < l + 1)
itemWidths[ix] = l + 1;
}
}
}
......@@ -1991,7 +1990,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
for (uint16_t cix : order)
{
size_t w = columnWidths[cix];
size_t w = itemWidths[cix];
std::string_view s;
auto iv = r->get(cix);
......@@ -2031,12 +2030,12 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
// first find the indent level
size_t l = 0;
for (auto &col : m_columns)
for (auto &col : m_items)
{
std::string tag = '_' + m_name + '.' + col.m_name;
std::string item_name = '_' + m_name + '.' + col.m_name;
if (l < tag.length())
l = tag.length();
if (l < item_name.length())
l = item_name.length();
}
l += 3;
......@@ -2067,7 +2066,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
for (uint16_t cix : order)
{
auto &col = m_columns[cix];
auto &col = m_items[cix];
os << '_';
if (not m_name.empty())
......@@ -2108,10 +2107,10 @@ bool category::operator==(const category &rhs) const
using namespace std::placeholders;
// set<std::string> tagsA(a.fields()), tagsB(b.fields());
// set<std::string> item_namesA(a.items()), item_namesB(b.items());
//
// if (tagsA != tagsB)
// std::cout << "Unequal number of fields\n";
// if (item_namesA != item_namesB)
// std::cout << "Unequal number of items\n";
const category_validator *catValidator = nullptr;
......@@ -2120,40 +2119,40 @@ bool category::operator==(const category &rhs) const
catValidator = validator->get_validator_for_category(a.name());
typedef std::function<int(std::string_view, std::string_view)> compType;
std::vector<std::tuple<std::string, compType>> tags;
std::vector<std::tuple<std::string, compType>> item_names;
std::vector<std::string> keys;
std::vector<size_t> keyIx;
if (catValidator == nullptr)
{
for (auto &tag : a.get_columns())
for (auto &item_name : a.get_items())
{
tags.push_back(std::make_tuple(tag, [](std::string_view va, std::string_view vb)
item_names.push_back(std::make_tuple(item_name, [](std::string_view va, std::string_view vb)
{ return va.compare(vb); }));
keyIx.push_back(keys.size());
keys.push_back(tag);
keys.push_back(item_name);
}
}
else
{
keys = catValidator->m_keys;
for (auto &tag : a.key_fields())
for (auto &item_name : a.key_items())
{
auto iv = catValidator->get_validator_for_item(tag);
auto iv = catValidator->get_validator_for_item(item_name);
if (iv == nullptr)
throw std::runtime_error("missing item validator");
auto tv = iv->m_type;
if (tv == nullptr)
throw std::runtime_error("missing type validator");
tags.push_back(std::make_tuple(tag, std::bind(&cif::type_validator::compare, tv, std::placeholders::_1, std::placeholders::_2)));
item_names.push_back(std::make_tuple(item_name, std::bind(&cif::type_validator::compare, tv, std::placeholders::_1, std::placeholders::_2)));
auto pred = [tag](const std::string &s) -> bool
auto pred = [item_name](const std::string &s) -> bool
{
return cif::iequals(tag, s) == 0;
return cif::iequals(item_name, s) == 0;
};
if (find_if(keys.begin(), keys.end(), pred) == keys.end())
keyIx.push_back(tags.size() - 1);
keyIx.push_back(item_names.size() - 1);
}
}
......@@ -2166,12 +2165,12 @@ bool category::operator==(const category &rhs) const
for (auto kix : keyIx)
{
std::string tag;
std::string item_name;
compType compare;
std::tie(tag, compare) = tags[kix];
std::tie(item_name, compare) = item_names[kix];
d = compare(a[tag].text(), b[tag].text());
d = compare(a[item_name].text(), b[item_name].text());
if (d != 0)
break;
......@@ -2193,19 +2192,19 @@ bool category::operator==(const category &rhs) const
std::vector<std::string> missingA, missingB, different;
for (auto &tt : tags)
for (auto &tt : item_names)
{
std::string tag;
std::string item_name;
compType compare;
std::tie(tag, compare) = tt;
std::tie(item_name, compare) = tt;
// make it an option to compare unapplicable to empty or something
auto ta = ra[tag].text();
auto ta = ra[item_name].text();
if (ta == "." or ta == "?")
ta = "";
auto tb = rb[tag].text();
auto tb = rb[item_name].text();
if (tb == "." or tb == "?")
tb = "";
......
src/condition.cpp
......@@ -30,17 +30,17 @@
namespace cif
{
iset get_category_fields(const category &cat)
iset get_category_items(const category &cat)
{
return cat.key_fields();
return cat.key_items();
}
uint16_t get_column_ix(const category &cat, std::string_view col)
uint16_t get_item_ix(const category &cat, std::string_view col)
{
return cat.get_column_ix(col);
return cat.get_item_ix(col);
}
bool is_column_type_uchar(const category &cat, std::string_view col)
bool is_item_type_uchar(const category &cat, std::string_view col)
{
bool result = false;
......@@ -63,14 +63,14 @@ namespace detail
condition_impl *key_equals_condition_impl::prepare(const category &c)
{
m_item_ix = c.get_column_ix(m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
m_item_ix = c.get_item_ix(m_item_name);
m_icase = is_item_type_uchar(c, m_item_name);
if (c.get_cat_validator() != nullptr and
c.key_field_indices().contains(m_item_ix) and
c.key_field_indices().size() == 1)
c.key_item_indices().contains(m_item_ix) and
c.key_item_indices().size() == 1)
{
m_single_hit = c[{ { m_item_tag, m_value } }];
m_single_hit = c[{ { m_item_name, m_value } }];
}
return this;
......
src/datablock.cpp
......@@ -143,13 +143,6 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
if (iequals(name, i->name()))
{
is_new = false;
if (i != begin())
{
auto n = std::next(i);
splice(begin(), *this, i, n);
}
break;
}
......@@ -158,25 +151,24 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
if (is_new)
{
auto &c = emplace_back(name);
c.set_validator(m_validator, *this);
i = insert(end(), {name});
i->set_validator(m_validator, *this);
}
assert(end() != begin());
return std::make_tuple(std::prev(end()), is_new);
assert(i != end());
return std::make_tuple(i, is_new);
}
std::vector<std::string> datablock::get_tag_order() const
std::vector<std::string> datablock::get_item_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();
auto cto = ci->get_item_order();
result.insert(result.end(), cto.begin(), cto.end());
}
......@@ -184,7 +176,7 @@ std::vector<std::string> datablock::get_tag_order() const
{ return cat.name() == "audit_conform"; });
if (ci != end())
{
auto cto = ci->get_tag_order();
auto cto = ci->get_item_order();
result.insert(result.end(), cto.begin(), cto.end());
}
......@@ -192,7 +184,7 @@ std::vector<std::string> datablock::get_tag_order() const
{
if (cat.name() == "entry" or cat.name() == "audit_conform")
continue;
auto cto = cat.get_tag_order();
auto cto = cat.get_item_order();
result.insert(result.end(), cto.begin(), cto.end());
}
......@@ -253,12 +245,31 @@ void datablock::write(std::ostream &os) const
{
// If the dictionary declares an audit_conform category, put it in,
// but only if it does not exist already!
if (get("audit_conform") == nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
if (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);
auto *audit_conform = get("audit_conform");
if (audit_conform == nullptr or audit_conform->size() != 1) // There should be one entry here, I guess
audit_conform = nullptr;
else
{
// And the name and version should be filled in of course
auto &e = audit_conform->front();
if (e["dict_name"].empty() or e["dict_version"].empty())
audit_conform = nullptr;
}
if (not audit_conform)
{
category auditConform("audit_conform");
// clang-format off
auditConform.emplace({
{ "dict_name", m_validator->name() },
{ "dict_version", m_validator->version() }
});
// clang-format on
auditConform.write(os);
}
}
// base order on parent child relationships, parents first
......@@ -327,16 +338,16 @@ void datablock::write(std::ostream &os) const
}
}
void datablock::write(std::ostream &os, const std::vector<std::string> &tag_order)
void datablock::write(std::ostream &os, const std::vector<std::string> &item_name_order)
{
os << "data_" << m_name << '\n'
<< "# \n";
std::vector<std::string> cat_order;
for (auto &o : tag_order)
for (auto &o : item_name_order)
{
std::string cat_name, item_name;
std::tie(cat_name, item_name) = split_tag_name(o);
std::tie(cat_name, item_name) = split_item_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);
......@@ -349,10 +360,10 @@ void datablock::write(std::ostream &os, const std::vector<std::string> &tag_orde
continue;
std::vector<std::string> items;
for (auto &o : tag_order)
for (auto &o : item_name_order)
{
std::string cat_name, item_name;
std::tie(cat_name, item_name) = split_tag_name(o);
std::tie(cat_name, item_name) = split_item_name(o);
if (cat_name == c)
items.push_back(item_name);
......
src/dictionary_parser.cpp
......@@ -50,7 +50,7 @@ class dictionary_parser : public parser
try
{
while (m_lookahead != CIFToken::Eof)
while (m_lookahead != CIFToken::END_OF_FILE)
{
switch (m_lookahead)
{
......@@ -128,7 +128,7 @@ class dictionary_parser : public parser
datablock::iterator cat = dict.end();
match(CIFToken::SAVE_NAME);
while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::Tag)
while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::ITEM_NAME)
{
if (m_lookahead == CIFToken::LOOP)
{
......@@ -136,30 +136,30 @@ class dictionary_parser : public parser
match(CIFToken::LOOP);
std::vector<std::string> tags;
while (m_lookahead == CIFToken::Tag)
std::vector<std::string> item_names;
while (m_lookahead == CIFToken::ITEM_NAME)
{
std::string catName, item_name;
std::tie(catName, item_name) = split_tag_name(m_token_value);
std::tie(catName, item_name) = split_item_name(m_token_value);
if (cat == dict.end())
std::tie(cat, std::ignore) = dict.emplace(catName);
else if (not iequals(cat->name(), catName))
error("inconsistent categories in loop_");
tags.push_back(item_name);
match(CIFToken::Tag);
item_names.push_back(item_name);
match(CIFToken::ITEM_NAME);
}
while (m_lookahead == CIFToken::Value)
while (m_lookahead == CIFToken::VALUE)
{
cat->emplace({});
auto row = cat->back();
for (auto tag : tags)
for (auto item_name : item_names)
{
row[tag] = m_token_value;
match(CIFToken::Value);
row[item_name] = m_token_value;
match(CIFToken::VALUE);
}
}
......@@ -168,18 +168,18 @@ class dictionary_parser : public parser
else
{
std::string catName, item_name;
std::tie(catName, item_name) = split_tag_name(m_token_value);
std::tie(catName, item_name) = split_item_name(m_token_value);
if (cat == dict.end() or not iequals(cat->name(), catName))
std::tie(cat, std::ignore) = dict.emplace(catName);
match(CIFToken::Tag);
match(CIFToken::ITEM_NAME);
if (cat->empty())
cat->emplace({});
cat->back()[item_name] = m_token_value;
match(CIFToken::Value);
match(CIFToken::VALUE);
}
}
......@@ -191,7 +191,7 @@ class dictionary_parser : public parser
std::vector<std::string> keys;
for (auto k : dict["category_key"])
keys.push_back(std::get<1>(split_tag_name(k["name"].as<std::string>())));
keys.push_back(std::get<1>(split_item_name(k["name"].as<std::string>())));
iset groups;
for (auto g : dict["category_group"])
......@@ -234,17 +234,17 @@ class dictionary_parser : public parser
// collect the dict from our dataBlock and construct validators
for (auto i : dict["item"])
{
std::string tagName, category, mandatory;
cif::tie(tagName, category, mandatory) = i.get("name", "category_id", "mandatory_code");
std::string item, category, mandatory;
cif::tie(item, category, mandatory) = i.get("name", "category_id", "mandatory_code");
std::string cat_name, item_name;
std::tie(cat_name, item_name) = split_tag_name(tagName);
std::tie(cat_name, item_name) = split_item_name(item);
if (cat_name.empty() or item_name.empty())
error("Invalid tag name in _item.name " + tagName);
error("Invalid item name in _item.name " + item);
if (not iequals(category, cat_name) and not(category.empty() or category == "?"))
error("specified category id does match the implicit category name for tag '" + tagName + '\'');
error("specified category id does match the implicit category name for item '" + item + '\'');
else
category = cat_name;
......@@ -260,22 +260,22 @@ class dictionary_parser : public parser
{
if (VERBOSE > 2)
{
std::cerr << "inconsistent mandatory value for " << tagName << " in dictionary\n";
std::cerr << "inconsistent mandatory value for " << item << " in dictionary\n";
if (iequals(tagName, saveFrameName))
if (iequals(item, saveFrameName))
std::cerr << "choosing " << mandatory << '\n';
else
std::cerr << "choosing " << (vi->m_mandatory ? "Y" : "N") << '\n';
}
if (iequals(tagName, saveFrameName))
if (iequals(item, saveFrameName))
vi->m_mandatory = (iequals(mandatory, "yes"));
}
if (vi->m_type != nullptr and tv != nullptr and vi->m_type != tv)
{
if (VERBOSE > 1)
std::cerr << "inconsistent type for " << tagName << " in dictionary\n";
std::cerr << "inconsistent type for " << item << " in dictionary\n";
}
// vi->mMandatory = (iequals(mandatory, "yes"));
......@@ -358,7 +358,7 @@ class dictionary_parser : public parser
}
size_t ix = linkIndex.at(key);
addLink(ix, piv->m_tag, civ->m_tag);
addLink(ix, piv->m_item_name, civ->m_item_name);
}
// Only process inline linked items if the linked group list is absent
......@@ -386,7 +386,7 @@ class dictionary_parser : public parser
}
size_t ix = linkIndex.at(key);
addLink(ix, piv->m_tag, civ->m_tag);
addLink(ix, piv->m_item_name, civ->m_item_name);
}
}
......@@ -417,7 +417,7 @@ class dictionary_parser : public parser
for (auto &iv : cv.m_item_validators)
{
if (iv.m_type == nullptr and cif::VERBOSE >= 0)
std::cerr << "Missing item_type for " << iv.m_tag << '\n';
std::cerr << "Missing item_type for " << iv.m_item_name << '\n';
}
}
}
......
src/file.cpp
......@@ -158,13 +158,6 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
if (iequals(name, i->name()))
{
is_new = false;
if (i != begin())
{
auto n = std::next(i);
splice(begin(), *this, i, n);
}
break;
}
......@@ -173,12 +166,12 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
if (is_new)
{
auto &db = emplace_back(name);
db.set_validator(m_validator);
i = insert(end(), { name });
i->set_validator(m_validator);
}
assert(begin() != end());
return std::make_tuple(std::prev(end()), is_new);
assert(i != end());
return std::make_tuple(i, is_new);
}
void file::load(const std::filesystem::path &p)
......
src/item.cpp
......@@ -35,7 +35,7 @@ const item_handle item_handle::s_null_item;
row_handle s_null_row_handle;
item_handle::item_handle()
: m_column(std::numeric_limits<uint16_t>::max())
: m_item_ix(std::numeric_limits<uint16_t>::max())
, m_row_handle(s_null_row_handle)
{
}
......@@ -44,7 +44,7 @@ std::string_view item_handle::text() const
{
if (not m_row_handle.empty())
{
auto iv = m_row_handle.m_row->get(m_column);
auto iv = m_row_handle.m_row->get(m_item_ix);
if (iv != nullptr)
return iv->text();
}
......@@ -55,14 +55,14 @@ std::string_view item_handle::text() const
void item_handle::assign_value(const item &v)
{
assert(not m_row_handle.empty());
m_row_handle.assign(m_column, v.value(), true);
m_row_handle.assign(m_item_ix, v.value(), true);
}
void item_handle::swap(item_handle &b)
{
assert(m_column == b.m_column);
assert(m_item_ix == b.m_item_ix);
// assert(&m_row_handle.m_category == &b.m_row_handle.m_category);
m_row_handle.swap(m_column, b.m_row_handle);
m_row_handle.swap(m_item_ix, b.m_row_handle);
}
}
src/model.cpp
......@@ -163,9 +163,9 @@ int atom::atom_impl::get_charge() const
// const std::string atom::atom_impl::get_property(const std::string_view name) const
// {
// for (auto &&[tag, ref] : mCachedRefs)
// for (auto &&[item_name, ref] : mCachedRefs)
// {
// if (tag == name)
// if (item_name == name)
// return ref.as<std::string>();
// }
......@@ -175,9 +175,9 @@ int atom::atom_impl::get_charge() const
// void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
// {
// for (auto &&[tag, ref] : mCachedRefs)
// for (auto &&[item_name, ref] : mCachedRefs)
// {
// if (tag != name)
// if (item_name != name)
// continue;
// ref = value;
......
src/parser.cpp
......@@ -269,7 +269,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
{
const auto kEOF = std::char_traits<char>::eof();
CIFToken result = CIFToken::Unknown;
CIFToken result = CIFToken::UNKNOWN;
int quoteChar = 0;
State state = State::Start;
m_bol = false;
......@@ -279,7 +279,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
reserved_words_automaton dag;
while (result == CIFToken::Unknown)
while (result == CIFToken::UNKNOWN)
{
auto ch = get_next_char();
......@@ -287,7 +287,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
{
case State::Start:
if (ch == kEOF)
result = CIFToken::Eof;
result = CIFToken::END_OF_FILE;
else if (ch == '\n')
{
m_bol = true;
......@@ -298,9 +298,9 @@ sac_parser::CIFToken sac_parser::get_next_token()
else if (ch == '#')
state = State::Comment;
else if (ch == '_')
state = State::Tag;
state = State::ItemName;
else if (ch == ';' and m_bol)
state = State::TextField;
state = State::TextItem;
else if (ch == '?')
state = State::QuestionMark;
else if (ch == '\'' or ch == '"')
......@@ -316,7 +316,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
case State::White:
if (ch == kEOF)
result = CIFToken::Eof;
result = CIFToken::END_OF_FILE;
else if (not is_space(ch))
{
state = State::Start;
......@@ -335,7 +335,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
m_token_buffer.clear();
}
else if (ch == kEOF)
result = CIFToken::Eof;
result = CIFToken::END_OF_FILE;
else if (not is_any_print(ch))
error("invalid character in comment");
break;
......@@ -344,29 +344,29 @@ sac_parser::CIFToken sac_parser::get_next_token()
if (not is_non_blank(ch))
{
retract();
result = CIFToken::Value;
result = CIFToken::VALUE;
}
else
state = State::Value;
break;
case State::TextField:
case State::TextItem:
if (ch == '\n')
state = State::TextFieldNL;
state = State::TextItemNL;
else if (ch == kEOF)
error("unterminated textfield");
else if (not is_any_print(ch) and cif::VERBOSE > 2)
warning("invalid character in text field '" + std::string({static_cast<char>(ch)}) + "' (" + std::to_string((int)ch) + ")");
break;
case State::TextFieldNL:
case State::TextItemNL:
if (is_text_lead(ch) or ch == ' ' or ch == '\t')
state = State::TextField;
state = State::TextItem;
else if (ch == ';')
{
assert(m_token_buffer.size() >= 2);
m_token_value = std::string_view(m_token_buffer.data() + 1, m_token_buffer.size() - 3);
result = CIFToken::Value;
result = CIFToken::VALUE;
}
else if (ch == kEOF)
error("unterminated textfield");
......@@ -387,7 +387,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
if (is_white(ch))
{
retract();
result = CIFToken::Value;
result = CIFToken::VALUE;
if (m_token_buffer.size() < 2)
error("Invalid quoted string token");
......@@ -403,11 +403,11 @@ sac_parser::CIFToken sac_parser::get_next_token()
error("invalid character in quoted string");
break;
case State::Tag:
case State::ItemName:
if (not is_non_blank(ch))
{
retract();
result = CIFToken::Tag;
result = CIFToken::ITEM_NAME;
m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
}
break;
......@@ -422,7 +422,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
if (not is_non_blank(ch))
{
retract();
result = CIFToken::Value;
result = CIFToken::VALUE;
m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
}
else
......@@ -467,7 +467,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
if (not is_non_blank(ch))
{
retract();
result = CIFToken::Value;
result = CIFToken::VALUE;
m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
break;
}
......@@ -483,7 +483,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
if (VERBOSE >= 5)
{
std::cerr << get_token_name(result);
if (result != CIFToken::Eof)
if (result != CIFToken::END_OF_FILE)
std::cerr << " " << std::quoted(m_token_value);
std::cerr << '\n';
}
......@@ -710,7 +710,7 @@ bool sac_parser::parse_single_datablock(const std::string &datablock, const data
void sac_parser::parse_file()
{
while (m_lookahead != CIFToken::Eof)
while (m_lookahead != CIFToken::END_OF_FILE)
{
switch (m_lookahead)
{
......@@ -735,10 +735,10 @@ void sac_parser::parse_file()
void sac_parser::parse_global()
{
match(CIFToken::GLOBAL);
while (m_lookahead == CIFToken::Tag)
while (m_lookahead == CIFToken::ITEM_NAME)
{
match(CIFToken::Tag);
match(CIFToken::Value);
match(CIFToken::ITEM_NAME);
match(CIFToken::VALUE);
}
}
......@@ -747,7 +747,7 @@ void sac_parser::parse_datablock()
static const std::string kUnitializedCategory("<invalid>");
std::string cat = kUnitializedCategory; // intial value acts as a guard for empty category names
while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::Tag or m_lookahead == CIFToken::SAVE_NAME)
while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::ITEM_NAME or m_lookahead == CIFToken::SAVE_NAME)
{
switch (m_lookahead)
{
......@@ -757,12 +757,12 @@ void sac_parser::parse_datablock()
match(CIFToken::LOOP);
std::vector<std::string> tags;
std::vector<std::string> item_names;
while (m_lookahead == CIFToken::Tag)
while (m_lookahead == CIFToken::ITEM_NAME)
{
std::string catName, itemName;
std::tie(catName, itemName) = split_tag_name(m_token_value);
std::tie(catName, itemName) = split_item_name(m_token_value);
if (cat == kUnitializedCategory)
{
......@@ -772,19 +772,19 @@ void sac_parser::parse_datablock()
else if (not iequals(cat, catName))
error("inconsistent categories in loop_");
tags.push_back(itemName);
item_names.push_back(itemName);
match(CIFToken::Tag);
match(CIFToken::ITEM_NAME);
}
while (m_lookahead == CIFToken::Value)
while (m_lookahead == CIFToken::VALUE)
{
produce_row();
for (auto tag : tags)
for (auto item_name : item_names)
{
produce_item(cat, tag, m_token_value);
match(CIFToken::Value);
produce_item(cat, item_name, m_token_value);
match(CIFToken::VALUE);
}
}
......@@ -792,10 +792,10 @@ void sac_parser::parse_datablock()
break;
}
case CIFToken::Tag:
case CIFToken::ITEM_NAME:
{
std::string catName, itemName;
std::tie(catName, itemName) = split_tag_name(m_token_value);
std::tie(catName, itemName) = split_item_name(m_token_value);
if (not iequals(cat, catName))
{
......@@ -804,11 +804,11 @@ void sac_parser::parse_datablock()
produce_row();
}
match(CIFToken::Tag);
match(CIFToken::ITEM_NAME);
produce_item(cat, itemName, m_token_value);
match(CIFToken::Value);
match(CIFToken::VALUE);
break;
}
......
src/pdb/pdb2cif_remark_3.cpp
......@@ -1493,8 +1493,8 @@ bool Remark3Parser::parse(const std::string &expMethod, PDBRecord *r, cif::datab
auto r1 = cat1.front();
auto r2 = cat2.front();
for (auto column : cat1.key_fields())
r2[column] = r1[column].text();
for (auto item : cat1.key_items())
r2[item] = r1[item].text();
}
}
else
......
src/pdb/reconstruct.cpp
......@@ -237,20 +237,20 @@ void checkAtomRecords(datablock &db)
{ "auth_comp_id", auth_comp_id.value_or(*label_comp_id) },
{ "auth_atom_id", auth_atom_id.value_or(*label_atom_id) } });
// Rewrite the coordinates and other fields that look better in a fixed format
// Rewrite the coordinates and other items that look better in a fixed format
// Be careful not to nuke invalidly formatted data here
for (auto [tag, prec] : std::vector<std::tuple<std::string_view, std::string::size_type>>{
for (auto [item_name, prec] : std::vector<std::tuple<std::string_view, std::string::size_type>>{
{ "cartn_x", 3 },
{ "cartn_y", 3 },
{ "cartn_z", 3 },
{ "occupancy", 2 },
{ "b_iso_or_equiv", 2 } })
{
if (row[tag].empty())
if (row[item_name].empty())
continue;
float v;
auto s = row.get<std::string>(tag);
auto s = row.get<std::string>(item_name);
if (auto [ptr, ec] = cif::from_chars(s.data(), s.data() + s.length(), v); ec != std::errc())
continue;
......@@ -259,7 +259,7 @@ void checkAtomRecords(datablock &db)
char b[12];
if (auto [ptr, ec] = cif::to_chars(b, b + sizeof(b), v, cif::chars_format::fixed, prec); ec == std::errc())
row.assign(tag, { b, static_cast<std::string::size_type>(ptr - b) }, false, false);
row.assign(item_name, { b, static_cast<std::string::size_type>(ptr - b) }, false, false);
}
}
}
......@@ -267,22 +267,22 @@ void checkAtomRecords(datablock &db)
auto *cv = atom_site.get_cat_validator();
if (cv)
{
// See if there are columns that are no longer known
for (auto tag : atom_site.get_columns())
// See if there are items that are no longer known
for (auto item_name : atom_site.get_items())
{
if (cv->get_validator_for_item(tag) != nullptr)
if (cv->get_validator_for_item(item_name) != nullptr)
continue;
auto r = atom_site.find_first(key(tag) != null);
auto r = atom_site.find_first(key(item_name) != null);
if (not r)
{
if (cif::VERBOSE > 0)
std::clog << "Dropping unknown column " << tag << '\n';
std::clog << "Dropping unknown item " << item_name << '\n';
atom_site.remove_column(tag);
atom_site.remove_item(item_name);
}
else if (cif::VERBOSE > 0)
std::clog << "Keeping unknown column " << std::quoted(tag) << " in atom_site since it is not empty\n";
std::clog << "Keeping unknown item " << std::quoted(item_name) << " in atom_site since it is not empty\n";
}
}
}
......@@ -311,10 +311,10 @@ void createEntity(datablock &db)
auto &cf = compound_factory::instance();
auto &atom_site = db["atom_site"];
atom_site.add_column("label_entity_id");
atom_site.add_item("label_entity_id");
auto &struct_asym = db["struct_asym"];
struct_asym.add_column("entity_id");
struct_asym.add_item("entity_id");
std::map<std::string, std::vector<std::tuple<std::string, int>>> asyms;
......@@ -617,7 +617,7 @@ void comparePolySeqSchemes(datablock &db)
auto &ndb_poly_seq_scheme = db["ndb_poly_seq_scheme"];
auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
// Since often ndb_poly_seq_scheme only contains an id and mon_id field
// Since often ndb_poly_seq_scheme only contains an id and mon_id item
// we assume that it should match the accompanying pdbx_poly_seq
std::vector<std::string> asym_ids_ndb, asym_ids_pdbx;
......@@ -722,6 +722,7 @@ void reconstruct_pdbx(file &file, std::string_view dictionary)
std::vector<std::string> invalidCategories;
// clean up each category
for (auto &cat : db)
{
try
......@@ -730,21 +731,21 @@ void reconstruct_pdbx(file &file, std::string_view dictionary)
if (not cv)
continue;
// Start by renaming columns that may have old names based on alias info
// Start by renaming items that may have old names based on alias info
for (auto tag : cat.get_columns())
for (auto item_name : cat.get_items())
{
auto iv = cv->get_validator_for_item(tag);
if (iv) // know, must be OK then
auto iv = cv->get_validator_for_item(item_name);
if (iv) // know, must be OK then`
continue;
iv = cv->get_validator_for_aliased_item(tag);
iv = cv->get_validator_for_aliased_item(item_name);
if (not iv)
continue;
if (cif::VERBOSE > 0)
std::clog << "Renaming " << tag << " to " << iv->m_tag << " in category " << cat.name() << '\n';
cat.rename_column(tag, iv->m_tag);
std::clog << "Renaming " << item_name << " to " << iv->m_item_name << " in category " << cat.name() << '\n';
cat.rename_item(item_name, iv->m_item_name);
}
for (auto link : validator.get_links_for_child(cat.name()))
......@@ -767,14 +768,38 @@ void reconstruct_pdbx(file &file, std::string_view dictionary)
}
}
// Fill in all mandatory fields
for (auto key : cv->m_mandatory_fields)
// Fill in all mandatory items
for (auto key : cv->m_mandatory_items)
{
if (not cat.has_column(key))
if (not cat.has_item(key))
{
if (cif::VERBOSE > 0)
std::clog << "Adding mandatory key " << key << " to category " << cat.name() << '\n';
cat.add_column(key);
cat.add_item(key);
}
}
// validate all values, and if they do not validate replace the content with an unknown flag
for (auto item_name : cat.get_items())
{
auto iv = cv->get_validator_for_item(item_name);
if (not iv)
continue;
auto ix = cat.get_item_ix(item_name);
for (auto row : cat)
{
std::error_code ec;
std::string_view value = row[ix].text();
if (not iv->validate_value(value, ec))
{
if (cif::VERBOSE > 0)
std::clog << "Replacing value (" << std::quoted(value) << ") for item " << item_name << " since it does not validate\n";
row[ix] = "?";
}
}
}
......@@ -834,7 +859,7 @@ void reconstruct_pdbx(file &file, std::string_view dictionary)
if (cif::VERBOSE > 0)
std::clog << "Attempt to fix " << cat.name() << " failed: " << ex.what() << '\n';
// replace fields that do not define a relation to a parent
// replace items that do not define a relation to a parent
std::set<std::string> replaceableKeys;
for (auto key : cv->m_keys)
......
src/pdb/validate-pdbx.cpp
......@@ -69,26 +69,67 @@ condition get_parents_condition(const validator &validator, row_handle rh, const
bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
{
using namespace cif::literals;
std::error_code ec;
bool result = is_valid_pdbx_file(file, dictionary, ec);
if (ec != std::errc())
throw std::system_error(ec);
return result;
}
bool is_valid_pdbx_file(const file &file, std::error_code &ec)
{
bool result = false;
if (file.empty())
ec = make_error_code(validation_error::empty_file);
else
{
std::string dictionary = "mmcif_pdbx";
for (auto &db : file)
{
auto audit_conform = db.get("audit_conform");
if (audit_conform == nullptr)
continue;
if (not audit_conform->empty())
{
auto specified_dict = audit_conform->front()["dict_name"];
if (not specified_dict.empty())
dictionary = specified_dict.as<std::string>();
}
auto &cf = cif::compound_factory::instance();
auto &validator = cif::validator_factory::instance().operator[](dictionary);
break;
}
result = is_valid_pdbx_file(file, dictionary, ec);
}
return result;
}
bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::error_code &ec)
{
using namespace cif::literals;
bool result = true;
try
{
auto &cf = cif::compound_factory::instance();
auto &validator = cif::validator_factory::instance().operator[](dictionary);
if (file.empty())
throw validation_error("Empty file");
throw std::runtime_error("Empty file");
auto &db = file.front();
if (db.empty())
throw validation_error("Empty datablock");
throw std::runtime_error("Empty datablock");
auto &atom_site = db["atom_site"];
if (atom_site.empty())
throw validation_error("Empty or missing atom_site category");
throw std::runtime_error("Empty or missing atom_site category");
auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
......@@ -111,29 +152,29 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
auto p = pdbx_poly_seq_scheme.find(get_parents_condition(validator, r, pdbx_poly_seq_scheme));
if (p.size() != 1)
throw validation_error("For each residue in atom_site that is a residue in a polymer there should be exactly one pdbx_poly_seq_scheme record");
throw std::runtime_error("For each residue in atom_site that is a residue in a polymer there should be exactly one pdbx_poly_seq_scheme record");
}
auto &entity = db["entity"];
if (entity.empty())
throw validation_error("Entity category is missing or empty");
throw std::runtime_error("Entity category is missing or empty");
auto &entity_poly = db["entity_poly"];
if (entity_poly.empty())
throw validation_error("Entity_poly category is missing or empty");
throw std::runtime_error("Entity_poly category is missing or empty");
auto &entity_poly_seq = db["entity_poly_seq"];
if (entity_poly_seq.empty())
throw validation_error("Entity_poly_seq category is missing or empty");
throw std::runtime_error("Entity_poly_seq category is missing or empty");
auto &struct_asym = db["struct_asym"];
if (struct_asym.empty())
throw validation_error("struct_asym category is missing or empty");
throw std::runtime_error("struct_asym category is missing or empty");
for (auto entity_id : entity.find<std::string>("type"_key == "polymer", "id"))
{
if (entity_poly.count("entity_id"_key == entity_id) != 1)
throw validation_error("There should be exactly one entity_poly record per polymer entity");
throw std::runtime_error("There should be exactly one entity_poly record per polymer entity");
const auto entity_poly_type = entity_poly.find1<std::string>("entity_id"_key == entity_id, "type");
......@@ -151,7 +192,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
"seq_id"_key == num and
"hetero"_key == hetero) != 1)
{
throw validation_error("For each entity_poly_seq record there should be exactly one pdbx_poly_seq record");
throw std::runtime_error("For each entity_poly_seq record there should be exactly one pdbx_poly_seq record");
}
}
}
......@@ -163,11 +204,11 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
"num"_key == seq_id and
"hetero"_key == hetero) != 1)
{
throw validation_error("For each pdbx_poly_seq/struct_asym record there should be exactly one entity_poly_seq record");
throw std::runtime_error("For each pdbx_poly_seq/struct_asym record there should be exactly one entity_poly_seq record");
}
if ((mon_per_seq_id[seq_id].size() > 1) != hetero)
throw validation_error("Mismatch between the hetero flag in the poly seq schemes and the number residues per seq_id");
throw std::runtime_error("Mismatch between the hetero flag in the poly seq schemes and the number residues per seq_id");
}
for (const auto &[seq_id, mon_ids] : mon_per_seq_id)
......@@ -184,7 +225,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
"label_seq_id"_key == seq_id and not std::move(cond);
if (atom_site.contains(std::move(cond)))
throw validation_error("An atom_site record exists that has no parent in the poly seq scheme categories");
throw std::runtime_error("An atom_site record exists that has no parent in the poly seq scheme categories");
}
}
......@@ -250,7 +291,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
seq->erase(std::remove_if(seq->begin(), seq->end(), [](char ch) { return std::isspace(ch); }), seq->end());
if (not seq_match(false, seq->begin(), seq->end()))
throw validation_error("Sequences do not match for entity " + entity_id);
throw std::runtime_error("Sequences do not match for entity " + entity_id);
}
if (not seq_can.has_value())
......@@ -263,7 +304,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
seq_can->erase(std::remove_if(seq_can->begin(), seq_can->end(), [](char ch) { return std::isspace(ch); }), seq_can->end());
if (not seq_match(true, seq_can->begin(), seq_can->end()))
throw validation_error("Canonical sequences do not match for entity " + entity_id);
throw std::runtime_error("Canonical sequences do not match for entity " + entity_id);
}
}
......@@ -275,6 +316,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
result = false;
if (cif::VERBOSE > 0)
std::clog << ex.what() << '\n';
ec = make_error_code(validation_error::not_valid_pdbx);
}
return result;
......
src/row.cpp
......@@ -29,44 +29,44 @@
namespace cif
{
void row_handle::assign(uint16_t column, std::string_view value, bool updateLinked, bool validate)
void row_handle::assign(uint16_t item, std::string_view value, bool updateLinked, bool validate)
{
if (not m_category)
throw std::runtime_error("uninitialized row");
m_category->update_value(m_row, column, value, updateLinked, validate);
m_category->update_value(m_row, item, value, updateLinked, validate);
}
uint16_t row_handle::get_column_ix(std::string_view name) const
uint16_t row_handle::get_item_ix(std::string_view name) const
{
if (not m_category)
throw std::runtime_error("uninitialized row");
return m_category->get_column_ix(name);
return m_category->get_item_ix(name);
}
std::string_view row_handle::get_column_name(uint16_t ix) const
std::string_view row_handle::get_item_name(uint16_t ix) const
{
if (not m_category)
throw std::runtime_error("uninitialized row");
return m_category->get_column_name(ix);
return m_category->get_item_name(ix);
}
uint16_t row_handle::add_column(std::string_view name)
uint16_t row_handle::add_item(std::string_view name)
{
if (not m_category)
throw std::runtime_error("uninitialized row");
return m_category->add_column(name);
return m_category->add_item(name);
}
void row_handle::swap(uint16_t column, row_handle &b)
void row_handle::swap(uint16_t item, row_handle &b)
{
if (not m_category)
throw std::runtime_error("uninitialized row");
m_category->swap_item(column, *this, b);
m_category->swap_item(item, *this, b);
}
// --------------------------------------------------------------------
......@@ -86,7 +86,7 @@ row_initializer::row_initializer(row_handle rh)
auto &i = r->operator[](ix);
if (not i)
continue;
emplace_back(cat.get_column_name(ix), i.text());
emplace_back(cat.get_item_name(ix), i.text());
}
}
......
src/text.cpp
......@@ -215,19 +215,19 @@ std::string trim_copy(std::string_view s)
// --------------------------------------------------------------------
std::tuple<std::string, std::string> split_tag_name(std::string_view tag)
std::tuple<std::string, std::string> split_item_name(std::string_view item_name)
{
if (tag.empty())
throw std::runtime_error("empty tag");
if (tag[0] != '_')
throw std::runtime_error("tag '" + std::string { tag } + "' does not start with underscore");
if (item_name.empty())
throw std::runtime_error("empty item_name");
if (item_name[0] != '_')
throw std::runtime_error("item_name '" + std::string { item_name } + "' does not start with underscore");
auto s = tag.find('.');
auto s = item_name.find('.');
if (s == std::string::npos)
// throw std::runtime_error("tag does not contain dot (" + std::string{ tag } + ')');
return std::tuple<std::string, std::string>{ "", tag.substr(1) };
// throw std::runtime_error("item_name does not contain dot (" + std::string{ item_name } + ')');
return std::tuple<std::string, std::string>{ "", item_name.substr(1) };
else
return std::tuple<std::string, std::string>{tag.substr(1, s - 1), tag.substr(s + 1)};
return std::tuple<std::string, std::string>{item_name.substr(1, s - 1), item_name.substr(s + 1)};
}
// --------------------------------------------------------------------
......
src/validate.cpp
......@@ -39,10 +39,10 @@
// the code will use boost::regex instead.
#if USE_BOOST_REGEX
#include <boost/regex.hpp>
# include <boost/regex.hpp>
using boost::regex;
#else
#include <regex>
# include <regex>
using std::regex;
#endif
......@@ -57,20 +57,11 @@ struct regex_impl : public regex
}
};
validation_error::validation_error(const std::string &msg)
: m_msg(msg)
{
}
validation_error::validation_error(const std::string &cat, const std::string &item, const std::string &msg)
: m_msg("When validating _" + cat + '.' + item + ": " + msg)
{
}
// --------------------------------------------------------------------
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
{
ec = {};
DDL_PrimitiveType result;
if (iequals(s, "char"))
result = DDL_PrimitiveType::Char;
......@@ -79,7 +70,16 @@ DDL_PrimitiveType map_to_primitive_type(std::string_view s)
else if (iequals(s, "numb"))
result = DDL_PrimitiveType::Numb;
else
throw validation_error("Not a known primitive type");
ec = make_error_code(validation_error::not_a_known_primitive_type);
return result;
}
DDL_PrimitiveType map_to_primitive_type(std::string_view s)
{
std::error_code ec;
auto result = map_to_primitive_type(s, ec);
if (ec)
throw std::system_error(ec, std::string{ s });
return result;
}
......@@ -196,39 +196,26 @@ int type_validator::compare(std::string_view a, std::string_view b) const
// --------------------------------------------------------------------
// void ValidateItem::addLinked(ValidateItem* parent, const std::string& parentItem, const std::string& childItem)
//{
//// if (mParent != nullptr and VERBOSE)
//// cerr << "replacing parent in " << mCategory->m_name << " from " << mParent->mCategory->m_name << " to " << parent->mCategory->m_name << endl;
//// mParent = parent;
//
// if (m_type == nullptr and parent != nullptr)
// m_type = parent->m_type;
//
// if (parent != nullptr)
// {
// mLinked.push_back({parent, parentItem, childItem});
//
// parent->mChildren.insert(this);
////
//// if (mCategory->mKeys == std::vector<std::string>{mTag})
//// parent->mForeignKeys.insert(this);
// }
//}
void item_validator::operator()(std::string_view value) const
{
std::error_code ec;
if (not validate_value(value, ec))
throw std::system_error(ec, std::string{ value } + " does not match rx for " + m_item_name);
}
bool item_validator::validate_value(std::string_view value, std::error_code &ec) const noexcept
{
ec = {};
if (not value.empty() and value != "?" and value != ".")
{
if (m_type != nullptr and not regex_match(value.begin(), value.end(), *m_type->m_rx))
throw validation_error(m_category->m_name, m_tag, "Value '" + std::string{ value } + "' does not match type expression for type " + m_type->m_name);
if (not m_enums.empty())
{
if (m_enums.count(std::string{ value }) == 0)
throw validation_error(m_category->m_name, m_tag, "Value '" + std::string{ value } + "' is not in the list of allowed values");
}
ec = make_error_code(validation_error::value_does_not_match_rx);
else if (not m_enums.empty() and m_enums.count(std::string{ value }) == 0)
ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
}
return ec == std::errc();
}
// --------------------------------------------------------------------
......@@ -236,27 +223,27 @@ void item_validator::operator()(std::string_view value) const
void category_validator::add_item_validator(item_validator &&v)
{
if (v.m_mandatory)
m_mandatory_fields.insert(v.m_tag);
m_mandatory_items.insert(v.m_item_name);
v.m_category = this;
auto r = m_item_validators.insert(std::move(v));
if (not r.second and VERBOSE >= 4)
std::cout << "Could not add validator for item " << v.m_tag << " to category " << m_name << '\n';
std::cout << "Could not add validator for item " << v.m_item_name << " to category " << m_name << '\n';
}
const item_validator *category_validator::get_validator_for_item(std::string_view tag) const
const item_validator *category_validator::get_validator_for_item(std::string_view item_name) const
{
const item_validator *result = nullptr;
auto i = m_item_validators.find(item_validator{ std::string(tag) });
auto i = m_item_validators.find(item_validator{ std::string(item_name) });
if (i != m_item_validators.end())
result = &*i;
else if (VERBOSE > 4)
std::cout << "No validator for tag " << tag << '\n';
std::cout << "No validator for item " << item_name << '\n';
return result;
}
const item_validator *category_validator::get_validator_for_aliased_item(std::string_view tag) const
const item_validator *category_validator::get_validator_for_aliased_item(std::string_view item_name) const
{
const item_validator *result = nullptr;
......@@ -264,8 +251,8 @@ const item_validator *category_validator::get_validator_for_aliased_item(std::st
{
for (auto &ai : iv.m_aliases)
{
const auto &[cat, name] = split_tag_name(ai.m_name);
if (name == tag and cat == m_name)
const auto &[cat, name] = split_item_name(ai.m_name);
if (iequals(name, item_name) and iequals(cat, m_name))
{
result = &iv;
break;
......@@ -317,19 +304,19 @@ const category_validator *validator::get_validator_for_category(std::string_view
return result;
}
item_validator *validator::get_validator_for_item(std::string_view tag) const
item_validator *validator::get_validator_for_item(std::string_view item_name) const
{
item_validator *result = nullptr;
std::string cat, item;
std::tie(cat, item) = split_tag_name(tag);
std::tie(cat, item) = split_item_name(item_name);
auto *cv = get_validator_for_category(cat);
if (cv != nullptr)
result = const_cast<item_validator *>(cv->get_validator_for_item(item));
if (result == nullptr and VERBOSE > 4)
std::cout << "No validator for item " << tag << '\n';
std::cout << "No validator for item " << item_name << '\n';
return result;
}
......@@ -354,11 +341,11 @@ void validator::add_link_validator(link_validator &&v)
auto piv = pcv->get_validator_for_item(v.m_parent_keys[i]);
if (piv == nullptr)
throw std::runtime_error("unknown parent tag _" + v.m_parent_category + '.' + v.m_parent_keys[i]);
throw std::runtime_error("unknown parent item _" + v.m_parent_category + '.' + v.m_parent_keys[i]);
auto civ = ccv->get_validator_for_item(v.m_child_keys[i]);
if (civ == nullptr)
throw std::runtime_error("unknown child tag _" + v.m_child_category + '.' + v.m_child_keys[i]);
throw std::runtime_error("unknown child item _" + v.m_child_category + '.' + v.m_child_keys[i]);
if (civ->m_type == nullptr and piv->m_type != nullptr)
const_cast<item_validator *>(civ)->m_type = piv->m_type;
......@@ -373,7 +360,7 @@ std::vector<const link_validator *> validator::get_links_for_parent(std::string_
for (auto &l : m_link_validators)
{
if (l.m_parent_category == category)
if (iequals(l.m_parent_category, category))
result.push_back(&l);
}
......@@ -386,19 +373,41 @@ std::vector<const link_validator *> validator::get_links_for_child(std::string_v
for (auto &l : m_link_validators)
{
if (l.m_child_category == category)
if (iequals(l.m_child_category, category))
result.push_back(&l);
}
return result;
}
void validator::report_error(const std::string &msg, bool fatal) const
// void validator::report_error(const std::string &msg, bool fatal) const
// {
// if (m_strict or fatal)
// throw validation_error(msg);
// else if (VERBOSE > 0)
// std::cerr << msg << '\n';
// }
void validator::report_error(std::error_code ec, bool fatal) const
{
if (m_strict or fatal)
throw validation_error(msg);
else if (VERBOSE > 0)
std::cerr << msg << '\n';
throw std::system_error(ec);
else
std::cerr << ec.message() << '\n';
}
void validator::report_error(std::error_code ec, std::string_view category,
std::string_view item, bool fatal) const
{
std::ostringstream os;
os << "category: "<< category;
if (not item.empty())
os << "; item: " << item;
if (m_strict or fatal)
throw std::system_error(ec, os.str());
else
std::cerr << ec.message() << ": " << os.str() << '\n';
}
// --------------------------------------------------------------------
......@@ -460,12 +469,12 @@ const validator &validator_factory::operator[](std::string_view dictionary_name)
if (not std::filesystem::exists(p, ec) or ec)
{
for (const char *dir : {
#if defined(CACHE_DIR)
# if defined(CACHE_DIR)
CACHE_DIR,
#endif
#if defined(DATA_DIR)
# endif
# if defined(DATA_DIR)
DATA_DIR
#endif
# endif
})
{
auto p2 = std::filesystem::path(dir) / p;
......
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