Added rename_column

Added item_alias
Rename columns in reconstruct

include/cif++/category.hpp

@@ -1041,6 +1041,9 @@ class category
 	 */
 	 */
 	void remove_column(std::string_view column_name);
 	void remove_column(std::string_view column_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 Return whether a column with name @a name exists in this category
 	/// @brief Return whether a column with name @a name exists in this category
 	/// @param name The name of the column
 	/// @param name The name of the column
 	/// @return True if the column exists
 	/// @return True if the column exists

include/cif++/validate.hpp

@@ -146,6 +146,16 @@ struct type_validator
 	int compare(std::string_view a, std::string_view b) const;
 	int compare(std::string_view a, std::string_view b) const;
 };
 };
 
 
+/** @brief Item alias, items can be renamed over time
+ */
+
+struct item_alias
+{
+	std::string m_name; ///< The alias_name
+	std::string m_dict; ///< The dictionary in which it was known
+	std::string m_vers; ///< The version of the dictionary
+};
+
 /**
 /**
  * @brief An item_validator binds a type_validator to an item in
  * @brief An item_validator binds a type_validator to an item in
  * a category along with other information found in the dictionary.
  * a category along with other information found in the dictionary.
@@ -163,6 +173,7 @@ struct item_validator
 	cif::iset m_enums;                        ///< If filled, the set of allowed values
 	cif::iset m_enums;                        ///< If filled, the set of allowed values
 	std::string m_default;                    ///< If filled, a default value for this item
 	std::string m_default;                    ///< If filled, a default value for this item
 	category_validator *m_category = nullptr; ///< The category_validator this item_validator belongs to
 	category_validator *m_category = nullptr; ///< The category_validator this item_validator belongs to
+	std::vector<item_alias> m_aliases;        ///< The aliases for this item
 
 
 	/// @brief Compare based on the name
 	/// @brief Compare based on the name
 	bool operator<(const item_validator &rhs) const
 	bool operator<(const item_validator &rhs) const
@@ -191,7 +202,7 @@ struct category_validator
 {
 {
 	std::string m_name;                         ///< The name of the category
 	std::string m_name;                         ///< The name of the category
 	std::vector<std::string> m_keys;            ///< The list of items that make up the key
 	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_groups;                         ///< The category groups this category belongs to
 	cif::iset m_mandatory_fields;               ///< The mandatory fields for this category
 	cif::iset m_mandatory_fields;               ///< The mandatory fields for this category
 	std::set<item_validator> m_item_validators; ///< The item validators for the items in this category
 	std::set<item_validator> m_item_validators; ///< The item validators for the items in this category
 
 
@@ -206,6 +217,9 @@ struct category_validator
 
 
 	/// @brief Return the item_validator for item @a tag, may return nullptr
 	/// @brief Return the item_validator for item @a tag, may return nullptr
 	const item_validator *get_validator_for_item(std::string_view tag) const;
 	const item_validator *get_validator_for_item(std::string_view tag) 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;
 };
 };
 
 
 /**
 /**

src/category.cpp

@@ -614,6 +614,20 @@ void category::remove_column(std::string_view column_name)
 	}
 	}
 }
 }
 
 
+void category::rename_column(std::string_view from_name, std::string_view to_name)
+{
+	for (size_t ix = 0; ix < m_columns.size(); ++ix)
+	{
+		if (not iequals(from_name, m_columns[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;
+
+		break;
+	}
+}
+
 iset category::get_columns() const
 iset category::get_columns() const
 {
 {
 	iset result;
 	iset result;

src/dictionary_parser.cpp

@@ -224,6 +224,13 @@ class dictionary_parser : public parser
 			// 	}
 			// 	}
 			// }
 			// }
 
 
+			std::vector<item_alias> aliases;
+			for (const auto &[alias_name, dictionary, version] :
+				dict["item_aliases"].rows<std::string,std::string,std::string>("alias_name", "dictionary", "version"))
+			{
+				aliases.emplace_back(alias_name, dictionary, version);
+			}
+
 			// collect the dict from our dataBlock and construct validators
 			// collect the dict from our dataBlock and construct validators
 			for (auto i : dict["item"])
 			for (auto i : dict["item"])
 			{
 			{
@@ -245,7 +252,7 @@ class dictionary_parser : public parser
 
 
 				auto vi = find(ivs.begin(), ivs.end(), item_validator{ item_name });
 				auto vi = find(ivs.begin(), ivs.end(), item_validator{ item_name });
 				if (vi == ivs.end())
 				if (vi == ivs.end())
-					ivs.push_back(item_validator{ item_name, iequals(mandatory, "yes"), tv, ess, defaultValue /*, defaultIsNull*/ });
+					ivs.push_back(item_validator{ item_name, iequals(mandatory, "yes"), tv, ess, defaultValue, nullptr, std::move(aliases) });
 				else
 				else
 				{
 				{
 					// need to update the itemValidator?
 					// need to update the itemValidator?

src/pdb/reconstruct.cpp

@@ -683,9 +683,6 @@ void comparePolySeqSchemes(datablock &db)
 			}
 			}
 		}
 		}
 	}
 	}
-
-	if (ndb_poly_seq_scheme.empty())
-		db.erase(std::remove(db.begin(), db.end(), ndb_poly_seq_scheme), db.end());
 }
 }
 
 
 void reconstruct_pdbx(file &file, std::string_view dictionary)
 void reconstruct_pdbx(file &file, std::string_view dictionary)
@@ -732,6 +729,23 @@ void reconstruct_pdbx(file &file, std::string_view dictionary)
 			auto cv = validator.get_validator_for_category(cat.name());
 			auto cv = validator.get_validator_for_category(cat.name());
 			if (not cv)
 			if (not cv)
 				continue;
 				continue;
+			
+			// Start by renaming columns that may have old names based on alias info
+
+			for (auto tag : cat.get_columns())
+			{
+				auto iv = cv->get_validator_for_item(tag);
+				if (iv)	// know, must be OK then
+					continue;
+				
+				iv = cv->get_validator_for_aliased_item(tag);
+				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);
+			}
 
 
 			for (auto link : validator.get_links_for_child(cat.name()))
 			for (auto link : validator.get_links_for_child(cat.name()))
 			{
 			{

src/validate.cpp

@@ -256,6 +256,28 @@ const item_validator *category_validator::get_validator_for_item(std::string_vie
 	return result;
 	return result;
 }
 }
 
 
+const item_validator *category_validator::get_validator_for_aliased_item(std::string_view tag) const
+{
+	const item_validator *result = nullptr;
+
+	for (auto &iv : m_item_validators)
+	{
+		for (auto &ai : iv.m_aliases)
+		{
+			const auto &[cat, name] = split_tag_name(ai.m_name);
+			if (name == tag and cat == m_name)
+			{
+				result = &iv;
+				break;
+			}
+		}
+		if (result)
+			break;
+	}
+
+	return result;
+}
+
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 
 
 void validator::add_type_validator(type_validator &&v)
 void validator::add_type_validator(type_validator &&v)