Update validation code, added pdbx_item_enumeration check and test case-sensitive when required.

include/cif++/validate.hpp

@@ -196,7 +196,7 @@ class validation_exception : public std::runtime_error
   public:
 	// Constructors
 	/// @cond
-	
+
 	validation_exception(validation_error err)
 		: validation_exception(make_error_code(err))
 	{
@@ -337,7 +337,7 @@ struct item_validator
 	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
+	std::set<std::string> m_enums;     ///< If filled, the set of allowed values
 	std::string m_default;             ///< If filled, a default value for this item
 	std::string m_category;            ///< The category this item_validator belongs to
 	std::vector<item_alias> m_aliases; ///< The aliases for this item
@@ -502,15 +502,29 @@ class validator
 	/// @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 value, std::string_view category,
+		std::string_view item, bool fatal = true) const
+	{
+		report_error(make_error_code(err), value, category, item, fatal);
+	}
+
 	/// @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);
+		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
+	{
+		report_error(ec, "", category, item, fatal);
+	}
+
+	/// @brief Bottleneck function to report an error in validation
+	void report_error(std::error_code ec, std::string value, std::string_view category,
 		std::string_view item, bool fatal = true) const;
 
 	/// @brief Write out the audit_conform data for this validator

src/category.cpp

@@ -749,16 +749,38 @@ void category::set_validator(const validator *v, datablock &db)
 
 		bool number = type->m_primitive_type == DDL_PrimitiveType::Numb;
 		if (number)
-			continue;
-
-		for (auto row = m_head; row != nullptr; row = row->m_next)
 		{
-			if (cix >= row->size() or row->operator[](cix).empty())
-				continue;
+			for (auto row = m_head; row != nullptr; row = row->m_next)
+			{
+				if (cix >= row->size() or row->operator[](cix).empty())
+					continue;
 
-			item_value &v = row->operator[](cix);
-			if (v.is_number())
-				v = v.str();
+				item_value &v = row->operator[](cix);
+				if (not v.is_number())
+				{
+					// Try cast the value to a number and throw in case of failure
+					try
+					{
+						v.cast_to_int();
+					}
+					catch (...)
+					{
+						v.cast_to_float();
+					}
+				}
+			}
+		}
+		else
+		{
+			for (auto row = m_head; row != nullptr; row = row->m_next)
+			{
+				if (cix >= row->size() or row->operator[](cix).empty())
+					continue;
+
+				item_value &v = row->operator[](cix);
+				if (v.is_number())
+					v = v.str();
+			}
 		}
 	}
 
@@ -890,11 +912,13 @@ bool category::is_valid() const
 				seen = true;
 				std::error_code ec;
 
-				iv->validate_value(*ri->get(cix), ec);
+				auto &v = *ri->get(cix);
+
+				iv->validate_value(v, ec);
 
 				if (ec != std::errc{})
 				{
-					m_validator->report_error(ec, m_name, m_items[cix].m_name, false);
+					m_validator->report_error(ec, v.str(), m_name, m_items[cix].m_name, false);
 					continue;
 				}
 			}

src/dictionary_parser.cpp

@@ -25,6 +25,8 @@
  */
 
 #include "cif++/cif++.hpp"
+#include "cif++/text.hpp"
+#include "cif++/validate.hpp"
 
 #include <cstddef>
 #include <exception>
@@ -103,7 +105,19 @@ class dictionary_parser : public parser
 				error("Undefined category '" + iv.first);
 
 			for (auto &v : iv.second)
+			{
+				// enums, make lower case if needed
+				auto tv = v.m_type;
+				if (tv and tv->m_primitive_type == DDL_PrimitiveType::UChar)
+				{
+					std::set<std::string> es;
+					for (auto &e : v.m_enums)
+						es.emplace(cif::to_lower_copy(e));
+					std::swap(es, v.m_enums);
+				}
+
 				const_cast<category_validator *>(cv)->add_item_validator(std::move(v));
+			}
 		}
 
 		// check all item validators for having a typeValidator
@@ -275,9 +289,11 @@ class dictionary_parser : public parser
 			if (typeCode.has_value())
 				tv = m_validator.get_validator_for_type(*typeCode);
 
-			iset ess;
+			std::set<std::string> ess;
 			for (auto e : dict["item_enumeration"])
 				ess.insert(e["value"].get<std::string>());
+			for (auto e : dict["pdbx_item_enumeration"])
+				ess.insert(e["value"].get<std::string>());
 
 			std::string defaultValue;
 			if (auto &cat = dict["item_default"]; not cat.empty())

src/pdb/pdb2cif.cpp

@@ -2193,7 +2193,7 @@ void PDBFileParser::ParseRemarks()
 							if (std::regex_match(line, m, rx))
 							{
 								models[0] = std::stoi(m[1].str());
-								models[1] = stoi(m[2].str());
+								models[1] = std::stoi(m[2].str());
 							}
 							else
 								headerSeen = cif::contains(line, "RES C SSSEQI");

src/validate.cpp

@@ -27,6 +27,7 @@
 #include "cif++/validate.hpp"
 
 #include "cif++/cif++.hpp"
+#include "cif++/text.hpp"
 
 #include <cassert>
 #include <charconv>
@@ -245,8 +246,17 @@ bool item_validator::validate_value(const item_value &value, std::error_code &ec
 						ec = make_error_code(validation_error::value_does_not_match_rx);
 					}
 
-					if (ec == std::errc{} and not m_enums.empty() and m_enums.count(value.str()) == 0)
-						ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
+					if (ec == std::errc{} and not m_enums.empty())
+					{
+						bool valid =
+							m_type->m_primitive_type == DDL_PrimitiveType::UChar ? //
+								m_enums.contains(cif::to_lower_copy(value.sv()))
+																				 : //
+								m_enums.contains(std::string{ value.sv() });
+
+						if (not valid)
+							ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
+					}
 				}
 			}
 		}
@@ -436,8 +446,8 @@ void validator::report_error(std::error_code ec, bool fatal) const
 		std::cerr << ec.message() << '\n';
 }
 
-void validator::report_error(std::error_code ec, std::string_view category,
-	std::string_view item, bool fatal) const
+void validator::report_error(std::error_code ec, std::string value,
+	std::string_view category, std::string_view item, bool fatal) const
 {
 	if (m_strict or fatal)
 	{
@@ -448,10 +458,19 @@ void validator::report_error(std::error_code ec, std::string_view category,
 	}
 
 	if (VERBOSE > 0)
-		std::cerr << ec.message()
-				  << "; category: " << std::quoted(category)
-				  << " item: " << std::quoted(item)
-				  << '\n';
+	{
+		if (value.empty())
+			std::cerr << ec.message()
+					  << "; category: " << std::quoted(category)
+					  << " item: " << std::quoted(item)
+					  << '\n';
+		else
+			std::cerr << ec.message()
+					  << "; value: " << std::quoted(value)
+					  << "; category: " << std::quoted(category)
+					  << " item: " << std::quoted(item)
+					  << '\n';
+	}
 }
 
 void validator::fill_audit_conform(category &audit_conform) const

test/model-test.cpp

@@ -443,8 +443,6 @@ TEST_CASE("test_alternates_1")
 	const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
 	cif::file file(example.string());
 
-	auto &db = file.front();
-
 	cif::mm::structure s(file);
 
 	for (auto atom : s.atoms())