address/port

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@472 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Cif++.h

@@ -101,6 +101,7 @@ class Validator;
 
 struct ValidateItem;
 struct ValidateCategory;
+struct ValidateLink;
 
 struct ItemColumn;
 struct ItemRow;
@@ -207,6 +208,8 @@ class Datablock
 	std::tuple<iterator,bool> emplace(const std::string& name);
 	
 	bool isValid();
+	void validateLinks() const;
+
 	void setValidator(Validator* v);
 
 	// this one only looks up a Category, returns nullptr if it does not exist
@@ -1105,7 +1108,7 @@ class Category
 		bool operator!=(const const_iterator& rhs) const	{ return not (mCurrent == rhs.mCurrent); } 
 		
 	  private:
-		const Row mCurrent;
+		Row mCurrent;
 	};
 
 	const_iterator begin() const;
@@ -1121,7 +1124,7 @@ class Category
 	
 	Row operator[](Condition&& cond);
 	RowSet find(Condition&& cond);
-	bool exists(Condition&& cond);
+	bool exists(Condition&& cond) const;
 	
 	RowSet orderBy(const string& Item)
 		{ return orderBy({ Item }); }
@@ -1147,8 +1150,10 @@ class Category
 	/// an orphan is a row that is the child side of one or more
 	/// links and for which there is no single parent left.
 	bool isOrphan(Row r);
+	bool hasParent(Row r, const Category& parentCat, const ValidateLink& link) const;
 
 	bool isValid();
+	void validateLinks() const;
 
 	const Validator& getValidator() const;
 	const ValidateCategory* getCatValidator() const		{ return mCatValidator; }
@@ -1225,6 +1230,7 @@ class File
 	void loadDictionary(std::istream& is);		// load dictionary from input stream
 
 	bool isValid();
+	void validateLinks() const;
 	
 	Datablock& firstDatablock()			{ return *mHead; }
 	void append(Datablock* e);

include/cif++/CifValidator.h

@@ -118,6 +118,7 @@ struct ValidateLink
 	std::vector<std::string>	mParentKeys;
 	std::string					mChildCategory;
 	std::vector<std::string>	mChildKeys;
+	std::string					mLinkGroupLabel;
 };
 
 // --------------------------------------------------------------------

src/Cif++.cpp

@@ -361,6 +361,12 @@ bool Datablock::isValid()
 	return result;
 }
 
+void Datablock::validateLinks() const
+{
+	for (auto& cat: *this)
+		cat.validateLinks();
+}
+
 void Datablock::setValidator(Validator* v)
 {
 	mValidator = v;
@@ -1333,7 +1339,7 @@ RowSet Category::find(Condition&& cond)
 	return result;
 }
 
-bool Category::exists(Condition&& cond)
+bool Category::exists(Condition&& cond) const
 {
 	bool result = false;
 
@@ -1597,6 +1603,21 @@ Category::const_iterator Category::end() const
 	return const_iterator(nullptr);
 }
 
+bool Category::hasParent(Row r, const Category& parentCat, const ValidateLink& link) const
+{
+	Condition cond;
+	for (size_t ix = 0; ix < link.mChildKeys.size(); ++ix)
+	{
+		const char* value = r[link.mChildKeys[ix]].c_str();
+		cond = move(cond) && (Key(link.mParentKeys[ix]) == value);
+	}
+
+	if (VERBOSE > 2)
+		cerr << "Check condition '" << cond << "' in parent category " << link.mParentCategory << " for child cat " << mName << endl;
+
+	return parentCat.exists(std::move(cond));
+}
+
 bool Category::isOrphan(Row r)
 {
 	// be safe
@@ -1728,6 +1749,29 @@ bool Category::isValid()
 	return result;
 }
 
+void Category::validateLinks() const
+{
+	auto& validator = getValidator();
+
+	for (auto linkValidator: validator.getLinksForChild(mName))
+	{
+		auto parent = mDb.get(linkValidator->mParentCategory);
+		if (parent == nullptr)
+			continue;
+
+		size_t missing = 0;
+		for (auto r: *this)
+			if (not hasParent(r, *parent, *linkValidator))
+				++missing;
+		
+		if (missing)
+		{
+			cerr << "Links for " << linkValidator->mLinkGroupLabel << " are incomplete" << endl
+				 << "  There are " << missing << " items in " << mName << " that don't have matching parent items in " << parent->mName << endl;
+		}
+	}
+}
+
 const Validator& Category::getValidator() const
 {
 	if (mValidator == nullptr)
@@ -1792,6 +1836,12 @@ auto Category::iterator::operator++() -> iterator&
 	return *this;
 }
 
+auto Category::const_iterator::operator++() -> const_iterator&
+{
+	mCurrent = Row(mCurrent.data()->mNext);
+	return *this;
+}
+
 namespace detail
 {
 
@@ -2592,6 +2642,12 @@ bool File::isValid()
 	return result;
 }
 
+void File::validateLinks() const
+{
+	for (auto d = mHead; d != nullptr; d = d->mNext)
+		d->validateLinks();
+}
+
 const Validator& File::getValidator() const
 {
 	if (mValidator == nullptr)

src/CifParser.cpp

@@ -915,6 +915,8 @@ void DictParser::linkItems()
 //		keys.insert(civ->mTag);
 //	}
 	
+	auto& linkedGroup = dict["pdbx_item_linked_group"];
+
 	// now store the links in the validator
 	for (auto& kv: linkIndex)
 	{
@@ -922,7 +924,14 @@ void DictParser::linkItems()
 		std::tie(link.mParentCategory, link.mChildCategory, link.mLinkGroupId) = kv.first;
 		
 		std::tie(link.mParentKeys, link.mChildKeys) = linkKeys[kv.second];
-		
+
+		// look up the label
+		for (auto r:  linkedGroup.find(cif::Key("category_id") == link.mChildCategory and cif::Key("link_group_id") == link.mLinkGroupId))
+		{
+			link.mLinkGroupLabel = r["label"].as<string>();
+			break;
+		}
+
 		mValidator.addLinkValidator(move(link));
 	}