Semantically validates XML files using CVMappings and a ControlledVocabulary. More...

#include <OpenMS/FORMAT/VALIDATORS/SemanticValidator.h>

Inheritance diagram for SemanticValidator:

Classes
struct	CVTerm
	Representation of a parsed CV term. More...
Public Member Functions
	SemanticValidator (const CVMappings &mapping, const ControlledVocabulary &cv)
	Constructor.
virtual	~SemanticValidator ()
	Destructor.
bool	validate (const String &filename, StringList &errors, StringList &warnings)
	Semantically validates an XML file.
bool	locateTerm (const String &path, const CVTerm &parsed_term) const
	Checks if a CVTerm is allowed in a given path.
void	setTag (const String &tag)
	Sets the CV parameter tag name (default: 'cvParam').
void	setAccessionAttribute (const String &accession)
	Sets the name of the attribute for accessions in the CV parameter tag name (default: 'accession').
void	setNameAttribute (const String &name)
	Sets the name of the attribute for accessions in the CV parameter tag name (default: 'name').
void	setValueAttribute (const String &value)
	Sets the name of the attribute for accessions in the CV parameter tag name (default: 'value').
void	setCheckTermValueTypes (bool check)
	Set if CV term value types should be check (enabled by default).
void	setCheckUnits (bool check)
	Set if CV term units should be check (disabled by default).
void	setUnitAccessionAttribute (const String &accession)
	Sets the name of the unit accession attribute (default: 'unitAccession').
void	setUnitNameAttribute (const String &name)
	Sets the name of the unit name attribute (default: 'unitName').
Protected Member Functions
void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
void	characters (const XMLCh *const chars, const XMLSize_t)
virtual String	getPath_ (UInt remove_from_end=0) const
	Returns the current element path.
virtual void	getCVTerm_ (const xercesc::Attributes &attributes, CVTerm &parsed_term)
	Parses the CV term accession (required), name (required) and value (optional) from the XML attributes.
virtual void	handleTerm_ (const String &path, const CVTerm &parsed_term)
	Handling of the term.
Protected Attributes
const CVMappings &	mapping_
	Reference to the mappings.
const ControlledVocabulary &	cv_
	Reference to the CVs.
StringList	errors_
	Validation erros.
StringList	warnings_
	Validation warnings.
StringList	open_tags_
	List of open tags.
Map< String, std::vector < CVMappingRule > >	rules_
	Rules (location => rule).
Map< String, Map< String, Map < String, UInt > > >	fulfilled_
Tag and attribute names

String	cv_tag_
String	accession_att_
String	name_att_
String	value_att_
String	unit_accession_att_
String	unit_name_att_
bool	check_term_value_types_
bool	check_units_
Private Member Functions
	SemanticValidator ()
	Not implemented.
	SemanticValidator (const SemanticValidator &rhs)
	Not implemented.
SemanticValidator &	operator= (const SemanticValidator &rhs)
	Not implemented.

Detailed Description

Semantically validates XML files using CVMappings and a ControlledVocabulary.

This is the general validator.
Specialized validators for specific file formats are derived from this class.

Constructor & Destructor Documentation

SemanticValidator	(	const CVMappings &	mapping,
		const ControlledVocabulary &	cv
	)

Constructor.

Parameters:

	mapping	The mapping rules
	cv	All controlled vocabularies required for the mapping

virtual ~SemanticValidator ( ) [virtual]

Destructor.

SemanticValidator ( ) [private]

Not implemented.

SemanticValidator ( const SemanticValidator & rhs ) [private]

Not implemented.

Member Function Documentation

void characters	(	const XMLCh *const	chars,
		const	XMLSize_t
	)			`[protected]`

void endElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname
	)			`[protected]`

virtual void getCVTerm_	(	const xercesc::Attributes &	attributes,
		CVTerm &	parsed_term
	)			`[protected, virtual]`

Parses the CV term accession (required), name (required) and value (optional) from the XML attributes.

virtual String getPath_ ( UInt remove_from_end = 0 ) const [protected, virtual]

Returns the current element path.

Reimplemented in MzMLValidator.

virtual void handleTerm_	(	const String &	path,
		const CVTerm &	parsed_term
	)			`[protected, virtual]`

Handling of the term.

Reimplemented in MzDataValidator, and MzMLValidator.

bool locateTerm	(	const String &	path,
		const CVTerm &	parsed_term
	)			const

Checks if a CVTerm is allowed in a given path.

SemanticValidator& operator= ( const SemanticValidator & rhs ) [private]

Not implemented.

void setAccessionAttribute ( const String & accession )

Sets the name of the attribute for accessions in the CV parameter tag name (default: 'accession').

void setCheckTermValueTypes ( bool check )

Set if CV term value types should be check (enabled by default).

If set to true, the xsd value types are checked, and errors are given in the cases

CVTerm needs value but has none
CVTerm has value but must not have one
CVTerm has value, needs value but value is of wrong type

void setCheckUnits ( bool check )

Set if CV term units should be check (disabled by default).

If set to true additional checks for CVTerms are performed:

CVTerm that must have a unit, but has none
CVTerm that has a wrong unit

void setNameAttribute ( const String & name )

Sets the name of the attribute for accessions in the CV parameter tag name (default: 'name').

void setTag ( const String & tag )

Sets the CV parameter tag name (default: 'cvParam').

void setUnitAccessionAttribute ( const String & accession )

Sets the name of the unit accession attribute (default: 'unitAccession').

void setUnitNameAttribute ( const String & name )

Sets the name of the unit name attribute (default: 'unitName').

void setValueAttribute ( const String & value )

Sets the name of the attribute for accessions in the CV parameter tag name (default: 'value').

void startElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attributes
	)			`[protected]`

Reimplemented in MzMLValidator.

bool validate	(	const String &	filename,
		StringList &	errors,
		StringList &	warnings
	)

Semantically validates an XML file.

Parameters:

	filename	The file to validate
	errors	Errors during the validation are returned in this output parameter.
	warnings	Warnings during the validation are returned in this output parameter.

Returns:: true if the validation was successfull, false otherwise.

Exceptions:

Exception::FileNotFound

is thrown if the file could not be opened

Member Data Documentation

String accession_att_ [protected]

bool check_term_value_types_ [protected]

bool check_units_ [protected]

const ControlledVocabulary& cv_ [protected]

Reference to the CVs.

String cv_tag_ [protected]

StringList errors_ [protected]

Validation erros.

Map<String, Map<String, Map<String, UInt> > > fulfilled_ [protected]

Fulfilled rules (location => rule ID => term ID => term count ) When a tag is closed, the fulfilled rules of the current location are checked against the required rules The fulfilled rules for that location are then deleted.

const CVMappings& mapping_ [protected]

Reference to the mappings.

String name_att_ [protected]

StringList open_tags_ [protected]

List of open tags.

Map<String, std::vector<CVMappingRule> > rules_ [protected]

Rules (location => rule).

String unit_accession_att_ [protected]

String unit_name_att_ [protected]

String value_att_ [protected]

StringList warnings_ [protected]

Validation warnings.