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

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

Inheritance diagram for SemanticValidator:

Collaboration diagram for SemanticValidator:

Classes
struct	CVTerm
	Representation of a parsed CV term. More...

Public Member Functions
	SemanticValidator (const CVMappings &mapping, const ControlledVocabulary &cv)
	Constructor. More...

	~SemanticValidator () override
	Destructor. More...

bool	validate (const String &filename, StringList &errors, StringList &warnings)
	Semantically validates an XML file. More...

bool	locateTerm (const String &path, const CVTerm &parsed_term) const
	Checks if a CVTerm is allowed in a given path. More...

void	setTag (const String &tag)
	Sets the CV parameter tag name (default: 'cvParam') More...

void	setAccessionAttribute (const String &accession)
	Sets the name of the attribute for accessions in the CV parameter tag name (default: 'accession') More...

void	setNameAttribute (const String &name)
	Sets the name of the attribute for accessions in the CV parameter tag name (default: 'name') More...

void	setValueAttribute (const String &value)
	Sets the name of the attribute for accessions in the CV parameter tag name (default: 'value') More...

void	setCheckTermValueTypes (bool check)
	Set if CV term value types should be check (enabled by default) More...

void	setCheckUnits (bool check)
	Set if CV term units should be check (disabled by default) More...

void	setUnitAccessionAttribute (const String &accession)
	Sets the name of the unit accession attribute (default: 'unitAccession') More...

void	setUnitNameAttribute (const String &name)
	Sets the name of the unit name attribute (default: 'unitName') More...

Public Member Functions inherited from XMLFile
	XMLFile ()
	Default constructor. More...

	XMLFile (const String &schema_location, const String &version)
	Constructor that sets the schema location. More...

virtual	~XMLFile ()
	Destructor. More...

bool	isValid (const String &filename, std::ostream &os)
	Checks if a file validates against the XML schema. More...

const String &	getVersion () const
	return the version of the schema More...

Protected Member Functions
void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes) override

void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname) override

void	characters (const XMLCh *const chars, const XMLSize_t) override

virtual String	getPath_ (UInt remove_from_end=0) const
	Returns the current element path. More...

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. More...

virtual void	handleTerm_ (const String &path, const CVTerm &parsed_term)
	Handling of the term. More...

Protected Member Functions inherited from XMLHandler
void	writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file. More...

Int	asInt_ (const String &in) const
	Conversion of a String to an integer value. More...

Int	asInt_ (const XMLCh *in) const
	Conversion of a Xerces string to an integer value. More...

UInt	asUInt_ (const String &in) const
	Conversion of a String to an unsigned integer value. More...

double	asDouble_ (const String &in) const
	Conversion of a String to a double value. More...

float	asFloat_ (const String &in) const
	Conversion of a String to a float value. More...

bool	asBool_ (const String &in) const
	Conversion of a string to a boolean value. More...

DateTime	asDateTime_ (String date_string) const
	Conversion of a xs:datetime string to a DateTime value. More...

bool	equal_ (const XMLCh a, const XMLCh b) const
	Returns if two Xerces strings are equal. More...

SignedSize	cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)

String	attributeAsString_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a String. More...

Int	attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a Int. More...

double	attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a double. More...

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a DoubleList. More...

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an IntList. More...

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an StringList. More...

bool	optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present. More...

bool	optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the Int value if the attribute is present. More...

bool	optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the UInt value if the attribute is present. More...

bool	optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the double value if the attribute is present. More...

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present. More...

bool	optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the StringList value if the attribute is present. More...

bool	optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the IntList value if the attribute is present. More...

String	attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a String. More...

Int	attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a Int. More...

double	attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a double. More...

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a DoubleList. More...

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a IntList. More...

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a StringList. More...

bool	optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the String value if the attribute is present. More...

bool	optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the Int value if the attribute is present. More...

bool	optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the UInt value if the attribute is present. More...

bool	optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the double value if the attribute is present. More...

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present. More...

bool	optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the IntList value if the attribute is present. More...

bool	optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the StringList value if the attribute is present. More...

	XMLHandler (const String &filename, const String &version)
	Default constructor. More...

	~XMLHandler () override
	Destructor. More...

void	reset ()
	Release internal memory used for parsing (call. More...

void	fatalError (const xercesc::SAXParseException &exception) override

void	error (const xercesc::SAXParseException &exception) override

void	warning (const xercesc::SAXParseException &exception) override

void	fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception. More...

void	error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors. More...

void	warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Warning handler. More...

void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Parsing method for character data. More...

void	startElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
	Parsing method for opening tags. More...

void	endElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname) override
	Parsing method for closing tags. More...

virtual void	writeTo (std::ostream &)
	Writes the contents to a stream. More...

virtual LOADDETAIL	getLoadDetail () const
	handler which support partial loading, implement this method More...

virtual void	setLoadDetail (const LOADDETAIL d)
	handler which support partial loading, implement this method More...

DataValue	cvParamToValue (const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...

DataValue	cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...

void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const

Protected Member Functions inherited from XMLFile
void	parse_ (const String &filename, XMLHandler *handler)
	Parses the XML file given by `filename` using the handler given by `handler`. More...

void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parses the in-memory buffer given by `buffer` using the handler given by `handler`. More...

void	save_ (const String &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by `handler` in the file given by `filename`. More...

void	enforceEncoding_ (const String &encoding)

	XMLFile ()
	Default constructor. More...

	XMLFile (const String &schema_location, const String &version)
	Constructor that sets the schema location. More...

virtual	~XMLFile ()
	Destructor. More...

bool	isValid (const String &filename, std::ostream &os)
	Checks if a file validates against the XML schema. More...

const String &	getVersion () const
	return the version of the schema More...

Protected Attributes
const CVMappings &	mapping_
	Reference to the mappings. More...

const ControlledVocabulary &	cv_
	Reference to the CVs. More...

StringList	errors_
	Validation errors. More...

StringList	warnings_
	Validation warnings. More...

StringList	open_tags_
	List of open tags. More...

std::map< String, std::vector< CVMappingRule > >	rules_
	Rules (location => rule) More...

std::map< String, std::map< String, std::map< String, UInt > > >	fulfilled_

Protected Attributes inherited from XMLHandler
String	file_
	File name. More...

String	version_
	Schema version. More...

StringManager	sm_
	Helper class for string conversion. More...

std::vector< String >	open_tags_
	Stack of open XML tags. More...

LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes More...

std::vector< std::vector< String > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children) More...

Protected Attributes inherited from XMLFile
String	schema_location_
	XML schema file location. More...

String	schema_version_
	Version string. More...

String	enforced_encoding_
	Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...

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_

	SemanticValidator ()
	Not implemented. More...

	SemanticValidator (const SemanticValidator &rhs)
	Not implemented. More...

SemanticValidator &	operator= (const SemanticValidator &rhs)
	Not implemented. More...

Additional Inherited Members
Protected Types inherited from XMLHandler
enum	ActionMode { LOAD , STORE }
	Action to set the current mode (for error messages) More...

enum	LOADDETAIL { LD_ALLDATA , LD_RAWCOUNTS , LD_COUNTS_WITHOPTIONS }

Static Protected Member Functions inherited from XMLHandler
static String	writeXMLEscape (const String &to_escape)
	Escapes a string and returns the escaped string. More...

static DataValue	fromXSDString (const String &type, const String &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue. More...

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.

Class Documentation

◆ OpenMS::Internal::SemanticValidator::CVTerm

struct OpenMS::Internal::SemanticValidator::CVTerm

Representation of a parsed CV term.

Collaboration diagram for SemanticValidator::CVTerm:

[legend]

Class Members
String	accession
bool	has_unit_accession
bool	has_unit_name
bool	has_value
String	name
String	unit_accession
String	unit_name
String	value

Constructor & Destructor Documentation

◆ SemanticValidator() [1/3]

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

Constructor.

Parameters

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

◆ ~SemanticValidator()

~SemanticValidator ( )

override

Destructor.

◆ SemanticValidator() [2/3]

SemanticValidator ( )

private

Not implemented.

◆ SemanticValidator() [3/3]

SemanticValidator ( const SemanticValidator & rhs )

private

Not implemented.

Member Function Documentation

◆ characters()

void characters	(	const XMLCh *const	chars,
		const	XMLSize_t
	)

overrideprotected

◆ endElement()

void endElement	(	const XMLCh * const	,
		const XMLCh * const	,
		const XMLCh *const	qname
	)

overrideprotected

◆ getCVTerm_()

virtual void getCVTerm_	(	const xercesc::Attributes &	attributes,
		CVTerm &	parsed_term
	)

protectedvirtual

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

◆ getPath_()

virtual String getPath_ ( UInt remove_from_end = 0 ) const

protectedvirtual

Returns the current element path.

Reimplemented in MzMLValidator.

◆ handleTerm_()

virtual void handleTerm_	(	const String &	path,
		const CVTerm &	parsed_term
	)

protectedvirtual

Handling of the term.

Reimplemented in MzMLValidator, and MzDataValidator.

◆ locateTerm()

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

Checks if a CVTerm is allowed in a given path.

◆ operator=()

SemanticValidator& operator= ( const SemanticValidator & rhs )

private

Not implemented.

◆ setAccessionAttribute()

void setAccessionAttribute ( const String & accession )

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

◆ setCheckTermValueTypes()

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

◆ setCheckUnits()

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

◆ setNameAttribute()

void setNameAttribute ( const String & name )

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

◆ setTag()

void setTag ( const String & tag )

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

◆ setUnitAccessionAttribute()

void setUnitAccessionAttribute ( const String & accession )

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

◆ setUnitNameAttribute()

void setUnitNameAttribute ( const String & name )

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

◆ setValueAttribute()

void setValueAttribute ( const String & value )

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

◆ startElement()

void startElement	(	const XMLCh * const	,
		const XMLCh * const	,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attributes
	)

overrideprotected

◆ validate()

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 successful, false otherwise.

Exceptions

Exception::FileNotFound is thrown if the file could not be opened

Member Data Documentation

◆ accession_att_

String accession_att_

protected

◆ check_term_value_types_

bool check_term_value_types_

protected

◆ check_units_

bool check_units_

protected

◆ cv_

const ControlledVocabulary& cv_

protected

Reference to the CVs.

◆ cv_tag_

String cv_tag_

protected

◆ errors_

StringList errors_

protected

Validation errors.

◆ fulfilled_

std::map<String, std::map<String, std::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.

◆ mapping_

const CVMappings& mapping_

protected

Reference to the mappings.

◆ name_att_

String name_att_

protected

◆ open_tags_

StringList open_tags_

protected

List of open tags.

◆ rules_

std::map<String, std::vector<CVMappingRule> > rules_

protected

Rules (location => rule)

◆ unit_accession_att_

String unit_accession_att_

protected

◆ unit_name_att_

String unit_name_att_

protected

◆ value_att_

String value_att_

protected

◆ warnings_

StringList warnings_

protected

Validation warnings.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Tag and attribute names

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::Internal::SemanticValidator::CVTerm

Constructor & Destructor Documentation

◆ SemanticValidator() [1/3]

◆ ~SemanticValidator()

◆ SemanticValidator() [2/3]

◆ SemanticValidator() [3/3]

Member Function Documentation

◆ characters()

◆ endElement()

◆ getCVTerm_()

◆ getPath_()

◆ handleTerm_()

◆ locateTerm()

◆ operator=()

◆ setAccessionAttribute()

◆ setCheckTermValueTypes()

◆ setCheckUnits()

◆ setNameAttribute()

◆ setTag()

◆ setUnitAccessionAttribute()

◆ setUnitNameAttribute()

◆ setValueAttribute()

◆ startElement()

◆ validate()

Member Data Documentation

◆ accession_att_

◆ check_term_value_types_

◆ check_units_

◆ cv_

◆ cv_tag_

◆ errors_

◆ fulfilled_

◆ mapping_

◆ name_att_

◆ open_tags_

◆ rules_

◆ unit_accession_att_

◆ unit_name_att_

◆ value_att_

◆ warnings_