Package de.isas.mztab2.validation

Class CvMappingValidator

java.lang.Object

de.isas.mztab2.validation.CvMappingValidator

All Implemented Interfaces:

de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab>

public class CvMappingValidator
extends Object
implements de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab>

Validator implementation that uses a provided xml mapping file with rules for required, recommended and optional CV parameters to assert that an mzTab follows these rules. First, all preValidators are run, then, the cv parameter validation is executed, before finally, the postValidators are run. Each validator can add validation messages to the output.

Author:

nilshoffmann

Constructor Summary

Constructors

Constructor	Description
CvMappingValidator()

Method Summary

Modifier and Type	Method	Description
static CvMappingValidator	of(info.psidev.cvmapping.CvMapping mapping, CvParameterLookupService client, boolean errorIfTermNotInRule)	Create a new instance of CvMappingValidator.
static CvMappingValidator	of(File mappingFile, boolean errorIfTermNotInRule)	Create a new instance of CvMappingValidator.
static CvMappingValidator	of(File mappingFile, CvParameterLookupService client, boolean errorIfTermNotInRule)	Create a new instance of CvMappingValidator.
static CvMappingValidator	of(URL mappingFile, boolean errorIfTermNotInRule)	Create a new instance of CvMappingValidator.
static CvMappingValidator	of(URL mappingFile, CvParameterLookupService client, boolean errorIfTermNotInRule)	Create a new instance of CvMappingValidator.
List<de.isas.mztab2.model.ValidationMessage>	validate(de.isas.mztab2.model.MzTab mzTab)
CvMappingValidator	withPostValidator(de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab> postValidator)	Add the provided validator implementation to the list of validators that run last.
CvMappingValidator	withPreValidator(de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab> preValidator)	Add the provided validator implementation to the list of validators that run first.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CvMappingValidator

public CvMappingValidator()

Method Detail

of

public static CvMappingValidator of(File mappingFile,
                                    boolean errorIfTermNotInRule)
                             throws JAXBException

Create a new instance of CvMappingValidator. Uses a default instance of the CvParameterLookupService.

Parameters:

mappingFile - the mapping file to use

errorIfTermNotInRule - raise an error if a term is not defined within an otherwise matching rule for the element

Returns:

a new CvMappingValidator instance

Throws:

JAXBException - if errors occur during unmarshalling of the mapping xml file.

of

public static CvMappingValidator of(File mappingFile,
                                    CvParameterLookupService client,
                                    boolean errorIfTermNotInRule)
                             throws JAXBException

Create a new instance of CvMappingValidator. Uses the provided CvParameterLookupService.

Parameters:

mappingFile - the mapping file to use

client - the ontology lookup service client

errorIfTermNotInRule - raise an error if a term is not defined within an otherwise matching rule for the element

Returns:

a new CvMappingValidator instance

Throws:

JAXBException - if errors occur during unmarshalling of the mapping xml file.

withPreValidator

public CvMappingValidator withPreValidator(de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab> preValidator)

Add the provided validator implementation to the list of validators that run first.

Parameters:

preValidator - the validator

Returns:

an instance of this object

withPostValidator

public CvMappingValidator withPostValidator(de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab> postValidator)

Add the provided validator implementation to the list of validators that run last.

Parameters:

postValidator - the validator

Returns:

an instance of this object

of

public static CvMappingValidator of(URL mappingFile,
                                    boolean errorIfTermNotInRule)
                             throws JAXBException

Create a new instance of CvMappingValidator. Uses a default instance of the CvParameterLookupService.

Parameters:

mappingFile - the mapping file URL to use

errorIfTermNotInRule - raise an error if a term is not defined within an otherwise matching rule for the element

Returns:

a new CvMappingValidator instance

Throws:

JAXBException - if errors occur during unmarshalling of the mapping xml file.

of

public static CvMappingValidator of(URL mappingFile,
                                    CvParameterLookupService client,
                                    boolean errorIfTermNotInRule)
                             throws JAXBException

Create a new instance of CvMappingValidator. Uses the provided CvParameterLookupService.

Parameters:

mappingFile - the mapping file URL to use

client - the ontology lookup service client

errorIfTermNotInRule - raise an error if a term is not defined within an otherwise matching rule for the element

Returns:

a new CvMappingValidator instance

Throws:

JAXBException - if errors occur during unmarshalling of the mapping xml file.

of

public static CvMappingValidator of(info.psidev.cvmapping.CvMapping mapping,
                                    CvParameterLookupService client,
                                    boolean errorIfTermNotInRule)

Create a new instance of CvMappingValidator. Uses the provided CvParameterLookupService.

Parameters:

mapping - the cv mapping to use

client - the ontology lookup service client

errorIfTermNotInRule - raise an error if a term is not defined within an otherwise matching rule for the element

Returns:

a new CvMappingValidator instance

validate

public List<de.isas.mztab2.model.ValidationMessage> validate(de.isas.mztab2.model.MzTab mzTab)

Specified by:

validate in interface de.isas.lipidomics.mztab2.validation.Validator<de.isas.mztab2.model.MzTab>