org.biopax.validator
Class BiopaxValidatorClient

java.lang.Object
  org.biopax.validator.BiopaxValidatorClient

public class BiopaxValidatorClient
extends java.lang.Object

Simple (example) BioPAX Validator client to upload and check BioPAX OWL files.

Author:

rodche

Nested Class Summary

static class

BiopaxValidatorClient.RetFormat

Field Summary

static java.lang.String

DEFAULT_VALIDATOR_URL Default BioPAX Validator's URL

Constructor Summary

BiopaxValidatorClient()
Default Constructor It configures for the default validator (defined by DEFAULT_VALIDATOR_URL constant) to return XML result.

BiopaxValidatorClient(java.lang.String url)
Main Constructor It configures for the validator's URL (defined by DEFAULT_VALIDATOR_URL constant) and result format ().

Method Summary

java.lang.String	getUrl()
void	setUrl(java.lang.String url)
static ValidatorResponse	unmarshal(java.lang.String xml)
void	validate(boolean autofix, boolean normalize, BiopaxValidatorClient.RetFormat retFormat, Behavior filterBy, java.lang.Integer maxErrs, java.lang.String biopaxUrl, java.io.File[] biopaxFiles, java.io.OutputStream out) Checks a BioPAX OWL file(s) or resource using the online BioPAX Validator and prints the results to the output stream.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VALIDATOR_URL

public static final java.lang.String DEFAULT_VALIDATOR_URL

Default BioPAX Validator's URL

See Also:

Constant Field Values

Constructor Detail

BiopaxValidatorClient

public BiopaxValidatorClient(java.lang.String url)

Main Constructor It configures for the validator's URL (defined by DEFAULT_VALIDATOR_URL constant) and result format ().

Parameters:

url - - validator's file-upload form address

BiopaxValidatorClient

public BiopaxValidatorClient()

Default Constructor It configures for the default validator (defined by DEFAULT_VALIDATOR_URL constant) to return XML result.

Method Detail

validate

public void validate(boolean autofix,
                     boolean normalize,
                     BiopaxValidatorClient.RetFormat retFormat,
                     Behavior filterBy,
                     java.lang.Integer maxErrs,
                     java.lang.String biopaxUrl,
                     java.io.File[] biopaxFiles,
                     java.io.OutputStream out)
              throws java.io.IOException

Checks a BioPAX OWL file(s) or resource using the online BioPAX Validator and prints the results to the output stream.

Parameters:

autofix - true/false (experimental)

normalize - true/false (experimental)

retFormat - xml, html, or owl (no errors, just modified owl, - when 'autofix' or 'normalize' is true); see also BiopaxValidatorClient.RetFormat

biopaxUrl - check the BioPAX at the URL

biopaxFiles - an array of BioPAX files to validate

out -

Throws:

java.io.IOException

setUrl

public void setUrl(java.lang.String url)

getUrl

public java.lang.String getUrl()

unmarshal

public static ValidatorResponse unmarshal(java.lang.String xml)
                                   throws javax.xml.bind.JAXBException

Parameters:

xml -

Returns:

Throws:

javax.xml.bind.JAXBException