org.biopax.paxtools.client

Class BiopaxValidatorClient

java.lang.Object

org.biopax.paxtools.client.BiopaxValidatorClient

public class BiopaxValidatorClient
extends Object

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

Author:

rodche

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BiopaxValidatorClient.RetFormat

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_VALIDATOR_URL Default BioPAX Validator's URL
static String	JVM_PROPERTY_URL The Java Option to set a BioPAX Validator URL (if set, overrides the default and URL provided by the Constructor arg.)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
String	getUrl()
void	setUrl(String url)
static org.biopax.validator.jaxb.ValidatorResponse	unmarshal(String xml) Converts a biopax-validator XML response to the java object.
void	validate(boolean autofix, String profile, BiopaxValidatorClient.RetFormat retFormat, org.biopax.validator.jaxb.Behavior filterBy, Integer maxErrs, String biopaxUrl, File[] biopaxFiles, 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 String DEFAULT_VALIDATOR_URL

Default BioPAX Validator's URL

See Also:

Constant Field Values

JVM_PROPERTY_URL

public static final String JVM_PROPERTY_URL

The Java Option to set a BioPAX Validator URL (if set, overrides the default and URL provided by the Constructor arg.)

See Also:

Constant Field Values

Constructor Detail

BiopaxValidatorClient

public BiopaxValidatorClient(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 URL.

Method Detail

validate

public void validate(boolean autofix,
                     String profile,
                     BiopaxValidatorClient.RetFormat retFormat,
                     org.biopax.validator.jaxb.Behavior filterBy,
                     Integer maxErrs,
                     String biopaxUrl,
                     File[] biopaxFiles,
                     OutputStream out)
              throws 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)

profile - validation profile name

retFormat - xml, html, or owl (no errors, just modified owl, if autofix=true)

filterBy - filter validation issues by the error/warning level

maxErrs - errors threshold - max no. critical errors to collect before quitting (warnings not counted; null/0/negative value means unlimited)

biopaxUrl - check the BioPAX at the URL

biopaxFiles - an array of BioPAX files to validate

out - validation report data output stream

Throws:

IOException - when there is an I/O error

setUrl

public void setUrl(String url)

getUrl

public String getUrl()

unmarshal

public static org.biopax.validator.jaxb.ValidatorResponse unmarshal(String xml)
                                                             throws JAXBException

Converts a biopax-validator XML response to the java object.

Parameters:

xml - input XML data - validation report - to import

Returns:

validation report object

Throws:

JAXBException - when there is an JAXB unmarshalling error