public class BiopaxValidatorClient extends Object
Modifier and Type | Class and Description |
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static class |
BiopaxValidatorClient.RetFormat |
Modifier and Type | Field and Description |
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static String |
DEFAULT_VALIDATOR_URL
Default BioPAX Validator's URL
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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.)
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Constructor and Description |
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BiopaxValidatorClient()
Default Constructor
It configures for the default validator URL.
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BiopaxValidatorClient(String url)
Main Constructor
It configures for the validator's URL
(defined by DEFAULT_VALIDATOR_URL constant)
and result format ().
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Modifier and Type | Method and Description |
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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.
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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.
|
public static final String DEFAULT_VALIDATOR_URL
public static final String JVM_PROPERTY_URL
public BiopaxValidatorClient(String url)
url
- - validator's file-upload form addresspublic BiopaxValidatorClient()
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
autofix
- true/false (experimental)profile
- validation profile nameretFormat
- xml, html, or owl (no errors, just modified owl, if autofix=true)filterBy
- filter validation issues by the error/warning levelmaxErrs
- 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 URLbiopaxFiles
- an array of BioPAX files to validateout
- validation report data output streamIOException
- when there is an I/O errorpublic static org.biopax.validator.jaxb.ValidatorResponse unmarshal(String xml) throws JAXBException
xml
- input XML data - validation report - to importJAXBException
- when there is an JAXB unmarshalling errorCopyright © 2015 BioPAX. All rights reserved.