owltools.ontologyrelease
Class OboOntologyReleaseRunner

java.lang.Object
  extended by owltools.ontologyrelease.OboOntologyReleaseRunner

public class OboOntologyReleaseRunner
extends Object

This class is a command line utility which builds an ontology release. The command line argument --h or --help provides usage documentation of this utility. This tool called through bin/ontology-release-runner.

Author:
Shahid Manzoor

Field Summary
protected static org.apache.log4j.Logger logger
           
 
Constructor Summary
OboOntologyReleaseRunner(OortConfiguration oortConfig, File base)
           
 
Method Summary
protected  boolean allowFileOverwrite(File file)
          Hook method to handle an unexpected file overwrite request.
protected  File checkNew(File file)
          Check whether the file is new.
 boolean createRelease(Vector<String> paths)
           
static void main(String[] args)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

logger

protected static final org.apache.log4j.Logger logger
Constructor Detail

OboOntologyReleaseRunner

public OboOntologyReleaseRunner(OortConfiguration oortConfig,
                                File base)
                         throws IOException
Throws:
IOException
Method Detail

checkNew

protected File checkNew(File file)
                 throws IOException
Check whether the file is new. Throw an IOException, if the file already exists and OortConfiguration.isAllowFileOverWrite() is not set to true.

Parameters:
file -
Returns:
file return the same file to allow chaining with other operations
Throws:
IOException

allowFileOverwrite

protected boolean allowFileOverwrite(File file)
                              throws IOException
Hook method to handle an unexpected file overwrite request. Returns true, if the overwrite is allowed.

Parameters:
file -
Returns:
boolean
Throws:
IOException

main

public static void main(String[] args)
                 throws IOException,
                        org.semanticweb.owlapi.model.OWLOntologyCreationException,
                        org.semanticweb.owlapi.model.OWLOntologyStorageException,
                        org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException

createRelease

public boolean createRelease(Vector<String> paths)
                      throws IOException,
                             org.semanticweb.owlapi.model.OWLOntologyCreationException,
                             FileNotFoundException,
                             org.semanticweb.owlapi.model.OWLOntologyStorageException,
                             OboOntologyReleaseRunnerCheckException,
                             OntologyMetaDataTools.AnnotationCardinalityException
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
FileNotFoundException
org.semanticweb.owlapi.model.OWLOntologyStorageException
OboOntologyReleaseRunnerCheckException
OntologyMetaDataTools.AnnotationCardinalityException


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