public class CommandRunner extends Object
CLIMethod
annotation, to designate the relevant methods.GafCommandRunner
,
JsCommandRunner
,
SimCommandRunner
,
SolrCommandRunner
,
TaxonCommandRunner
Modifier and Type | Field and Description |
---|---|
boolean |
exitOnException |
OWLGraphWrapper |
g |
boolean |
isDisposeReasonerOnExit |
Set<org.semanticweb.owlapi.model.OWLObject> |
owlObjectCachedSet |
protected ParserWrapper |
pw |
org.semanticweb.owlapi.model.OWLOntology |
queryOntology |
org.semanticweb.owlapi.reasoner.OWLReasoner |
reasoner |
String |
reasonerName |
Constructor and Description |
---|
CommandRunner() |
Modifier and Type | Method and Description |
---|---|
void |
assertAboxInferences(Opts opts) |
void |
assertInferredSubClassAxioms(Opts opts) |
void |
createBioChebi(Opts opts) |
void |
createExternalMappings(Opts opts) |
void |
createPartOfLinks(Opts opts)
GeneOntology specific function to create links between molecular
functions and their corresponding processes.
|
void |
createSlim(Opts opts) |
void |
createSubsetTags(Opts opts)
Simple helper to create a subset tag for matching entities, allows to specify exceptions
|
protected void |
exit(int code) |
void |
extractAnnotationValue(Opts opts) |
void |
extractExtensionFile(Opts opts)
Extract all xps (
OWLEquivalentClassesAxiom ) from the loaded
ontology. |
void |
filterExtensionFile(Opts opts)
Retain only subclass of axioms and intersection of axioms if they contain
a class in it's signature of a given set of parent terms.
|
protected OWLPrettyPrinter |
getPrettyPrinter() |
void |
handlePrettyPrinter(Opts opts) |
void |
help() |
void |
helpFooter() |
void |
jsonLdToRdf(Opts opts) |
void |
rdfToJsonLd(Opts opts) |
void |
removeRedundantInferredSuperClassAxioms(Opts opts) |
void |
removeRedundantSubclasses(Opts opts) |
void |
removeSubsetEntities(Opts opts) |
org.semanticweb.owlapi.model.OWLClass |
resolveClass(String id) |
List<org.semanticweb.owlapi.model.OWLClass> |
resolveClassList(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(String id) |
Set<org.semanticweb.owlapi.model.OWLObject> |
resolveEntityList(Opts opts) |
org.semanticweb.owlapi.model.OWLObjectProperty |
resolveObjectProperty(String id) |
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyList(Opts opts) |
List<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyListAsList(Opts opts) |
void |
run(Opts opts) |
void |
run(String[] args) |
void |
runDAGCheck(Opts opts) |
void |
runSingleIteration(Opts opts) |
void |
runSingleIteration(String[] args) |
void |
summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont) |
void |
verifyChanges(Opts opts) |
public OWLGraphWrapper g
public org.semanticweb.owlapi.model.OWLOntology queryOntology
public boolean exitOnException
public boolean isDisposeReasonerOnExit
public org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
public String reasonerName
public Set<org.semanticweb.owlapi.model.OWLObject> owlObjectCachedSet
protected ParserWrapper pw
public void createExternalMappings(Opts opts) throws Exception
Exception
public void assertInferredSubClassAxioms(Opts opts) throws Exception
Exception
public void removeRedundantSubclasses(Opts opts) throws Exception
Exception
public void createPartOfLinks(Opts opts) throws Exception
opts
- Exception
public void removeRedundantInferredSuperClassAxioms(Opts opts) throws Exception
Exception
public void createSubsetTags(Opts opts) throws Exception
opts
- Exception
public void extractAnnotationValue(Opts opts) throws Exception
Exception
public void extractExtensionFile(Opts opts) throws Exception
OWLEquivalentClassesAxiom
) from the loaded
ontology. Requires a set of roots classes to restrict the set of
extracted xps.opts
- Exception
public void filterExtensionFile(Opts opts) throws Exception
opts
- Exception
protected void exit(int code)
protected OWLPrettyPrinter getPrettyPrinter()
public void summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont)
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyList(Opts opts)
public List<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyListAsList(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(String id)
public org.semanticweb.owlapi.model.OWLObjectProperty resolveObjectProperty(String id)
public org.semanticweb.owlapi.model.OWLClass resolveClass(String id)
public void help()
public void helpFooter()
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