public class OortConfiguration extends Object
OboOntologyReleaseRunner
. Contains methods
to read and write the configuration from Properties
.Modifier and Type | Class and Description |
---|---|
static class |
OortConfiguration.MacroStrategy |
Constructor and Description |
---|
OortConfiguration() |
Modifier and Type | Method and Description |
---|---|
void |
addBridgeOntology(String bridgeOntology) |
void |
addPath(String path) |
void |
addRewriteIRIMap(org.semanticweb.owlapi.model.IRI from,
org.semanticweb.owlapi.model.IRI to)
Adds entry to rewrite map
|
void |
addSourceOntologyPrefix(String prefix) |
void |
addToSkipFormatSet(String fmt) |
static void |
addValues(String s,
Collection<String> values)
Only public for testing purposes.
|
static OortConfiguration |
createOortConfig(Properties properties)
Create an
OortConfiguration from the given Properties . |
static Properties |
createProperties(OortConfiguration config)
Create a
Properties object for the given configuration. |
static CharSequence |
escape(String s,
char escapeChar)
Only public for testing purposes.
|
static List<OntologyCheck> |
getAvailableChecks()
Provide a list of all
OntologyCheck 's known to this configuration. |
File |
getBase() |
List<String> |
getBridgeOntologies() |
String |
getCatalogXML() |
org.semanticweb.owlapi.model.OWLDocumentFormat |
getDefaultFormat() |
String |
getErrorReportFile() |
List<String> |
getFilterSimpleProperties() |
Set<String> |
getIgnoreSelectedEquivalentPairSet() |
String |
getJustifyAssertedSubclassesFrom() |
OortConfiguration.MacroStrategy |
getMacroStrategy() |
static OntologyCheck |
getOntologyCheck(String shortName) |
List<OntologyCheck> |
getOntologyChecks() |
static String |
getOntologyCheckShortName(OntologyCheck check) |
org.semanticweb.owlapi.model.OWLDocumentFormat |
getOwlOfnFormat() |
org.semanticweb.owlapi.model.OWLDocumentFormat |
getOwlXMLFormat() |
Vector<String> |
getPaths() |
Set<PropertyView> |
getPropertyViews() |
String |
getQueryOntology() |
String |
getQueryOntologyReference() |
String |
getReasonerName() |
Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> |
getRewriteIRIMap() |
Set<String> |
getSkipFormatSet() |
Set<String> |
getSourceOntologyPrefixes() |
int |
getThreads() |
String |
getTraceReportFile() |
String |
getVersionSubdirectory() |
boolean |
isAddImportsFromSupports() |
boolean |
isAddSupportFromImports() |
boolean |
isAllowEquivalentNamedClassPairs() |
boolean |
isAllowFileOverWrite() |
boolean |
isAsserted() |
boolean |
isAutoDetectBridgingOntology() |
boolean |
isCheckConsistency() |
boolean |
isCheckPotentialRedundant() |
boolean |
isCreateErrorModules() |
boolean |
isEnforceEL() |
boolean |
isExecuteOntologyChecks() |
boolean |
isExpandMacros() |
boolean |
isExpandShortcutRelations() |
boolean |
isExpandXrefs() |
boolean |
isForceRelease() |
boolean |
isGafToOwl() |
boolean |
isIgnoreLockFile() |
boolean |
isJustifyAssertedSubclasses() |
boolean |
isQueryOntologyReferenceIsIRI() |
boolean |
isRecreateMireot() |
boolean |
isRelaxed() |
boolean |
isRemoveDanglingBeforeReasoning() |
boolean |
isRemoveQueryOntologyReference() |
boolean |
isRemoveRedunantAxioms() |
boolean |
isRemoveTrailingQualifiers() |
boolean |
isRepairAnnotationCardinality() |
boolean |
isRunOboBasicDagCheck() |
boolean |
isSimple() |
boolean |
isSkipFormat(String fmt) |
boolean |
isTranslateDisjointsToEquivalents() |
boolean |
isUseIsInferred() |
boolean |
isUseQueryOntology() |
boolean |
isUseReleaseFolder() |
boolean |
isVersionReportFiles() |
boolean |
isWriteELOntology() |
boolean |
isWriteLabelOWL() |
boolean |
isWriteMetadata() |
boolean |
isWriteSubsets() |
static void |
loadConfig(File file,
OortConfiguration config)
Load the configuration from a property file into the
given
OortConfiguration . |
static void |
loadOortConfig(Properties properties,
OortConfiguration config)
Load the given
Properties into the OortConfiguration . |
static OortConfiguration |
readConfig(File file)
Read from a configuration property file and load it
into a new
OortConfiguration object. |
void |
removeFromSkipFormatSet(String fmt) |
void |
setAddImportsFromSupports(boolean addImportsFromSupports) |
void |
setAddSupportFromImports(boolean addSupportFromImports) |
void |
setAllowEquivalentNamedClassPairs(boolean allowEquivalentNamedClassPairs) |
void |
setAllowFileOverWrite(boolean allowFileOverWrite)
Set allowFileOverWrite
|
void |
setAsserted(boolean asserted)
Set asserted
|
void |
setAutoDetectBridgingOntology(boolean isAutoDetectBridgingOntology) |
void |
setBase(File base) |
void |
setBridgeOntologies(List<String> bridgeOntologies) |
void |
setCatalogXML(String catalogXML) |
void |
setCheckConsistency(boolean checkConsistency) |
void |
setCheckPotentialRedundant(boolean checkPotentialRedundant) |
void |
setCreateErrorModules(boolean createErrorModules) |
void |
setEnforceEL(boolean enforceEL) |
void |
setErrorReportFile(String errorReportFile) |
void |
setExecuteOntologyChecks(boolean executeOntologyChecks) |
void |
setExpandMacros(boolean expandMacros) |
void |
setExpandShortcutRelations(boolean expandShortcutRelations) |
void |
setExpandXrefs(boolean expandXrefs)
Set export bridges
|
void |
setFilterSimpleProperties(List<String> filterSimpleProperties) |
void |
setForceRelease(boolean forceRelease) |
void |
setGafToOwl(boolean gafToOwl) |
void |
setIgnoreLockFile(boolean ignoreLockFile) |
void |
setIgnoreSelectedEquivalentPairSet(Set<String> ignoreSelectedEquivalentPairSet) |
void |
setJustifyAssertedSubclasses(boolean isJustifyAssertedSubclasses) |
void |
setJustifyAssertedSubclassesFrom(String justifyAssertedSubclassesFrom) |
void |
setMacroStrategy(OortConfiguration.MacroStrategy macroStrategy)
Set the
OortConfiguration.MacroStrategy |
void |
setOntologyChecks(List<OntologyCheck> ontologyChecks) |
void |
setPropertyViews(Set<PropertyView> propertyViews) |
void |
setQueryOntology(String queryOntology) |
void |
setQueryOntologyReference(String queryOntologyReference) |
void |
setQueryOntologyReferenceIsIRI(boolean queryOntologyReferenceIsIRI) |
void |
setReasonerName(String reasonerName)
Set the reasoner name
|
void |
setRecreateMireot(boolean recreateMireot)
Set recreateMireot
|
void |
setRelaxed(boolean relaxed) |
void |
setRemoveDanglingBeforeReasoning(boolean removeDanglingBeforeReasoning) |
void |
setRemoveQueryOntologyReference(boolean removeQueryOntologyReference) |
void |
setRemoveRedunantAxioms(boolean removeRedunantAxioms) |
void |
setRemoveTrailingQualifiers(boolean removeTrailingQualifiers) |
void |
setRepairAnnotationCardinality(boolean repairAnnotationCardinality) |
void |
setRewriteIRIMap(Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> rewriteIRIMap) |
void |
setRunOboBasicDagCheck(boolean runOboBasicDagCheck) |
void |
setSimple(boolean simple)
Set simple.
|
void |
setSkipFormatSet(Set<String> skipFormatSet) |
void |
setSourceOntologyPrefixes(Set<String> sourceOntologyPrefixes) |
void |
setThreads(int threads) |
void |
setTraceReportFile(String traceReportFile) |
void |
setTranslateDisjointsToEquivalents(boolean translateDisjointsToEquivalents) |
void |
setUseIsInferred(boolean useIsInferred) |
void |
setUseQueryOntology(boolean useQueryOntology) |
void |
setUseReleaseFolder(boolean useReleaseFolder) |
void |
setVersionReportFiles(boolean versionReportFiles) |
void |
setVersionSubdirectory(String versionSubdirectory) |
void |
setWriteELOntology(boolean writeELOntology) |
void |
setWriteLabelOWL(boolean writeLabelOWL) |
void |
setWriteMetadata(boolean writeMetadata) |
void |
setWriteSubsets(boolean isWriteSubsets) |
String |
toString() |
static String |
unescape(String s)
Only public for testing purposes.
|
static void |
writeConfig(File file,
OortConfiguration config)
Write the given
OortConfiguration into the file as properties. |
public static OntologyCheck getOntologyCheck(String shortName)
public static String getOntologyCheckShortName(OntologyCheck check)
public static List<OntologyCheck> getAvailableChecks()
OntologyCheck
's known to this configuration.public String getReasonerName()
public void setReasonerName(String reasonerName)
reasonerName
- public boolean isAsserted()
public void setAsserted(boolean asserted)
asserted
- public boolean isSimple()
public void setSimple(boolean simple)
simple
- public List<String> getFilterSimpleProperties()
public void setFilterSimpleProperties(List<String> filterSimpleProperties)
filterSimpleProperties
- the filterSimpleProperties to setpublic boolean isRelaxed()
public void setRelaxed(boolean relaxed)
relaxed
- the relaxed to setpublic boolean isExpandXrefs()
public void setExpandXrefs(boolean expandXrefs)
expandXrefs
- public boolean isAllowFileOverWrite()
public void setAllowFileOverWrite(boolean allowFileOverWrite)
allowFileOverWrite
- public OortConfiguration.MacroStrategy getMacroStrategy()
OortConfiguration.MacroStrategy
public void setMacroStrategy(OortConfiguration.MacroStrategy macroStrategy)
OortConfiguration.MacroStrategy
macroStrategy
- public boolean isRecreateMireot()
public void setRecreateMireot(boolean recreateMireot)
recreateMireot
- public boolean isExpandShortcutRelations()
public void setExpandShortcutRelations(boolean expandShortcutRelations)
public boolean isEnforceEL()
public void setEnforceEL(boolean enforceEL)
public boolean isWriteELOntology()
public void setWriteELOntology(boolean writeELOntology)
public void addToSkipFormatSet(String fmt)
public void removeFromSkipFormatSet(String fmt)
public boolean isSkipFormat(String fmt)
public void addSourceOntologyPrefix(String prefix)
public void setBridgeOntologies(List<String> bridgeOntologies)
bridgeOntologies
- the bridgeOntologies to setpublic void addBridgeOntology(String bridgeOntology)
public boolean isExecuteOntologyChecks()
public void setExecuteOntologyChecks(boolean executeOntologyChecks)
public boolean isAllowEquivalentNamedClassPairs()
public void setAllowEquivalentNamedClassPairs(boolean allowEquivalentNamedClassPairs)
public boolean isWriteSubsets()
public void setWriteSubsets(boolean isWriteSubsets)
public boolean isJustifyAssertedSubclasses()
public void setJustifyAssertedSubclasses(boolean isJustifyAssertedSubclasses)
public boolean isUseIsInferred()
public void setUseIsInferred(boolean useIsInferred)
useIsInferred
- the useIsInferred to setpublic boolean isRemoveTrailingQualifiers()
public void setRemoveTrailingQualifiers(boolean removeTrailingQualifiers)
removeTrailingQualifiers
- the removeTrailingQualifiers to setpublic boolean isAutoDetectBridgingOntology()
public void setAutoDetectBridgingOntology(boolean isAutoDetectBridgingOntology)
public boolean isExpandMacros()
public void setExpandMacros(boolean expandMacros)
expandMacros
- isExpandMacros to setpublic boolean isForceRelease()
public void setForceRelease(boolean forceRelease)
forceRelease
- forceRelease to setpublic boolean isCheckConsistency()
public void setCheckConsistency(boolean checkConsistency)
checkConsistency
- the checkConsistency to setpublic boolean isRemoveDanglingBeforeReasoning()
public void setRemoveDanglingBeforeReasoning(boolean removeDanglingBeforeReasoning)
public boolean isAddSupportFromImports()
public void setAddSupportFromImports(boolean addSupportFromImports)
public boolean isAddImportsFromSupports()
public void setAddImportsFromSupports(boolean addImportsFromSupports)
public boolean isTranslateDisjointsToEquivalents()
public void setTranslateDisjointsToEquivalents(boolean translateDisjointsToEquivalents)
public boolean isWriteMetadata()
public void setWriteMetadata(boolean writeMetadata)
writeMetadata
- the writeMetadata to setpublic Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> getRewriteIRIMap()
public void setRewriteIRIMap(Map<org.semanticweb.owlapi.model.IRI,org.semanticweb.owlapi.model.IRI> rewriteIRIMap)
rewriteIRIMap
- map of IRIs to be rewritten public void addRewriteIRIMap(org.semanticweb.owlapi.model.IRI from, org.semanticweb.owlapi.model.IRI to)
from
- to
- public org.semanticweb.owlapi.model.OWLDocumentFormat getDefaultFormat()
public org.semanticweb.owlapi.model.OWLDocumentFormat getOwlXMLFormat()
public void addPath(String path)
path
- the path to add to the setpublic File getBase()
public void setBase(File base)
base
- the base to setpublic boolean isRepairAnnotationCardinality()
public void setRepairAnnotationCardinality(boolean repairAnnotationCardinality)
repairAnnotationCardinality
- the repairAnnotationCardinality to setpublic Set<PropertyView> getPropertyViews()
public void setPropertyViews(Set<PropertyView> propertyViews)
public boolean isUseReleaseFolder()
public void setUseReleaseFolder(boolean useReleaseFolder)
useReleaseFolder
- the useReleaseFolder to setpublic boolean isGafToOwl()
public void setGafToOwl(boolean gafToOwl)
gafToOwl
- the gafToOwl to setpublic String getCatalogXML()
public void setCatalogXML(String catalogXML)
catalogXML
- the catalogXML to setpublic String getVersionSubdirectory()
public void setVersionSubdirectory(String versionSubdirectory)
versionSubdirectory
- the versionSubdirectory to setpublic boolean isUseQueryOntology()
public void setUseQueryOntology(boolean useQueryOntology)
useQueryOntology
- the useQueryOntology to setpublic String getQueryOntology()
public void setQueryOntology(String queryOntology)
queryOntology
- the queryOntology to setpublic String getQueryOntologyReference()
public void setQueryOntologyReference(String queryOntologyReference)
queryOntologyReference
- the queryOntologyReference to setpublic boolean isQueryOntologyReferenceIsIRI()
public void setQueryOntologyReferenceIsIRI(boolean queryOntologyReferenceIsIRI)
queryOntologyReferenceIsIRI
- the queryOntologyReferenceIsIRI to setpublic boolean isRemoveQueryOntologyReference()
public boolean isWriteLabelOWL()
public void setWriteLabelOWL(boolean writeLabelOWL)
writeLabelOWL
- the writeLabelOWL to setpublic org.semanticweb.owlapi.model.OWLDocumentFormat getOwlOfnFormat()
public void setRemoveQueryOntologyReference(boolean removeQueryOntologyReference)
removeQueryOntologyReference
- the removeQueryOntologyReference to setpublic String getJustifyAssertedSubclassesFrom()
public void setJustifyAssertedSubclassesFrom(String justifyAssertedSubclassesFrom)
justifyAssertedSubclassesFrom
- the justifyAssertedSubclassesFrom to setpublic boolean isIgnoreLockFile()
public void setIgnoreLockFile(boolean ignoreLockFile)
ignoreLockFile
- the ignoreLockFile to setpublic List<OntologyCheck> getOntologyChecks()
public void setOntologyChecks(List<OntologyCheck> ontologyChecks)
ontologyChecks
- the ontologyChecks to setpublic int getThreads()
public void setThreads(int threads)
threads
- the threads to setpublic boolean isRunOboBasicDagCheck()
public void setRunOboBasicDagCheck(boolean runOboBasicDagCheck)
runOboBasicDagCheck
- the runOboBasicDagCheck to setpublic String getErrorReportFile()
public void setErrorReportFile(String errorReportFile)
errorReportFile
- the errorReportFile to setpublic String getTraceReportFile()
public void setTraceReportFile(String traceReportFile)
traceReportFile
- the traceReportFile to setpublic boolean isRemoveRedunantAxioms()
public void setRemoveRedunantAxioms(boolean removeRedunantAxioms)
removeRedunantAxioms
- the removeRedunantAxioms to setpublic boolean isCheckPotentialRedundant()
public void setCheckPotentialRedundant(boolean checkPotentialRedundant)
checkPotentialRedundant
- the checkPotentialRedundant to setpublic boolean isVersionReportFiles()
public void setVersionReportFiles(boolean versionReportFiles)
versionReportFiles
- the versionReportFiles to setpublic boolean isCreateErrorModules()
public void setCreateErrorModules(boolean createErrorModules)
createErrorModules
- the createErrorModules to setpublic Set<String> getIgnoreSelectedEquivalentPairSet()
public void setIgnoreSelectedEquivalentPairSet(Set<String> ignoreSelectedEquivalentPairSet)
ignoreSelectedEquivalentPairSet
- the ignoreSelectedEquivalentPairSet to setpublic static Properties createProperties(OortConfiguration config)
Properties
object for the given configuration.config
- public static OortConfiguration createOortConfig(Properties properties)
OortConfiguration
from the given Properties
.properties
- public static void loadOortConfig(Properties properties, OortConfiguration config)
Properties
into the OortConfiguration
.properties
- config
- public static void addValues(String s, Collection<String> values)
s
- values
- public static CharSequence escape(String s, char escapeChar)
s
- escapeChar
- public static String unescape(String s)
s
- public static OortConfiguration readConfig(File file) throws IOException
OortConfiguration
object.file
- IOException
public static void loadConfig(File file, OortConfiguration config) throws IOException
OortConfiguration
.file
- source property fileconfig
- target configurationIOException
public static void writeConfig(File file, OortConfiguration config) throws IOException
OortConfiguration
into the file as properties.file
- target fileconfig
- IOException
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