VIVO-366 change to annotation-to-PropertyConfig converter to deal with multiple values
This commit is contained in:
brianjlowe
parent
e33070b3a8
commit
cd28028fb3
2 changed files with 70 additions and 77 deletions
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@ -93,18 +93,6 @@ public class KnowledgeBaseUpdater {
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List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
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AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
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// Only modify the TBox and migration metadata the first time
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if(updateRequired(servletContext)) {
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//process the TBox before the ABox
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try {
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log.debug("\tupdating tbox annotations");
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updateTBoxAnnotations();
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} catch (Exception e) {
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log.error(e,e);
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}
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}
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// update ABox data any time
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log.info("performing SPARQL CONSTRUCT additions");
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@ -124,6 +112,18 @@ public class KnowledgeBaseUpdater {
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performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/",
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settings.getRDFService(), RETRACT);
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// Only modify the TBox and migration metadata the first time
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if(updateRequired(servletContext)) {
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//process the TBox before the ABox
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try {
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log.debug("\tupdating tbox annotations");
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updateTBoxAnnotations();
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} catch (Exception e) {
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log.error(e,e);
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}
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}
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}
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@ -450,90 +450,69 @@ public class TBoxUpdater {
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}
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public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
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Dataset dataset = new RDFServiceDataset(settings.getRDFService());
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Model userAnnotationsModel = dataset.getNamedModel(
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JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
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if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
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mergePropertyAnnotationsToPropertyConfig(changeObj, userAnnotationsModel);
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mergePropertyAnnotationsToPropertyConfig(changeObj, siteModel);
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}
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Resource renamedProperty = userAnnotationsModel.getResource(changeObj.getSourceURI());
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userAnnotationsModel.removeAll(renamedProperty, null, (RDFNode) null);
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userAnnotationsModel.removeAll(null, null, renamedProperty);
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Resource renamedProperty = siteModel.getResource(changeObj.getSourceURI());
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siteModel.removeAll(renamedProperty, null, (RDFNode) null);
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siteModel.removeAll(null, null, renamedProperty);
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}
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private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj,
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Model userAnnotationsModel) throws IOException {
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String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
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String oldPropertyURI = changeObj.getSourceURI();
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Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
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String propertyAnnotationsQuery =
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"PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
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"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
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"CONSTRUCT { \n" +
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" <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
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" <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
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" <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
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" <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
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" <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
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" <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
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" <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
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"} WHERE { \n" +
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" { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
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" UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
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" UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
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" UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
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" UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
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" UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
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" { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
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" UNION { <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
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" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
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"} \n" ;
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Model userChangesModel = construct(
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propertyAnnotationsQuery, userAnnotationsModel).difference(
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construct(propertyAnnotationsQuery, oldAnnotationsModel));
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String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
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"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
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"CONSTRUCT { \n" +
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" ?configuration config:propertyGroup ?group . \n" +
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" ?configuration config:displayName ?label . \n" +
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" ?configuration vitro:displayRankAnnot ?displayRank . \n" +
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" ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
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" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
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" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
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"} WHERE { \n" +
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" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
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"} \n" ;
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if(userChangesModel.size() == 0) {
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return;
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} else {
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log.info("Updating PropertyConfig.n3 to include locally-changed " +
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"settings from old property " + oldPropertyURI);
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}
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String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
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String newQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
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"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
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"CONSTRUCT { \n" +
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" <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" +
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" ?configuration config:displayName ?rlabel . \n" +
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" ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" +
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" ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
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" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
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" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +
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" ?configuration config:propertyGroup ?group . \n" +
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" ?configuration config:displayName ?label . \n" +
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" ?configuration ?vitroProp ?vitroValue . \n" +
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"} WHERE { \n" +
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" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
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" ?configuration config:propertyGroup ?rgroup } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
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" ?configuration config:displayName ?rlabel . \n " +
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" FILTER(?rlabel != ?label) } \n " +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
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" ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
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" ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
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" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
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" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " +
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" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
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" OPTIONAL { <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
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" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
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"} \n" ;
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String existingQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
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"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
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"CONSTRUCT { \n" +
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" ?configuration config:propertyGroup ?group . \n" +
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" ?configuration config:displayName ?label . \n" +
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" ?configuration ?vitroProp ?vitroValue . \n" +
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"} WHERE { \n" +
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" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
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" OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
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" OPTIONAL { ?configuration config:displayName ?label } \n" +
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" OPTIONAL { ?configuration ?vitroProp ?vitroValue \n" +
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" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
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"} \n" ;
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Model configModel = ModelFactory.createDefaultModel();
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@ -542,17 +521,31 @@ public class TBoxUpdater {
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FileInputStream fis = new FileInputStream(file);
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configModel.read(fis, null, "N3");
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Model union = ModelFactory.createUnion(configModel,
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userChangesModel);
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Model currentUnion = ModelFactory.createUnion(configModel,
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userAnnotationsModel);
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Model additions = construct(addQuery, union);
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Model retractions = construct(retractQuery, union);
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Model userAnnotationsAsConfig = construct(newQuery, currentUnion);
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Model currentDefaultConfig = construct(existingQuery, currentUnion);
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if (additions.size() > 0 || retractions.size() > 0) {
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configModel.remove(retractions);
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log.info("Removing " + retractions.size() + " statements from " + contextURI);
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Model additions = userAnnotationsAsConfig.difference(currentDefaultConfig);
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Model retractions = currentDefaultConfig.difference(userAnnotationsAsConfig);
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// filter the retractions so we won't remove a value for a given predicate
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// unless the additions model contains at least one value for the same predicate
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Model filteredRetractions = ModelFactory.createDefaultModel();
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StmtIterator retractIt = retractions.listStatements();
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while(retractIt.hasNext()) {
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Statement candidate = retractIt.nextStatement();
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if(additions.contains(null, candidate.getPredicate(), (RDFNode) null)) {
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filteredRetractions.add(candidate);
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}
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}
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if (additions.size() > 0 || filteredRetractions.size() > 0) {
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configModel.remove(filteredRetractions);
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log.debug("Removing " + filteredRetractions.size() + " statements from " + contextURI);
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configModel.add(additions);
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log.info("Adding " + additions.size() + " statements from " + contextURI);
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log.debug("Adding " + additions.size() + " statements from " + contextURI);
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FileOutputStream fos = new FileOutputStream(file);
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configModel.write(fos, "N3");
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}
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