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VIVO-366 change to annotation-to-PropertyConfig converter to deal with multiple values

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This commit is contained in:
brianjlowe 2013-10-15 15:48:25 -04:00
parent e33070b3a8
commit cd28028fb3
2 changed files with 70 additions and 77 deletions
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24
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -93,18 +93,6 @@ public class KnowledgeBaseUpdater {
List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges(); List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel()); AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
// Only modify the TBox and migration metadata the first time
if(updateRequired(servletContext)) {
//process the TBox before the ABox
try {
log.debug("\tupdating tbox annotations");
updateTBoxAnnotations();
} catch (Exception e) {
log.error(e,e);
}
}
// update ABox data any time // update ABox data any time
log.info("performing SPARQL CONSTRUCT additions"); log.info("performing SPARQL CONSTRUCT additions");
@ -124,6 +112,18 @@ public class KnowledgeBaseUpdater {
performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/", performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/",
settings.getRDFService(), RETRACT); settings.getRDFService(), RETRACT);
// Only modify the TBox and migration metadata the first time
if(updateRequired(servletContext)) {
//process the TBox before the ABox
try {
log.debug("\tupdating tbox annotations");
updateTBoxAnnotations();
} catch (Exception e) {
log.error(e,e);
}
}
} }

123
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -450,90 +450,69 @@ public class TBoxUpdater {
} }
public void renameProperty(AtomicOntologyChange changeObj) throws IOException { public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
Dataset dataset = new RDFServiceDataset(settings.getRDFService());
Model userAnnotationsModel = dataset.getNamedModel(
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) { if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
mergePropertyAnnotationsToPropertyConfig(changeObj, userAnnotationsModel); mergePropertyAnnotationsToPropertyConfig(changeObj, siteModel);
} }
Resource renamedProperty = userAnnotationsModel.getResource(changeObj.getSourceURI()); Resource renamedProperty = siteModel.getResource(changeObj.getSourceURI());
userAnnotationsModel.removeAll(renamedProperty, null, (RDFNode) null); siteModel.removeAll(renamedProperty, null, (RDFNode) null);
userAnnotationsModel.removeAll(null, null, renamedProperty); siteModel.removeAll(null, null, renamedProperty);
} }
private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj, private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj,
Model userAnnotationsModel) throws IOException { Model userAnnotationsModel) throws IOException {
String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3); String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
String oldPropertyURI = changeObj.getSourceURI(); String oldPropertyURI = changeObj.getSourceURI();
Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel(); Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
String propertyAnnotationsQuery = String propertyAnnotationsQuery =
"PREFIX config: <" + VitroVocabulary.configURI + "> \n" + "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" + "PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
"CONSTRUCT { \n" + "CONSTRUCT { \n" +
" <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
" <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" + " <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
" <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" + " <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
" <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
" <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
" <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
"} WHERE { \n" + "} WHERE { \n" +
" { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" + " { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
" UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" + " UNION { <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
" UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" + " FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
" UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
" UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
" UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
"} \n" ; "} \n" ;
Model userChangesModel = construct( Model userChangesModel = construct(
propertyAnnotationsQuery, userAnnotationsModel).difference( propertyAnnotationsQuery, userAnnotationsModel).difference(
construct(propertyAnnotationsQuery, oldAnnotationsModel)); construct(propertyAnnotationsQuery, oldAnnotationsModel));
String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" + if(userChangesModel.size() == 0) {
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" + return;
"CONSTRUCT { \n" + } else {
" ?configuration config:propertyGroup ?group . \n" + log.info("Updating PropertyConfig.n3 to include locally-changed " +
" ?configuration config:displayName ?label . \n" + "settings from old property " + oldPropertyURI);
" ?configuration vitro:displayRankAnnot ?displayRank . \n" + }
" ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
"} WHERE { \n" +
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
"} \n" ;
String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" + String newQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" + "PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
"CONSTRUCT { \n" + "CONSTRUCT { \n" +
" <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" + " ?configuration config:propertyGroup ?group . \n" +
" ?configuration config:displayName ?rlabel . \n" + " ?configuration config:displayName ?label . \n" +
" ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" + " ?configuration ?vitroProp ?vitroValue . \n" +
" ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +
"} WHERE { \n" + "} WHERE { \n" +
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" + " <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" + " OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
" ?configuration config:propertyGroup ?rgroup } \n" + " OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" + " OPTIONAL { <" + oldPropertyURI + "> ?vitroProp ?vitroValue \n" +
" ?configuration config:displayName ?rlabel . \n " + " FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
" FILTER(?rlabel != ?label) } \n " + "} \n" ;
" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
" ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " + String existingQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" + "PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
" ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" + "CONSTRUCT { \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" + " ?configuration config:propertyGroup ?group . \n" +
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" + " ?configuration config:displayName ?label . \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " + " ?configuration ?vitroProp ?vitroValue . \n" +
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " + "} WHERE { \n" +
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
" OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
" OPTIONAL { ?configuration config:displayName ?label } \n" +
" OPTIONAL { ?configuration ?vitroProp ?vitroValue \n" +
" FILTER (regex(str(?vitroProp), \"" + VitroVocabulary.vitroURI + "\")) } \n" +
"} \n" ; "} \n" ;
Model configModel = ModelFactory.createDefaultModel(); Model configModel = ModelFactory.createDefaultModel();
@ -542,17 +521,31 @@ public class TBoxUpdater {
FileInputStream fis = new FileInputStream(file); FileInputStream fis = new FileInputStream(file);
configModel.read(fis, null, "N3"); configModel.read(fis, null, "N3");
Model union = ModelFactory.createUnion(configModel, Model currentUnion = ModelFactory.createUnion(configModel,
userChangesModel); userAnnotationsModel);
Model additions = construct(addQuery, union); Model userAnnotationsAsConfig = construct(newQuery, currentUnion);
Model retractions = construct(retractQuery, union); Model currentDefaultConfig = construct(existingQuery, currentUnion);
if (additions.size() > 0 || retractions.size() > 0) { Model additions = userAnnotationsAsConfig.difference(currentDefaultConfig);
configModel.remove(retractions); Model retractions = currentDefaultConfig.difference(userAnnotationsAsConfig);
log.info("Removing " + retractions.size() + " statements from " + contextURI);
// filter the retractions so we won't remove a value for a given predicate
// unless the additions model contains at least one value for the same predicate
Model filteredRetractions = ModelFactory.createDefaultModel();
StmtIterator retractIt = retractions.listStatements();
while(retractIt.hasNext()) {
Statement candidate = retractIt.nextStatement();
if(additions.contains(null, candidate.getPredicate(), (RDFNode) null)) {
filteredRetractions.add(candidate);
}
}
if (additions.size() > 0 || filteredRetractions.size() > 0) {
configModel.remove(filteredRetractions);
log.debug("Removing " + filteredRetractions.size() + " statements from " + contextURI);
configModel.add(additions); configModel.add(additions);
log.info("Adding " + additions.size() + " statements from " + contextURI); log.debug("Adding " + additions.size() + " statements from " + contextURI);
FileOutputStream fos = new FileOutputStream(file); FileOutputStream fos = new FileOutputStream(file);
configModel.write(fos, "N3"); configModel.write(fos, "N3");
} }