updates to knowledge base migration
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stellamit
parent
2fcebd1c5f
commit
7f67559db4
5 changed files with 73 additions and 101 deletions
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@ -28,6 +28,7 @@ import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.shared.Lock;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
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/**
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@ -51,18 +52,12 @@ public class KnowledgeBaseUpdater {
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this.record = new SimpleChangeRecord(settings.getAddedDataFile(), settings.getRemovedDataFile());
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}
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public boolean update() throws IOException {
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// Check to see if the update is necessary.
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boolean updateRequired = updateRequired();
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if (updateRequired) {
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public void update() throws IOException {
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if (this.logger == null) {
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this.logger = new SimpleChangeLogger(settings.getLogFile(), settings.getErrorLogFile());
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}
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long startTime = System.currentTimeMillis();
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System.out.println("Migrating the knowledge base");
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log.info("Migrating the knowledge base");
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@ -87,29 +82,29 @@ public class KnowledgeBaseUpdater {
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long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;
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System.out.println("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
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log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
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return;
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}
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return updateRequired;
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}
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private void performUpdate() throws IOException {
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log.info("\tperforming SPARQL construct additions (abox)");
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performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getAssertionOntModelSelector().getABoxModel());
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log.info("finished sparql construct additions");
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log.info("\tperforming SPARQL construct deletions (infenences)");
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performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getInferenceOntModelSelector().getABoxModel());
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log.info("finished sparql construct retractions");
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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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//process the TBox before the ABox
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updateTBoxAnnotations();
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log.info("finished updating tbox annotations");
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log.info("\tupdating tbox annotations");
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updateTBoxAnnotations();
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log.info("\tupdating the abox");
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updateABox(changes);
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log.info("finished updating abox");
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}
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private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel aboxModel) throws IOException {
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@ -195,7 +190,7 @@ public class KnowledgeBaseUpdater {
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fileContents.append(ln).append('\n');
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}
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try {
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log.info("processing SPARQL construct query from file " + sparqlFiles[i].getName());
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log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName());
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Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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@ -269,7 +264,7 @@ public class KnowledgeBaseUpdater {
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boolean required = false;
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String sparqlQueryStr = loadSparqlQuery(settings.getAskQueryFile());
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String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile());
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if (sparqlQueryStr == null) {
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return required;
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}
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@ -286,12 +281,10 @@ public class KnowledgeBaseUpdater {
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required = false;
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} else {
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required = true;
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Model tbox = settings.getAssertionOntModelSelector().getTBoxModel();
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String sparqlQueryStr2 = loadSparqlQuery(settings.getAskEmptyQueryFile());
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if (sparqlQueryStr2 != null) {
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Query query2 = QueryFactory.create(sparqlQueryStr2);
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QueryExecution isNotEmpty = QueryExecutionFactory.create(query2, tbox);
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required = isNotEmpty.execAsk();
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if (JenaDataSourceSetupBase.isFirstStartup()) {
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assertSuccess();
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log.info("The application is starting with a fresh DB, an indication will be added to the DB that a knowledge base migration to the current version is not required.");
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required = false;
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}
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}
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@ -328,15 +321,19 @@ public class KnowledgeBaseUpdater {
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m.enterCriticalSection(Lock.WRITE);
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try {
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m.read(inStream, null, settings.getSuccessRDFFormat());
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if (logger != null) {
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logger.logWithDate("Finished knowledge base migration");
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}
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} finally {
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m.leaveCriticalSection();
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}
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} catch (Exception e) {
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if (logger != null) {
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logger.logError(" unable to make RDF assertions about successful " +
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" update to new ontology version: " + e.getMessage());
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}
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}
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}
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/**
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* A class that allows to access two different ontology change lists,
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@ -12,9 +12,7 @@ public class UpdateSettings {
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private String sparqlConstructAdditionsDir;
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private String sparqlConstructAdditionsPass2Dir;
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private String sparqlConstructDeletionsDir;
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private String askQueryFile;
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private String askEmptyQueryFile;
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private String askEverQueryFile;
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private String askUpdatedQueryFile;
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private String successAssertionsFile;
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private String successRDFFormat = "N3";
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private String diffFile;
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@ -54,23 +52,11 @@ public class UpdateSettings {
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public void setSparqlConstructDeletionsDir(String sparqlConstructDeletionsDir) {
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this.sparqlConstructDeletionsDir = sparqlConstructDeletionsDir;
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}
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public String getAskQueryFile() {
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return askQueryFile;
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public String getAskUpdatedQueryFile() {
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return askUpdatedQueryFile;
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}
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public void setAskQueryFile(String askQueryFile) {
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this.askQueryFile = askQueryFile;
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}
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public String getAskEverQueryFile() {
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return askEverQueryFile;
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}
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public void setAskEverQueryFile(String askEverQueryFile) {
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this.askEverQueryFile = askEverQueryFile;
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}
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public String getAskEmptyQueryFile() {
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return askEmptyQueryFile;
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}
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public void setAskEmptyQueryFile(String askEmptyQueryFile) {
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this.askEmptyQueryFile = askEmptyQueryFile;
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public void setAskUpdatedQueryFile(String askQueryFile) {
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this.askUpdatedQueryFile = askQueryFile;
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}
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public String getSuccessAssertionsFile() {
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return successAssertionsFile;
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@ -156,5 +142,4 @@ public class UpdateSettings {
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public void setNewTBoxAnnotationsModel(OntModel newTBoxAnnotationsModel) {
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this.newTBoxAnnotationsModel = newTBoxAnnotationsModel;
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}
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}
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@ -86,7 +86,7 @@ public class FileGraphSetup implements ServletContextListener {
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if ( (aboxChanged || tboxChanged) && !isUpdateRequired(sce.getServletContext()) ) {
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log.info("a full recompute of the Abox will be performed because" +
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" the filegraph abox(s) and/or tbox(s) have changed." );
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" the filegraph abox(s) and/or tbox(s) have changed or are being read for the first time." );
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SimpleReasonerSetup.setRecomputeRequired(sce.getServletContext());
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}
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}
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@ -259,7 +259,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
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RDB, SDB
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}
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protected boolean isFirstStartup() {
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public static boolean isFirstStartup() {
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return firstStartup;
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}
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@ -48,8 +48,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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private static final String DATA_DIR = "/WEB-INF/ontologies/update/";
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private static final String LOG_DIR = "logs/";
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private static final String CHANGED_DATA_DIR = "changedData/";
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private static final String ASK_QUERY_FILE = DATA_DIR + "ask.sparql";
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private static final String ASK_EMPTY_QUERY_FILE = DATA_DIR + "askEmpty.sparql";
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private static final String ASK_QUERY_FILE = DATA_DIR + "askUpdated.sparql";
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private static final String SUCCESS_ASSERTIONS_FILE = DATA_DIR + "success.n3";
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private static final String SUCCESS_RDF_FORMAT = "N3";
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private static final String DIFF_FILE = DATA_DIR + "diff.tab.txt";
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@ -77,8 +76,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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String errorLogFileName = DATA_DIR + LOG_DIR + timestampedFileName("knowledgeBaseUpdate.error", "log");
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UpdateSettings settings = new UpdateSettings();
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settings.setAskQueryFile(getAskQueryPath(ctx));
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settings.setAskEmptyQueryFile(getAskEmptyQueryPath(ctx));
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settings.setAskUpdatedQueryFile(getAskUpdatedQueryPath(ctx));
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settings.setDataDir(ctx.getRealPath(DATA_DIR));
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settings.setSparqlConstructAdditionsDir(ctx.getRealPath(SPARQL_CONSTRUCT_ADDITIONS_DIR));
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settings.setSparqlConstructDeletionsDir(ctx.getRealPath(SPARQL_CONSTRUCT_DELETIONS_DIR));
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@ -110,7 +108,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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}
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try {
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KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
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try {
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@ -119,13 +116,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
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//doMiscAppMetadataReplacements(ctx.getRealPath(MISC_REPLACEMENTS_FILE), oms);
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reloadDisplayModel(ctx);
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}
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} catch (Throwable t){
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log.warn("warning", t);
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}
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ontologyUpdater.update();
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}
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} catch (IOException ioe) {
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String errMsg = "IOException updating knowledge base " +
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"for ontology changes: ";
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@ -135,7 +127,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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ioe.printStackTrace();
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throw new RuntimeException(errMsg, ioe);
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}
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} catch (Throwable t){
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log.warn("warning", t);
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}
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} catch (Throwable t) {
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t.printStackTrace();
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}
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@ -244,13 +238,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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// nothing to do
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}
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public static String getAskQueryPath(ServletContext ctx) {
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public static String getAskUpdatedQueryPath(ServletContext ctx) {
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return ctx.getRealPath(ASK_QUERY_FILE);
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}
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public static String getAskEmptyQueryPath(ServletContext ctx) {
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return ctx.getRealPath(ASK_EMPTY_QUERY_FILE);
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}
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private static String timestampedFileName(String prefix, String suffix) {
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