improvement to app metadata setup to avoid null model if empty
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bjl23
parent
4c1bbde7d9
commit
d6f19324f8
1 changed files with 71 additions and 55 deletions
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@ -101,6 +101,9 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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// SDB setup
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// union default graph
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SDB.getContext().set(SDB.unionDefaultGraph, true) ;
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StoreDesc storeDesc = makeStoreDesc();
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setApplicationStoreDesc(storeDesc, sce.getServletContext());
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@ -182,26 +185,24 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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// Application metadata model is cached in memory.
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try {
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Model applicationMetadataModelDB = makeDBModel(bds, JENA_APPLICATION_METADATA_MODEL, DB_ONT_MODEL_SPEC, TripleStoreType.SDB);
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if (applicationMetadataModelDB == null || applicationMetadataModelDB.size() == 0) {
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repairAppMetadataModel(store, aboxAssertions, aboxInferences);
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}
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OntModel applicationMetadataModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
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if (applicationMetadataModelDB != null && applicationMetadataModelDB.size() > 0) {
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long startTime = System.currentTimeMillis();
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System.out.println("Copying cached application metadata model into memory");
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applicationMetadataModel.add(applicationMetadataModelDB);
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System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load application metadata model assertions of size " + applicationMetadataModel.size());
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applicationMetadataModel.getBaseModel().register(new ModelSynchronizer(applicationMetadataModelDB));
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baseOms.setApplicationMetadataModel(applicationMetadataModel);
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inferenceOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
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unionOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
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} else {
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log.error("The application metadata model was not found");
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long startTime = System.currentTimeMillis();
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System.out.println("Copying cached application metadata model into memory");
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applicationMetadataModel.add(applicationMetadataModelDB);
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System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load application metadata model assertions of size " + applicationMetadataModel.size());
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applicationMetadataModel.getBaseModel().register(new ModelSynchronizer(applicationMetadataModelDB));
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if (applicationMetadataModelDB.size() == 0) {
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repairAppMetadataModel(applicationMetadataModel, aboxAssertions, aboxInferences);
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}
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baseOms.setApplicationMetadataModel(applicationMetadataModel);
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inferenceOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
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unionOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
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} catch (Throwable e) {
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log.error("Unable to load application metadata model cache from DB", e);
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}
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@ -498,10 +499,11 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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return;
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}
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private static void repairAppMetadataModel(Store store, Model aboxAssertions, Model aboxInferences) {
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private static void repairAppMetadataModel(Model applicationMetadataModel,
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Model aboxAssertions,
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Model aboxInferences) {
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log.info("Repairing the application metadata model");
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Model applicationMetadataModel = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
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log.info("Moving application metadata from ABox to dedicated model");
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getAppMetadata(aboxAssertions, applicationMetadataModel);
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getAppMetadata(aboxInferences, applicationMetadataModel);
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aboxAssertions.remove(applicationMetadataModel);
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@ -534,46 +536,60 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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store.getTableFormatter().create();
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store.getTableFormatter().truncate();
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// This is a one-time copy of stored KB data - from a Jena RDB store
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// to a Jena SDB store. In the process, we will also separate out the
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// TBox from the Abox; these are in the same graph in pre 1.2 VIVO
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// versions and will now be stored and maintained in separate models
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// Access to the Jena RDB data is through the OntModelSelectors that have
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// been set up earlier in the current session by
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// JenaPersistentDataSourceSetup.java
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// In the code below, note that the current getABoxModel() methods on
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// the OntModelSelectors return a graph with both ABox and TBox data.
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OntModel submodels = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
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readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
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store.getTableFormatter().dropIndexes(); // improve load performance
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Model tboxAssertions = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxAssertions = ModelFactory.createDefaultModel();
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getTBoxModel(memModel, submodels, memTboxAssertions);
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tboxAssertions.add(memTboxAssertions);
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try {
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Model tboxInferences = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxInferences = ModelFactory.createDefaultModel();
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getTBoxModel(inferenceModel, submodels, memTboxInferences);
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tboxInferences.add(memTboxInferences);
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// This is a one-time copy of stored KB data - from a Jena RDB store
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// to a Jena SDB store. In the process, we will also separate out the
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// TBox from the Abox; these are in the same graph in pre 1.2 VIVO
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// versions and will now be stored and maintained in separate models
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// Access to the Jena RDB data is through the OntModelSelectors that have
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// been set up earlier in the current session by
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// JenaPersistentDataSourceSetup.java
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// In the code below, note that the current getABoxModel() methods on
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// the OntModelSelectors return a graph with both ABox and TBox data.
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Model aboxAssertions = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_DB_MODEL);
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copyDifference(memModel, memTboxAssertions, aboxAssertions);
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Model aboxInferences = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_INF_MODEL);
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copyDifference(inferenceModel, memTboxInferences, aboxInferences);
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OntModel submodels = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
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readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
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Model tboxAssertions = SDBFactory.connectNamedModel(
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store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxAssertions = ModelFactory.createDefaultModel();
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getTBoxModel(memModel, submodels, memTboxAssertions);
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tboxAssertions.add(memTboxAssertions);
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Model tboxInferences = SDBFactory.connectNamedModel(
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store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxInferences = ModelFactory.createDefaultModel();
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getTBoxModel(inferenceModel, submodels, memTboxInferences);
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tboxInferences.add(memTboxInferences);
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Model aboxAssertions = SDBFactory.connectNamedModel(
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store, JenaDataSourceSetupBase.JENA_DB_MODEL);
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copyDifference(memModel, memTboxAssertions, aboxAssertions);
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// Set up the application metadata model
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Model applicationMetadataModel = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
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getAppMetadata(memModel, applicationMetadataModel);
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log.info("During initial SDB setup, created an application metadata model of size " + applicationMetadataModel.size());
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// Make sure the reasoner takes into account the newly-set-up data.
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SimpleReasonerSetup.setRecomputeRequired(ctx);
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Model aboxInferences = SDBFactory.connectNamedModel(
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store, JenaDataSourceSetupBase.JENA_INF_MODEL);
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copyDifference(inferenceModel, memTboxInferences, aboxInferences);
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// Set up the application metadata model
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Model applicationMetadataModel = SDBFactory.connectNamedModel(
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store, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
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getAppMetadata(memModel, applicationMetadataModel);
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log.info("During initial SDB setup, created an application metadata model of size "
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+ applicationMetadataModel.size());
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// Make sure the reasoner takes into account the newly-set-up data.
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SimpleReasonerSetup.setRecomputeRequired(ctx);
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} finally {
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store.getTableFormatter().addIndexes();
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}
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}
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/**
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