Added ART API for stored model

minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java

@@ -551,9 +551,12 @@ public void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCreatio
 		}
 	}
 
-
 	@Override
 	public OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationException {
+		return loadModelABox(modelId, null);
+	}
+	@Override
+	public OWLOntology loadModelABox(IRI modelId, OWLOntologyManager manager) throws OWLOntologyCreationException {
 		LOG.info("Load model abox: " + modelId + " from database");
 		try {
 			BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();
@@ -568,7 +571,13 @@ public OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationExceptio
 						connection.getStatements(null, null, null, false, new URIImpl(modelId.toString()));
 				//setting minimal to true will give an OWL abox with triples that won't be connected to the tbox, hence e.g. object properties might not be recognized.  
 				boolean minimal = true;
-				OWLOntology abox = loadOntologyDocumentSource(new RioMemoryTripleSource(statements), minimal);
+				OWLOntology abox;
+				if(manager ==null) {
+					abox = loadOntologyDocumentSource(new RioMemoryTripleSource(statements), minimal);
+				} else {
+					abox = loadOntologyDocumentSource(new RioMemoryTripleSource(statements), minimal, manager);
+				}
+
 				statements.close();
 				abox = postLoadFileFilter(abox);
 				return abox;

minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java

@@ -840,6 +840,14 @@ public boolean isModelModified(IRI modelId) {
 	 * @throws OWLOntologyCreationException
 	 */
 	protected abstract OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationException;
+
+	/**
+	 * @param modelId
+	 * @param manager
+	 * @return ontology
+	 * @throws OWLOntologyCreationException
+	 */
+	protected abstract OWLOntology loadModelABox(IRI modelId, OWLOntologyManager manager) throws OWLOntologyCreationException;
 
 	/**
 	 * @param id

minerva-server/.gitignore

@@ -1 +1,2 @@
 target/
+.temp*

minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java

@@ -451,12 +451,14 @@ public static Server startUp(UndoAwareMolecularModelManager models, MinervaStart
 		//		JsonOrJsonpSeedHandler seedHandler = new JsonOrJsonpSeedHandler(models, conf.defaultModelState, conf.golrSeedUrl, ecoMapper );
 	//	SPARQLHandler sparqlHandler = new SPARQLHandler(models, conf.sparqlEndpointTimeout);
 		ModelSearchHandler searchHandler = new ModelSearchHandler(models);
+		ModelARTHandler artHandler = new ModelARTHandler(models, ipc);
+
 		LocalDate d = LocalDate.now();
 		LocalTime t = LocalTime.now(); 
 		String startup = d.toString()+" "+t.toString();
 		StatusHandler statusHandler = new StatusHandler(conf, ont_annos, startup); 
 		TaxonHandler taxonHandler = new TaxonHandler(models);
-		resourceConfig = resourceConfig.registerInstances(batchHandler, searchHandler, statusHandler, taxonHandler);
+		resourceConfig = resourceConfig.registerInstances(batchHandler, searchHandler,artHandler, statusHandler, taxonHandler);
 
 		// setup jetty server port, buffers and context path
 		Server server = new Server();

minerva-server/src/main/java/org/geneontology/minerva/server/handler/ModelARTHandler.java

@@ -0,0 +1,161 @@
+/**
+ * 
+ */
+package org.geneontology.minerva.server.handler;
+
+import static org.geneontology.minerva.server.handler.OperationsTools.createModelRenderer;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.ws.rs.Consumes;
+import javax.ws.rs.FormParam;
+import javax.ws.rs.GET;
+import javax.ws.rs.POST;
+import javax.ws.rs.Path;
+import javax.ws.rs.Produces;
+import javax.ws.rs.QueryParam;
+import javax.ws.rs.core.MediaType;
+
+import org.apache.commons.io.IOUtils;
+import org.geneontology.minerva.BlazegraphMolecularModelManager;
+import org.geneontology.minerva.BlazegraphOntologyManager;
+import org.geneontology.minerva.ModelContainer;
+import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException;
+import org.geneontology.minerva.curie.CurieHandler;
+import org.geneontology.minerva.json.InferenceProvider;
+import org.geneontology.minerva.json.JsonModel;
+import org.geneontology.minerva.json.MolecularModelJsonRenderer;
+import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse;
+import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.ResponseData;
+import org.geneontology.minerva.server.inferences.InferenceProviderCreator;
+import org.openrdf.query.Binding;
+import org.openrdf.query.BindingSet;
+import org.openrdf.query.MalformedQueryException;
+import org.openrdf.query.QueryEvaluationException; 
+import org.openrdf.query.QueryResult;
+import org.openrdf.query.TupleQueryResult;
+import org.openrdf.repository.RepositoryException;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.parameters.OntologyCopy;
+
+import com.google.gson.annotations.SerializedName;
+
+/**
+ * Gets Model readonly data for Annotation Review Tool
+ * Uses Jersey + JSONP
+ *
+ *
+ */
+@Path("/search/stored") //using store endpoint temporarily because thats what barista allows
+public class ModelARTHandler {
+
+	private final BlazegraphMolecularModelManager<?> m3;
+	private final BlazegraphOntologyManager go_lego;
+	private final CurieHandler curieHandler;
+	private final InferenceProviderCreator ipc;
+	/**
+	 * 
+	 */
+	public ModelARTHandler(BlazegraphMolecularModelManager<?> m3, InferenceProviderCreator ipc) {
+		this.m3 = m3;
+		this.go_lego  = m3.getGolego_repo();
+		this.curieHandler = m3.getCuriHandler();
+		this.ipc = ipc;
+	}
+
+	public class ModelARTResult {
+		private String id;
+		private JsonModel storedModel;
+		private JsonModel activeModel;
+		private JsonModel diffModel;
+
+		public String getId() {
+			return id;
+		}
+
+		public void setId(String id) {
+			this.id = id;
+		}
+
+		public void setStoredModel(JsonModel storedModel) {
+			this.storedModel = storedModel;
+		}
+
+		public JsonModel getStoredModel() {
+			return this.storedModel;
+		}
+
+		public void setActiveModel(JsonModel activeModel) {
+			this.activeModel = activeModel;
+		}
+
+		public JsonModel getActiveModel() {
+			return this.activeModel;
+		}
+	}	
+
+
+	@GET
+	@Produces(MediaType.APPLICATION_JSON)
+	public ModelARTResult storedGet(
+			@QueryParam("id") Set<String> id
+			) throws Exception{
+		ModelARTResult result = new ModelARTResult();
+		result = stored(id);
+		return result;
+	}
+
+	public ModelARTResult stored(Set<String> ids) throws Exception {
+		ModelARTResult result = new ModelARTResult();
+
+		for(String mid : ids) {
+			addToModel(mid, result);
+		}		
+
+		return result;
+	}
+
+	private void addToModel(String modelId, ModelARTResult result) throws Exception {
+
+		IRI modelIri = curieHandler.getIRI(modelId);
+		OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+		OWLOntology currentOntology = m3.getModelAbox(modelIri);
+		OWLOntology storedOntology = m3.loadModelABox(modelIri, manager);
+
+		//OWLOntology stored_ontology = man1.copyOntology(storedOntology, OntologyCopy.DEEP);	
+		ModelContainer storedMC = new ModelContainer(modelIri, null, storedOntology);		
+		final MolecularModelJsonRenderer storedRenderer = createModelRenderer(storedMC, go_lego, null, curieHandler);
+		JsonModel jsonStoredModel = storedRenderer.renderModel();			
+
+		ModelContainer activeMC = new ModelContainer(modelIri, null, currentOntology);		
+		InferenceProvider inferenceProvider = ipc.create(activeMC);
+		final MolecularModelJsonRenderer renderer = createModelRenderer(activeMC, go_lego, inferenceProvider, curieHandler);
+		JsonModel jsonActiveModel = renderer.renderModel();	
+
+		result.storedModel = jsonStoredModel;
+		result.activeModel = jsonActiveModel;
+		result.diffModel = getDiff(jsonStoredModel, jsonActiveModel);
+
+	}
+
+	private JsonModel getDiff(JsonModel storedOntology, JsonModel activeOntology) {
+		return new JsonModel();
+	}
+
+}