Added a basic robot diff operation to minerva m3batchhandler

#356

minerva-core/pom.xml

@@ -82,5 +82,10 @@
     		<artifactId>commons-math3</artifactId>
     		<version>3.6.1</version>
 		</dependency>
+		  	<dependency>
+  			<groupId>org.obolibrary.robot</groupId>
+  			<artifactId>robot-core</artifactId>
+ 			<version>1.7.1</version>
+		</dependency>
 	</dependencies>
 </project>

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

@@ -552,7 +552,7 @@ public void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCreatio
 
 
 	@Override
-	protected OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationException {
+	public OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationException {
 		LOG.info("Load model abox: " + modelId + " from database");
 		try {
 			BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection();

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

@@ -240,6 +240,7 @@ else if (Entity.meta == entity) {
 		if(!isConformant) {
 			response.data.validation_results = inferenceProvider.getValidation_results();
 		}
+		response.data.diffResult = values.diffResult;
 		response.data.modifiedFlag = Boolean.valueOf(values.model.isModified());
 		// These are required for an "okay" response.
 		response.messageType = M3BatchResponse.MESSAGE_TYPE_SUCCESS;

minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java

@@ -4,6 +4,7 @@
 import com.google.gson.annotations.SerializedName;
 import org.geneontology.minerva.json.*;
 import org.geneontology.minerva.validation.ValidationResultSet;
+import org.geneontology.owl.differ.Differ;
 
 import javax.ws.rs.*;
 import java.util.List;
@@ -63,6 +64,9 @@ public static enum Operation {
 		@SerializedName("reset")
 		resetModel,
 
+		@SerializedName("diff")
+		diffModel,
+
 		@SerializedName("update-imports")
 		updateImports,
 
@@ -114,6 +118,10 @@ public static class ResponseData extends JsonModel {
 			@SerializedName("modified-p")
 			public Boolean modifiedFlag;
 
+			//TODO starting out here with raw result from robot
+			@SerializedName("diff-result")
+			public String diffResult;
+
 			public Object undo;
 			public Object redo;
 

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

@@ -24,18 +24,23 @@
 import org.geneontology.minerva.server.handler.M3BatchHandler.Operation;
 import org.geneontology.minerva.server.handler.OperationsTools.MissingParameterException;
 import org.geneontology.minerva.server.validation.BeforeSaveModelValidator;
+import org.geneontology.owl.differ.Differ;
 import org.geneontology.rules.engine.WorkingMemory;
+import org.obolibrary.robot.DiffOperation;
+import org.obolibrary.robot.IOHelper;
 import org.openrdf.query.*;
 import org.openrdf.repository.RepositoryException;
 import org.openrdf.rio.RDFHandlerException;
 import org.openrdf.rio.RDFWriter;
 import org.openrdf.rio.Rio;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.OntologyCopy;
 import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.io.StringWriter;
 import java.util.*;
 
 import static org.geneontology.minerva.server.handler.OperationsTools.requireNotNull;
@@ -78,7 +83,8 @@ static class BatchHandlerValues implements VariableResolver {
 		boolean nonMeta = false;
 		ModelContainer model = null;
 		Map<String, OWLNamedIndividual> individualVariable = new HashMap<>();
-
+		String diffResult = null;
+
 		@Override
 		public boolean notVariable(String id) {
 			return individualVariable.containsKey(id) == false;
@@ -507,6 +513,26 @@ else if (Operation.resetModel == operation) {
 			//reset model values
 			values.model = checkModelId(null, request);
 			values.renderBulk = true;
+		}else if (Operation.diffModel == operation) {
+			values.nonMeta = true;
+			requireNotNull(request.arguments, "request.arguments");
+			//this won't change
+			values.model = checkModelId(values.model, request);
+			IRI model_iri = values.model.getModelId();
+			//run diff
+			OWLOntologyManager man1 = OWLManager.createOWLOntologyManager();
+			OWLOntology active_ontology = man1.copyOntology(values.model.getAboxOntology(), OntologyCopy.DEEP);			
+			OWLOntology stored_ontology = m3.loadModelABox(model_iri);
+			//TODO refine representation of diff result..
+			StringWriter writer = new StringWriter();
+		   // boolean actual = DiffOperation.compare(active_ontology, stored_ontology, writer);
+			Map<String, String> options = new HashMap<>();
+		    options.put("labels", "true");
+		    options.put("format", "html");
+		    DiffOperation.compare(active_ontology, stored_ontology, new IOHelper(), writer, options);
+			values.diffResult = writer.toString();
+			writer.close();
+			values.renderBulk = true;
 		}
 		else if (Operation.undo == operation) {
 			values.nonMeta = true;

minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelEditTest.java

@@ -142,6 +142,16 @@ public void testModelReset() throws Exception {
 		Set<OWLAxiom> mid_axioms = midModel.getABoxAxioms(null);
 		assertFalse(mid_axioms.equals(start_axioms));
 
+		//test diff command for comparison
+		r = new M3Request();
+		r.entity = Entity.model;
+		r.operation = Operation.diffModel;
+		r.arguments = new M3Argument();
+		r.arguments.modelId = modelId;
+		M3BatchResponse diffresp = executeBatch(r);
+		String dr = diffresp.data.diffResult;
+		assertFalse(dr.equals("Ontologies are identical\n"));
+
 		//now reset the model
 		r = new M3Request();
 		r.entity = Entity.model;
@@ -158,6 +168,16 @@ public void testModelReset() throws Exception {
 		OWLOntology endModel = man3.copyOntology(models.getModelAbox(IRI.create(modelId)), OntologyCopy.DEEP);
 		Set<OWLAxiom> end_axioms = endModel.getABoxAxioms(null);
 		assertTrue(start_axioms.equals(end_axioms));
+
+		//test diff command for comparison
+		r = new M3Request();
+		r.entity = Entity.model;
+		r.operation = Operation.diffModel;
+		r.arguments = new M3Argument();
+		r.arguments.modelId = modelId;
+		diffresp = executeBatch(r);
+		dr = diffresp.data.diffResult;
+		assertTrue(dr.equals("Ontologies are identical\n"));
 	}
 
 	@Test