Merge pull request #242 from geneontology/issue-212-validation-explan…

…ations-1

Added explanations for core shape failures

minerva-core/src/main/java/org/geneontology/minerva/json/InferenceProvider.java

@@ -4,15 +4,15 @@
 
 import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLNamedIndividual;
-import org.geneontology.minerva.server.validation.ModelValidationReport;
+import org.geneontology.minerva.server.validation.ValidationResultSet;
 
 public interface InferenceProvider {
 
 	public boolean isConsistent();
 
 	public Set<OWLClass> getTypes(OWLNamedIndividual i);
 
-	public Set<ModelValidationReport> getValidation_reports();
+	public ValidationResultSet  getValidation_results();
 
 	Set<OWLClass> getAllTypes(OWLNamedIndividual i);
 }

minerva-core/src/main/java/org/geneontology/minerva/server/validation/ValidationResultSet.java

@@ -0,0 +1,5 @@
+package org.geneontology.minerva.server.validation;
+
+public interface ValidationResultSet {
+
+}

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

@@ -348,6 +348,7 @@ public static Server startUp(final MinervaStartUpConfig conf)
 		// set pre and post file handlers
 		models.addPostLoadOntologyFilter(ModelReaderHelper.INSTANCE);
 		conf.shex.tbox_reasoner = models.getTbox_reasoner();
+		conf.shex.curieHandler = conf.curieHandler;
 		// start server
 		Server server = startUp(models, conf);
 		return server;

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

@@ -11,6 +11,7 @@
 import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.ResponseData;
 import org.geneontology.minerva.server.inferences.InferenceProviderCreator;
 import org.geneontology.minerva.server.validation.ModelValidationReport;
+import org.geneontology.minerva.server.validation.ValidationResultSet;
 import org.glassfish.jersey.server.JSONP;
 import org.semanticweb.owlapi.model.OWLObjectProperty;
 
@@ -206,15 +207,9 @@ else if (Entity.meta == entity) {
 			inferenceProvider = inferenceProviderCreator.create(values.model);
 			isConsistent = inferenceProvider.isConsistent();
 			response.setReasoned(true);
-			values.renderBulk = true; // to ensure that all indivuduals are in the response
-			//TODO @goodb fill in explanations for shape and owl validation
-			for(ModelValidationReport report : inferenceProvider.getValidation_reports()) {
-				//if any of the validation tests come back noncomformant, set nonconformant ("something is wrong") flag
-				if(!report.isConformant()) {
-					isConformant = false;
-					break;
-				}
-			}			
+			values.renderBulk = true; // to ensure that all individuals are in the response
+			ValidationResultSet validations = inferenceProvider.getValidation_results();
+			isConformant = validations.allConformant();	
 		}
 
 		// create response.data
@@ -244,8 +239,7 @@ else if (Entity.meta == entity) {
 			response.data.inconsistentFlag =  Boolean.TRUE;
 		}
 		if(!isConformant) {
-			response.data.nonconformantFlag = Boolean.TRUE;
-			response.data.validation_results = inferenceProvider.getValidation_reports();
+			response.data.validation_results = inferenceProvider.getValidation_results();
 		}
 		response.data.modifiedFlag = Boolean.valueOf(values.model.isModified());
 		// These are required for an "okay" response.

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.server.validation.ModelValidationReport;
+import org.geneontology.minerva.server.validation.ValidationResultSet;
 
 import javax.ws.rs.*;
 import java.util.List;
@@ -121,12 +122,9 @@ public static class ResponseData extends JsonModel {
 
 			@SerializedName("sparql-result")
 			public JsonObject sparqlResult;
-
-			@SerializedName("noncomformant-p")
-			public Boolean nonconformantFlag;
 
 			@SerializedName("validation-results")
-			public Set<ModelValidationReport> validation_results;
+			public ValidationResultSet validation_results;
 
 		}
 

minerva-server/src/main/java/org/geneontology/minerva/server/inferences/MapInferenceProvider.java

@@ -21,7 +21,7 @@ public class MapInferenceProvider implements InferenceProvider {
 	private final Map<OWLNamedIndividual, Set<OWLClass>> inferredTypes;
 	private final Map<OWLNamedIndividual, Set<OWLClass>> inferredTypesWithIndirects;
 	//for shex and other validation
-	private Set<ModelValidationReport> validation_reports;
+	private ValidationResultSet validation_results;
 
 	public static InferenceProvider create(OWLReasoner r, OWLOntology ont, ShexValidator shex) {
 		Map<OWLNamedIndividual, Set<OWLClass>> inferredTypes = new HashMap<>();
@@ -50,40 +50,36 @@ public static InferenceProvider create(OWLReasoner r, OWLOntology ont, ShexValid
 				inferredTypesWithIndirects.put(individual, all_inferred);
 			}
 		}
-		//Aim to support multiple validation regimes - e.g. reasoner, shex, gorules
-		Set<ModelValidationReport> all_validation_results = new HashSet<ModelValidationReport>();
 		//reasoner
-		ModelValidationReport reasoner_validation_report = new OWLValidationReport();
-		reasoner_validation_report.setConformant(isConsistent);
+		OWLValidationReport reasoner_validation = new OWLValidationReport();
+		reasoner_validation.setConformant(isConsistent);
 		if(!isConsistent) {
 			Violation i_v = new Violation("id of inconsistent node");
-			i_v.setCommentary("comment about why");
-			reasoner_validation_report.addViolation(i_v);
+			reasoner_validation.addViolation(i_v);
 		}
-		all_validation_results.add(reasoner_validation_report);
+
 		//shex
 		//generate an RDF model
 		Model model = JenaOwlTool.getJenaModel(ont);
 		//add superclasses to types used in model 
 		model = shex.enrichSuperClasses(model);
-		ModelValidationReport validation_report = null;
+		ShexValidationReport shex_validation = null;
 		try {
-			validation_report = shex.createValidationReport(model);
-			if(validation_report!=null) {
-				all_validation_results.add(validation_report);
-			}
+			boolean stream_output_for_debug = true;
+			shex_validation = shex.runShapeMapValidation(model, stream_output_for_debug);
 		} catch (Exception e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}	
-		return new MapInferenceProvider(isConsistent, inferredTypes, inferredTypesWithIndirects, all_validation_results);
+		ValidationResultSet all_validations = new ValidationResultSet(reasoner_validation, shex_validation);
+		return new MapInferenceProvider(isConsistent, inferredTypes, inferredTypesWithIndirects, all_validations);
 	}
 
-	MapInferenceProvider(boolean isConsistent, Map<OWLNamedIndividual, Set<OWLClass>> inferredTypes, Map<OWLNamedIndividual, Set<OWLClass>> inferredTypesWithIndirects, Set<ModelValidationReport> validation_reports) {
+	MapInferenceProvider(boolean isConsistent, Map<OWLNamedIndividual, Set<OWLClass>> inferredTypes, Map<OWLNamedIndividual, Set<OWLClass>> inferredTypesWithIndirects, ValidationResultSet validation_reports) {
 		this.isConsistent = isConsistent;
 		this.inferredTypes = inferredTypes;
 		this.inferredTypesWithIndirects = inferredTypesWithIndirects;
-		this.validation_reports = validation_reports;
+		this.validation_results = validation_reports;
 	}
 
 	@Override
@@ -114,7 +110,9 @@ public Set<OWLClass> getAllTypes(OWLNamedIndividual i) {
 		return result;
 	}
 
-	public Set<ModelValidationReport> getValidation_reports() {
-		return validation_reports;
+	public ValidationResultSet getValidation_results() {
+		return validation_results;
 	}
+
+
 }

minerva-server/src/main/java/org/geneontology/minerva/server/validation/ModelValidationReport.java

@@ -6,14 +6,20 @@
 import java.util.HashSet;
 import java.util.Set;
 
+import com.google.gson.annotations.SerializedName;
+
 /**
  * @author bgood
  *
  */
 public class ModelValidationReport {
 	final String id;
+
+	@SerializedName("is-conformant")
 	boolean conformant;
 	final String tracker;
+
+	@SerializedName("rule-file")
 	final String rulefile;
 	Set<Violation> violations;
 

minerva-server/src/main/java/org/geneontology/minerva/server/validation/ShexConstraint.java

@@ -3,32 +3,53 @@
  */
 package org.geneontology.minerva.server.validation;
 
+import java.util.Set;
+
+import com.google.gson.annotations.SerializedName;
+
 /**
  * @author bgood
  *
  */
 public class ShexConstraint {
-	String property_id;
-	String propery_range;
+	String object;
+	String property;
+
+	@SerializedName("intended-range-shapes")
+	Set<String> intended_range_shapes;
 	/**
 	 * 
 	 */
-	public ShexConstraint(String property_id, String propery_range) {
-		this.property_id = property_id;
-		this.propery_range = propery_range;
+
+
+	public ShexConstraint(String object, String property, Set<String> intended_range_shapes) {
+		super();
+		this.object = object;
+		this.property = property;
+		this.intended_range_shapes = intended_range_shapes;
+	}
+
+	public Set<String> getIntended_range_shapes() {
+		return intended_range_shapes;
+	}
+	public void setIntended_range_shapes(Set<String> intended_range_shapes) {
+		this.intended_range_shapes = intended_range_shapes;
 	}
 
-	public String getProperty_id() {
-		return property_id;
+	public String getObject() {
+		return object;
 	}
-	public void setProperty_id(String property_id) {
-		this.property_id = property_id;
+
+	public void setObject(String object) {
+		this.object = object;
 	}
-	public String getPropery_range() {
-		return propery_range;
+
+	public String getProperty() {
+		return property;
 	}
-	public void setPropery_range(String propery_range) {
-		this.propery_range = propery_range;
+
+	public void setProperty(String property) {
+		this.property = property;
 	}
 
 }

minerva-server/src/main/java/org/geneontology/minerva/server/validation/ShexExplanation.java

@@ -11,19 +11,19 @@
  *
  */
 public class ShexExplanation {
-	String shape_id;
+	String shape;
 	Set<ShexConstraint> constraints;
 	/**
 	 * 
 	 */
 	public ShexExplanation() {
 		constraints = new HashSet<ShexConstraint>();
 	}
-	public String getShape_id() {
-		return shape_id;
+	public String getShape() {
+		return shape;
 	}
-	public void setShape_id(String shape_id) {
-		this.shape_id = shape_id;
+	public void setShape(String shape) {
+		this.shape = shape;
 	}
 	public Set<ShexConstraint> getConstraints() {
 		return constraints;

minerva-server/src/main/java/org/geneontology/minerva/server/validation/ShexValidationReport.java

@@ -15,44 +15,51 @@
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.Resource;
 
+import com.google.gson.annotations.SerializedName;
+
+
 /**
  * @author bgood
  *
  */
 
 public class ShexValidationReport extends ModelValidationReport{
+	@SerializedName("report-type")
 	public static final String report_type_id = "SHEX_CORE_SCHEMA";
 	public static final String tracker = "https://github.com/geneontology/go-shapes/issues";
+
+	@SerializedName("rule-file")
 	public static final String rulefile = "https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex";
 
-	public boolean model_is_valid; 
+	@SerializedName("node-matched-shapes")
 	public Map<String, Set<String>> node_matched_shapes = new HashMap<String, Set<String>>();
-	public Map<String, Set<String>> node_unmatched_shapes = new HashMap<String, Set<String>>();
-	public Map<String, String> node_report = new HashMap<String, String>();
-	public Map<String, Boolean> node_is_valid = new HashMap<String, Boolean>();
-	public String model_report = "";
-	public String model_title = "";
 	/**
 	 * 
 	 */
 	public ShexValidationReport(String id, Model model) {
 		super(id, tracker, rulefile);
-		String q = "select ?cam ?title where {"
-				+ "?cam <http://purl.org/dc/elements/1.1/title> ?title }";
-		//	+ "?cam <"+DC.description.getURI()+"> ?title }";
-		QueryExecution qe = QueryExecutionFactory.create(q, model);
-		ResultSet results = qe.execSelect();
-		if (results.hasNext()) {
-			QuerySolution qs = results.next();
-			Resource model_id_resource = qs.getResource("cam");
-			Literal title = qs.getLiteral("title");
-			if(id==null) {
-				id = model_id_resource.getURI();
-			}
-			model_title = title.getString();
+	}
+
+	public String getAsText() {
+		String report = "report type id = "+report_type_id+"\nrulefile = "+rulefile+"\ntracker = "+tracker+"\n";
+		if(conformant) {
+			report+="No errors detected";
+			return report;
+		}
+		report+=getViolations().size()+" noncomformant nodes detected:\n";
+		for(Violation violation : getViolations()) {
+			report+="node: "+violation.getNode()+" ";
+			ShexViolation sv = (ShexViolation) violation;
+			for(ShexExplanation e : sv.getExplanations()) {
+				report+="was expected to match shape: "+e.shape;
+				report+=" but did not fit the following constraints:";
+				for(ShexConstraint c : e.getConstraints()) {
+					report+="\n\tthe objects of assertions made with "+c.getProperty()+" should be nodes that fit the one of these shapes: ";
+					report+="\n\t\t"+c.getIntended_range_shapes(); 
+					report+="\n\t\tbut, sadly, the object "+c.getObject()+" of one such assertion emanating from the failing node here did not.\n";
+				}
+			}  
 		}
-		qe.close();
-		model_report = "shape id\tnode uri\tvalidation status\n";
+		return report;
 	}
-
 }