Audit module (Change Tracking) (vivo-project#390)

* merged changeset_user_info

* changed default graph uri

* audit code

* Modified audit controller

* Audit controller added user information

* Add listener to RDFService configuration models

* added some filters for audit history

* More filtering options for audit controller

* added user id in audit history table

* Allow only admins to access audit page

* fix for prev commit

* Set default end date to be the next day to avoid empty results

* Removed not implemented AuditDaoFS implementation, added tests for AuditDatTDB

* added example configuration

* Fixed some typos

* Don't show empty changes on audit history page

* fix: release dataset before close

* remove empty test file

* chore: fixed formatting

* Don't delete TDB dataset from temporary directory as it results in test errors on Windows and the directory will be deleted at some point anyway.

* refactored and improved sparql queries

fixes

* style fixes

* fixes

* one more fix

---------

Co-authored-by: Georgy Litvinov <georgy.litvinov@tib.eu>

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/ApplicationImpl.java

@@ -8,6 +8,7 @@
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
+import edu.cornell.mannlib.vitro.webapp.audit.AuditModule;
 import org.apache.jena.ontology.OntDocumentManager;
 
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
@@ -41,6 +42,7 @@ public class ApplicationImpl implements Application {
 	private SearchIndexer searchIndexer;
 	private ImageProcessor imageProcessor;
 	private FileStorage fileStorage;
+	private AuditModule auditModule;
 	private ContentTripleSource contentTripleSource;
 	private ConfigurationTripleSource configurationTripleSource;
 	private TBoxReasonerModule tboxReasonerModule;
@@ -103,6 +105,15 @@ public void setFileStorage(FileStorage fs) {
 		fileStorage = fs;
 	}
 
+	@Override
+	public AuditModule getAuditModule() {
+		return auditModule;
+	}
+
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasAuditModule", minOccurs = 0, maxOccurs = 1)
+	public void setAuditModule(AuditModule am) {
+		auditModule = am;
+	}
 	@Override
 	public ContentTripleSource getContentTripleSource() {
 		return contentTripleSource;
@@ -165,6 +176,11 @@ public void contextInitialized(ServletContextEvent sce) {
 			fileStorage.startup(app, css);
 			ss.info(this, "Started the FileStorage system: " + fileStorage);
 
+			AuditModule auditModule = app.getAuditModule();
+			if (auditModule != null) {
+				auditModule.startup(app, css);
+			}
+
 			ContentTripleSource contentTripleSource = app
 					.getContentTripleSource();
 			contentTripleSource.startup(app, css);
@@ -213,6 +229,11 @@ public void contextDestroyed(ServletContextEvent sce) {
 			app.getFileStorage().shutdown(app);
 			app.getImageProcessor().shutdown(app);
 			app.getSearchEngine().shutdown(app);
+
+			AuditModule auditModule = app.getAuditModule();
+			if (auditModule != null) {
+				auditModule.shutdown(app);
+			}
 		}
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/audit/AbstractListStatementsMethod.java

@@ -0,0 +1,50 @@
+/* $This file is distributed under the terms of the license in LICENSE$ */
+
+package edu.cornell.mannlib.vitro.webapp.audit;
+
+import java.util.List;
+
+import freemarker.ext.beans.StringModel;
+import freemarker.template.SimpleScalar;
+import freemarker.template.TemplateMethodModelEx;
+import freemarker.template.TemplateModelException;
+
+/**
+ * Base helper method for Freemarker
+ */
+public abstract class AbstractListStatementsMethod implements TemplateMethodModelEx {
+    @Override
+    public Object exec(List arguments) throws TemplateModelException {
+        // We expect two arguments
+        // 1 - an AuditChangeSet
+        // 2 - a graph URI
+        if (arguments.size() == 2) {
+            Object arg1 = arguments.get(0);
+            Object arg2 = arguments.get(1);
+
+            // This looks odd, but the AuditChangeSet is wrapped in a StringModel
+            if (arg1 instanceof StringModel) {
+                arg1 = ((StringModel) arg1).getWrappedObject();
+            }
+
+            if (arg1 instanceof AuditChangeSet && arg2 instanceof SimpleScalar) {
+                AuditChangeSet dataset = (AuditChangeSet) arg1;
+                String graphUri = ((SimpleScalar) arg2).getAsString();
+
+                // Get the statements from the changeset for the named graph
+                return getStatements(dataset, graphUri);
+            }
+        }
+
+        throw new TemplateModelException("Wrong arguments");
+    }
+
+    /**
+     * Abstract method to be implemented for Added / Removed statements
+     *
+     * @param dataset
+     * @param graphUri
+     * @return
+     */
+    protected abstract Object getStatements(AuditChangeSet dataset, String graphUri);
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/audit/AuditChangeListener.java

@@ -0,0 +1,63 @@
+/* $This file is distributed under the terms of the license in LICENSE$ */
+
+package edu.cornell.mannlib.vitro.webapp.audit;
+
+import edu.cornell.mannlib.vitro.webapp.audit.storage.AuditDAOFactory;
+import edu.cornell.mannlib.vitro.webapp.audit.storage.AuditVocabulary;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.jena.rdf.listeners.StatementListener;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelChangedListener;
+
+/**
+ * Listener for changes in the RDFService
+ */
+public class AuditChangeListener extends StatementListener implements ModelChangedListener, ChangeListener {
+    private static final Log log = LogFactory.getLog(AuditChangeListener.class);
+
+    @Override
+    public void notifyModelChange(ModelChange modelChange) {
+
+        // Convert the serialized statements into a Jena Model
+        Model changes =
+                RDFServiceUtils.parseModel(modelChange.getSerializedModel(), modelChange.getSerializationFormat());
+
+        // Get the changeset for the current request
+        AuditChangeSet auditChangeset = new AuditChangeSet();
+        Model additions = auditChangeset.getAddedModel(modelChange.getGraphURI());
+
+        String userId = modelChange.getUserId();
+        if (StringUtils.isBlank(userId)) {
+            Exception e = new Exception();
+            log.debug("User id is not provided.", e);
+            userId = AuditVocabulary.RESOURCE_UNKNOWN;
+        }
+        auditChangeset.setUserId(userId);
+
+        // Is the change adding or removing statements?
+        if (modelChange.getOperation() == ModelChange.Operation.REMOVE) {
+            // If we are removing statements, make sure we don't retain them in the additions
+            additions.remove(changes);
+
+            // Record all of the changes in the Model of removed statements
+            Model removed = auditChangeset.getRemovedModel(modelChange.getGraphURI());
+            removed.add(changes);
+        } else {
+            // Record all of the changes in the Model of added statements
+            additions.add(changes);
+        }
+        if (!auditChangeset.isEmpty()) {
+            // Write the changes to the audit store
+            AuditDAOFactory.getAuditDAO().write(auditChangeset);
+        }
+    }
+
+    @Override
+    public void notifyEvent(String graphURI, Object event) {
+    }
+}