Bug fix. Fixed regression in the update aspects function UD-287. Also

fixed a bug that the update aspect function didn't update the
modification time of the network.

src/main/java/org/ndexbio/common/models/dao/postgresql/NetworkDAO.java

@@ -390,9 +390,10 @@ public void clearNetworkSummary(UUID networkId, long fileSize) throws SQLExcepti
 	 * @throws NdexException 
 	 * @throws JsonProcessingException 
 	 */
-	public void saveNetworkEntry(NetworkSummary networkSummary, MetaDataCollection metadata) throws SQLException, NdexException, JsonProcessingException {
+	public void saveNetworkEntry(NetworkSummary networkSummary, MetaDataCollection metadata, boolean setModificationTime) throws SQLException, NdexException, JsonProcessingException {
 		String sqlStr = "update network set name = ?, description = ?, version = ?, edgecount=?, nodecount=?, "
 				+ "properties = ? ::jsonb, cxmetadata = ? :: json, warnings = ?, subnetworkids = ?, "
+				+ (setModificationTime? "modification_time = localtimestamp, " : "") 
 				+ " is_validated =true where \"UUID\" = ? and is_deleted = false";
 		try (PreparedStatement pst = db.prepareStatement(sqlStr)) {
 			pst.setString(1,networkSummary.getName());

src/main/java/org/ndexbio/common/persistence/CXNetworkAspectsUpdater.java

@@ -46,10 +46,11 @@ public CXNetworkAspectsUpdater(UUID networkUUID, /*String ownerUserName,*/ Netwo
 	public void update() throws FileNotFoundException, IOException, DuplicateObjectException, ObjectNotFoundException, NdexException, SQLException {
 
 		try (	InputStream inputStream = new FileInputStream(Configuration.getInstance().getNdexRoot() + "/data/" + aspectsCXNetworkID.toString() + "/network.cx") ) {
-			  persistNetworkData(inputStream); 
+			  persistNetworkData(inputStream, true); 
 
 
 			  UUID networkUUID = getNetworkId();
+			  @SuppressWarnings("resource")
 			  NetworkDAO dao = getDAO();
 			  //handle the network properties 
 			  NetworkSummary summary = dao.getNetworkSummaryById(networkUUID);
@@ -65,21 +66,21 @@ public void update() throws FileNotFoundException, IOException, DuplicateObjectE
 			  if ( aspectTable.containsKey(NodesElement.ASPECT_NAME))
 				  summary.setNodeCount((int) aspectTable.get(NodesElement.ASPECT_NAME).getElementCount());
 
-				summary.setModificationTime(new Timestamp(Calendar.getInstance().getTimeInMillis()));
+			  //summary.setModificationTime(new Timestamp(Calendar.getInstance().getTimeInMillis()));
 
-				if ( aspectTable.containsKey(NetworkAttributesElement.ASPECT_NAME)) {
+			  if ( aspectTable.containsKey(NetworkAttributesElement.ASPECT_NAME)) {
 					summary.setProperties(properties);
 					summary.setName(this.networkName);
 					summary.setDescription(this.description);
 					summary.setVersion(this.version);
 					summary.setWarnings(warnings);
-				}
+			   }
 				if ( aspectTable.containsKey(SubNetworkElement.ASPECT_NAME)) {
 					summary.setSubnetworkIds(subNetworkIds);
 				}
 				try {
 				//	dao.saveNetworkEntry(summary, (this.provenanceHistory == null? null: provenanceHistory.getEntity()), metadata);
-					dao.saveNetworkEntry(summary, fullMetaData);
+					dao.saveNetworkEntry(summary, fullMetaData ,true);
 					dao.setFlag(getNetworkId(), "has_layout", fullMetaData.getMetaDataElement(CartesianLayoutElement.ASPECT_NAME)!=null);	
 					dao.commit();
 				} catch (SQLException e) {

src/main/java/org/ndexbio/common/persistence/CXNetworkLoader.java

@@ -146,7 +146,6 @@ public class CXNetworkLoader implements AutoCloseable {
 	private Set<String> indexedFields;
 
 //	protected String updatedBy;
-
 	public CXNetworkLoader(UUID networkUUID, boolean isUpdate, NetworkDAO networkDao, VisibilityType visibility, Set<String> IndexedFields, int sampleGenerationThreshold) {
 		super();
 
@@ -233,7 +232,7 @@ public void persistCXNetwork() throws IOException, DuplicateObjectException, Obj
 
 		  try (	InputStream inputStream = new FileInputStream(Configuration.getInstance().getNdexRoot() + "/data/" + networkId + "/network.cx") ) {
 
-			  persistNetworkData(inputStream); 
+			  persistNetworkData(inputStream, false); 
 
 		//	  logger.info("aspects have been stored.");
 
@@ -259,7 +258,7 @@ public void persistCXNetwork() throws IOException, DuplicateObjectException, Obj
 				summary.setSubnetworkIds(subNetworkIds);
 				try {
 				//	dao.saveNetworkEntry(summary, (this.provenanceHistory == null? null: provenanceHistory.getEntity()), metadata);
-					dao.saveNetworkEntry(summary, metadata);
+					dao.saveNetworkEntry(summary, metadata, false);
 
 					dao.commit();
 				} catch (SQLException e) {
@@ -435,12 +434,14 @@ public void importNetwork() throws IOException, DuplicateObjectException, Object
 
 	/** 
 	 * If it is called from a network import function ( db migrator), we don't remove the provenance entry from the metadata.
+	 * @param  isAspectUpdate set this flag if updating aspects in network. We are not check if node aspect is missing when 
+	 *          this parameter is set to true.
 	 * @throws IOException
 	 * @throws DuplicateObjectException
 	 * @throws NdexException
 	 * @throws ObjectNotFoundException
 	 */
-	protected void persistNetworkData(InputStream in/*, boolean isImport*/)
+	protected void persistNetworkData(InputStream in, boolean isAspectUpdate)
 			throws IOException, DuplicateObjectException, NdexException, ObjectNotFoundException {
 
 		CxElementReader2 cxreader = createCXReader(in);
@@ -529,7 +530,7 @@ protected void persistNetworkData(InputStream in/*, boolean isImport*/)
 
 		  if(metadata !=null) {
 
-			  if (metadata.getMetaDataElement(NodesElement.ASPECT_NAME) == null ) {
+			  if ( !isAspectUpdate && metadata.getMetaDataElement(NodesElement.ASPECT_NAME) == null ) {
 				  throw new NdexException ("Nodes aspect is missing.");
 			  }
 

src/main/java/org/ndexbio/rest/services/NetworkServiceV2.java

@@ -1832,7 +1832,8 @@ public void deleteNetwork(final @PathParam("networkid") String id) throws NdexEx
 					throw new NetworkConcurrentModificationException ();
 				}
 				  throw new NdexException("Can't delete a read-only network.");
-			}	
+			}
+			//TODO: need to check if the network actually exists and give an 404 error for that case.
 			throw new NdexException("Only network owner can delete a network.");	
 		} catch ( IOException e ) {
 			throw new NdexException ("Error occurred when deleting network: " + e.getMessage(), e);