ATLAS-1033: fix for issues flagged by Coverity scan

addons/falcon-bridge/src/main/java/org/apache/atlas/falcon/bridge/FalconBridge.java

@@ -28,6 +28,7 @@ import org.apache.atlas.hive.bridge.HiveMetaStoreBridge;
 import org.apache.atlas.hive.model.HiveDataModelGenerator;
 import org.apache.atlas.hive.model.HiveDataTypes;
 import org.apache.atlas.typesystem.Referenceable;
+import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.falcon.entity.CatalogStorage;
 import org.apache.falcon.entity.FeedHelper;
@@ -284,18 +285,26 @@ public class FalconBridge {
                                                         Feed feed) throws Exception {
         org.apache.falcon.entity.v0.feed.Cluster feedCluster = FeedHelper.getCluster(feed, cluster.getName());
 
-        final CatalogTable table = getTable(feedCluster, feed);
-        if (table != null) {
-            CatalogStorage storage = new CatalogStorage(cluster, table);
-            return createHiveTableInstance(cluster.getName(), storage.getDatabase().toLowerCase(),
-                    storage.getTable().toLowerCase());
-        } else {
-            List<Location> locations = FeedHelper.getLocations(feedCluster, feed);
-            Location dataLocation = FileSystemStorage.getLocation(locations, LocationType.DATA);
-            final String pathUri = normalize(dataLocation.getPath());
-            LOG.info("Registering DFS Path {} ", pathUri);
-            return fillHDFSDataSet(pathUri, cluster.getName());
+        if(feedCluster != null) {
+            final CatalogTable table = getTable(feedCluster, feed);
+            if (table != null) {
+                CatalogStorage storage = new CatalogStorage(cluster, table);
+                return createHiveTableInstance(cluster.getName(), storage.getDatabase().toLowerCase(),
+                        storage.getTable().toLowerCase());
+            } else {
+                List<Location> locations = FeedHelper.getLocations(feedCluster, feed);
+                if (CollectionUtils.isNotEmpty(locations)) {
+                    Location dataLocation = FileSystemStorage.getLocation(locations, LocationType.DATA);
+                    if (dataLocation != null) {
+                        final String pathUri = normalize(dataLocation.getPath());
+                        LOG.info("Registering DFS Path {} ", pathUri);
+                        return fillHDFSDataSet(pathUri, cluster.getName());
+                    }
+                }
+            }
         }
+
+        return null;
     }
 
     private static CatalogTable getTable(org.apache.falcon.entity.v0.feed.Cluster cluster, Feed feed) {

addons/hive-bridge/src/main/java/org/apache/atlas/hive/hook/HiveHook.java

@@ -56,6 +56,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.net.MalformedURLException;
+import java.net.URI;
 import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.Date;
@@ -491,37 +492,42 @@ public class HiveHook extends AtlasHook implements ExecuteWithHookContext {
             table = partition.getTable();
             db = dgiBridge.hiveClient.getDatabase(table.getDbName());
             break;
+
+        default:
+            LOG.info("{}: entity-type not handled by Atlas hook. Ignored", entity.getType());
         }
 
-        db = dgiBridge.hiveClient.getDatabase(db.getName());
-        Referenceable dbEntity = dgiBridge.createDBInstance(db);
+        if (db != null) {
+            db = dgiBridge.hiveClient.getDatabase(db.getName());
+            Referenceable dbEntity = dgiBridge.createDBInstance(db);
 
-        entities.add(dbEntity);
-        result.put(Type.DATABASE, dbEntity);
+            entities.add(dbEntity);
+            result.put(Type.DATABASE, dbEntity);
 
-        Referenceable tableEntity = null;
+            Referenceable tableEntity = null;
 
-        if (table != null) {
-            if (existTable != null) {
-                table = existTable;
-            } else {
-                table = dgiBridge.hiveClient.getTable(table.getDbName(), table.getTableName());
+            if (table != null) {
+                if (existTable != null) {
+                    table = existTable;
+                } else {
+                    table = dgiBridge.hiveClient.getTable(table.getDbName(), table.getTableName());
+                }
+                //If its an external table, even though the temp table skip flag is on,
+                // we create the table since we need the HDFS path to temp table lineage.
+                if (skipTempTables &&
+                        table.isTemporary() &&
+                        !TableType.EXTERNAL_TABLE.equals(table.getTableType())) {
+                    LOG.debug("Skipping temporary table registration {} since it is not an external table {} ", table.getTableName(), table.getTableType().name());
+
+                } else {
+                    tableEntity = dgiBridge.createTableInstance(dbEntity, table);
+                    entities.add(tableEntity);
+                    result.put(Type.TABLE, tableEntity);
+                }
             }
-            //If its an external table, even though the temp table skip flag is on,
-            // we create the table since we need the HDFS path to temp table lineage.
-            if (skipTempTables &&
-                table.isTemporary() &&
-                !TableType.EXTERNAL_TABLE.equals(table.getTableType())) {
-                LOG.debug("Skipping temporary table registration {} since it is not an external table {} ", table.getTableName(), table.getTableType().name());
 
-            } else {
-                tableEntity = dgiBridge.createTableInstance(dbEntity, table);
-                entities.add(tableEntity);
-                result.put(Type.TABLE, tableEntity);
-            }
+            event.addMessage(new HookNotification.EntityUpdateRequest(event.getUser(), entities));
         }
-
-        event.addMessage(new HookNotification.EntityUpdateRequest(event.getUser(), entities));
         return result;
     }
 
@@ -620,13 +626,16 @@ public class HiveHook extends AtlasHook implements ExecuteWithHookContext {
                 entities.addAll(result.values());
             }
         } else if (entity.getType() == Type.DFS_DIR) {
-            final String pathUri = lower(new Path(entity.getLocation()).toString());
-            LOG.debug("Registering DFS Path {} ", pathUri);
-            if (!dataSetsProcessed.contains(pathUri)) {
-                Referenceable hdfsPath = dgiBridge.fillHDFSDataSet(pathUri);
-                dataSets.put(entity, hdfsPath);
-                dataSetsProcessed.add(pathUri);
-                entities.add(hdfsPath);
+            URI location = entity.getLocation();
+            if(location != null) {
+                final String pathUri = lower(new Path(location).toString());
+                LOG.debug("Registering DFS Path {} ", pathUri);
+                if (!dataSetsProcessed.contains(pathUri)) {
+                    Referenceable hdfsPath = dgiBridge.fillHDFSDataSet(pathUri);
+                    dataSets.put(entity, hdfsPath);
+                    dataSetsProcessed.add(pathUri);
+                    entities.add(hdfsPath);
+                }
             }
         }
     }
@@ -666,13 +675,17 @@ public class HiveHook extends AtlasHook implements ExecuteWithHookContext {
     private void handleExternalTables(final HiveMetaStoreBridge dgiBridge, final HiveEventContext event, final LinkedHashMap<Type, Referenceable> tables) throws HiveException, MalformedURLException {
         List<Referenceable> entities = new ArrayList<>();
         final WriteEntity hiveEntity = (WriteEntity) getEntityByType(event.getOutputs(), Type.TABLE);
-        Table hiveTable = hiveEntity.getTable();
+
+        Table hiveTable = hiveEntity == null ? null : hiveEntity.getTable();
+
         //Refresh to get the correct location
-        hiveTable = dgiBridge.hiveClient.getTable(hiveTable.getDbName(), hiveTable.getTableName());
+        if(hiveTable != null) {
+            hiveTable = dgiBridge.hiveClient.getTable(hiveTable.getDbName(), hiveTable.getTableName());
+        }
 
-        final String location = lower(hiveTable.getDataLocation().toString());
         if (hiveTable != null && TableType.EXTERNAL_TABLE.equals(hiveTable.getTableType())) {
             LOG.info("Registering external table process {} ", event.getQueryStr());
+            final String location = lower(hiveTable.getDataLocation().toString());
             final ReadEntity dfsEntity = new ReadEntity();
             dfsEntity.setTyp(Type.DFS_DIR);
             dfsEntity.setName(location);
@@ -702,6 +715,7 @@ public class HiveHook extends AtlasHook implements ExecuteWithHookContext {
             entities.add(processReferenceable);
             event.addMessage(new HookNotification.EntityUpdateRequest(event.getUser(), entities));
         }
+
     }
 
     private boolean isCreateOp(HiveEventContext hiveEvent) {

authorization/src/main/java/org/apache/atlas/authorize/simple/PolicyParser.java

@@ -161,12 +161,7 @@ public class PolicyParser {
                 if (def.getUsers() != null) {
                     usersMap = def.getUsers();
                 }
-                List<AtlasActionTypes> userAutorities = usersMap.get(userAndRole[USERNAME]);
-                if (userAutorities == null) {
-
-                    userAutorities = new ArrayList<AtlasActionTypes>();
-                }
-                userAutorities = getListOfAutorities(userAndRole[USER_AUTHORITIES]);
+                List<AtlasActionTypes> userAutorities = getListOfAutorities(userAndRole[USER_AUTHORITIES]);
                 usersMap.put(userAndRole[USERNAME], userAutorities);
                 def.setUsers(usersMap);
             }
@@ -195,11 +190,7 @@ public class PolicyParser {
                 if (def.getGroups() != null) {
                     groupsMap = def.getGroups();
                 }
-                List<AtlasActionTypes> groupAutorities = groupsMap.get(groupAndRole[GROUPNAME]);
-                if (groupAutorities == null) {
-                    groupAutorities = new ArrayList<AtlasActionTypes>();
-                }
-                groupAutorities = getListOfAutorities(groupAndRole[GROUP_AUTHORITIES]);
+                List<AtlasActionTypes> groupAutorities = getListOfAutorities(groupAndRole[GROUP_AUTHORITIES]);
                 groupsMap.put(groupAndRole[GROUPNAME], groupAutorities);
                 def.setGroups(groupsMap);
             }

authorization/src/main/java/org/apache/atlas/authorize/simple/SimpleAtlasAuthorizer.java

@@ -32,6 +32,7 @@ import org.apache.atlas.authorize.AtlasAuthorizationException;
 import org.apache.atlas.authorize.AtlasAuthorizer;
 import org.apache.atlas.authorize.AtlasResourceTypes;
 import org.apache.atlas.utils.PropertiesUtil;
+import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.configuration.Configuration;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.IOCase;
@@ -224,10 +225,12 @@ public final class SimpleAtlasAuthorizer implements AtlasAuthorizer {
             LOG.debug("==> SimpleAtlasAuthorizer checkAccessForGroups");
         }
 
-        for (String group : groups) {
-            isAccessAllowed = checkAccess(group, resourceType, resource, map);
-            if (isAccessAllowed) {
-                break;
+        if(CollectionUtils.isNotEmpty(groups)) {
+            for (String group : groups) {
+                isAccessAllowed = checkAccess(group, resourceType, resource, map);
+                if (isAccessAllowed) {
+                    break;
+                }
             }
         }
 

client/src/main/java/org/apache/atlas/AtlasClient.java

@@ -144,8 +144,15 @@ public class AtlasClient {
 
     // New constuctor for Basic auth
     public AtlasClient(String[] baseUrl, String[] basicAuthUserNamepassword) {
-        this.basicAuthUser = basicAuthUserNamepassword[0];
-        this.basicAuthPassword = basicAuthUserNamepassword[1];
+        if (basicAuthUserNamepassword != null) {
+            if (basicAuthUserNamepassword.length > 0) {
+                this.basicAuthUser = basicAuthUserNamepassword[0];
+            }
+            if (basicAuthUserNamepassword.length > 1) {
+                this.basicAuthPassword = basicAuthUserNamepassword[1];
+            }
+        }
+
         initializeState(baseUrl, null, null);
     }
 
@@ -1119,7 +1126,8 @@ public class AtlasClient {
     private JSONObject callAPIWithResource(API api, WebResource resource, Object requestObject)
         throws AtlasServiceException {
         ClientResponse clientResponse = null;
-        for (int i = 0; i < getNumberOfRetries(); i++) {
+        int i = 0;
+        do {
             clientResponse = resource.accept(JSON_MEDIA_TYPE).type(JSON_MEDIA_TYPE)
                 .method(api.getMethod(), ClientResponse.class, requestObject);
 
@@ -1137,7 +1145,9 @@ public class AtlasClient {
                 LOG.error("Got a service unavailable when calling: {}, will retry..", resource);
                 sleepBetweenRetries();
             }
-        }
+
+            i++;
+        } while (i < getNumberOfRetries());
 
         throw new AtlasServiceException(api, clientResponse);
     }

client/src/main/java/org/apache/atlas/AtlasServiceException.java

@@ -37,8 +37,8 @@ public class AtlasServiceException extends Exception {
     }
 
     private AtlasServiceException(AtlasClient.API api, ClientResponse.Status status, String response) {
-        super("Metadata service API " + api + " failed with status " + status.getStatusCode() + "(" +
-                status.getReasonPhrase() + ") Response Body (" + response + ")");
+        super("Metadata service API " + api + " failed with status " + (status != null ? status.getStatusCode() : -1)
+                + " (" + status + ") Response Body (" + response + ")");
         this.status = status;
     }
 

common/src/main/java/org/apache/atlas/utils/ParamChecker.java

@@ -139,20 +139,6 @@ public final class ParamChecker {
     }
 
     /**
-     * Check that a list is not null and that none of its elements is null. If null or if the list has emtpy elements
-     * throws an IllegalArgumentException.
-     *  @param list the list of strings.
-     * @param name parameter name for the exception message.
-     */
-    public static Collection<String> notEmptyElements(Collection<String> list, String name) {
-        notEmpty(list, name);
-        for (String ele : list) {
-            notEmpty(ele, String.format("list %s element %s", name, ele));
-        }
-        return list;
-    }
-
-    /**
      * Checks that the given value is <= max value.
      * @param value
      * @param maxValue

notification/src/main/java/org/apache/atlas/hook/FailedMessagesLogger.java

@@ -77,13 +77,15 @@ public class FailedMessagesLogger {
         org.apache.log4j.Logger rootLogger = org.apache.log4j.Logger.getRootLogger();
 
         Enumeration allAppenders = rootLogger.getAllAppenders();
-        while (allAppenders.hasMoreElements()) {
-            Appender appender = (Appender) allAppenders.nextElement();
-            if (appender instanceof FileAppender) {
-                FileAppender fileAppender = (FileAppender) appender;
-                String rootLoggerFile = fileAppender.getFile();
-                rootLoggerDirectory = new File(rootLoggerFile).getParent();
-                break;
+        if (allAppenders != null) {
+            while (allAppenders.hasMoreElements()) {
+                Appender appender = (Appender) allAppenders.nextElement();
+                if (appender instanceof FileAppender) {
+                    FileAppender fileAppender = (FileAppender) appender;
+                    String rootLoggerFile = fileAppender.getFile();
+                    rootLoggerDirectory = new File(rootLoggerFile).getParent();
+                    break;
+                }
             }
         }
         return rootLoggerDirectory;

release-log.txt

@@ -6,6 +6,7 @@ INCOMPATIBLE CHANGES:
 
 
 ALL CHANGES:
+ATLAS-1033 fix for issues flagged by Coverity scan (mneethiraj via sumasai)
 ATLAS-1036 Compilation error on java 1.8 - GraphBackedDiscoveryService (shwethags via sumasai)
 ATLAS-1034 Incorrect Falcon hook impl class name in Falcon hook shim (mneethiraj via shwethags)
 ATLAS-347 Atlas search APIs should allow pagination of results (shwethags)

repository/src/main/java/org/apache/atlas/discovery/DataSetLineageService.java

@@ -101,7 +101,7 @@ public class DataSetLineageService implements LineageService {
     @GraphTransaction
     public String getOutputsGraph(String datasetName) throws AtlasException {
         LOG.info("Fetching lineage outputs graph for datasetName={}", datasetName);
-        ParamChecker.notEmpty(datasetName, "dataset name");
+        datasetName = ParamChecker.notEmpty(datasetName, "dataset name");
         ReferenceableInstance datasetInstance = validateDatasetNameExists(datasetName);
         return getOutputsGraphForId(datasetInstance.getId()._getId());
     }
@@ -116,7 +116,7 @@ public class DataSetLineageService implements LineageService {
     @GraphTransaction
     public String getInputsGraph(String tableName) throws AtlasException {
         LOG.info("Fetching lineage inputs graph for tableName={}", tableName);
-        ParamChecker.notEmpty(tableName, "table name");
+        tableName = ParamChecker.notEmpty(tableName, "table name");
         ReferenceableInstance datasetInstance = validateDatasetNameExists(tableName);
         return getInputsGraphForId(datasetInstance.getId()._getId());
     }
@@ -125,7 +125,7 @@ public class DataSetLineageService implements LineageService {
     @GraphTransaction
     public String getInputsGraphForEntity(String guid) throws AtlasException {
         LOG.info("Fetching lineage inputs graph for entity={}", guid);
-        ParamChecker.notEmpty(guid, "Entity id");
+        guid = ParamChecker.notEmpty(guid, "Entity id");
         validateDatasetExists(guid);
         return getInputsGraphForId(guid);
     }
@@ -143,7 +143,7 @@ public class DataSetLineageService implements LineageService {
     @GraphTransaction
     public String getOutputsGraphForEntity(String guid) throws AtlasException {
         LOG.info("Fetching lineage outputs graph for entity guid={}", guid);
-        ParamChecker.notEmpty(guid, "Entity id");
+        guid = ParamChecker.notEmpty(guid, "Entity id");
         validateDatasetExists(guid);
         return getOutputsGraphForId(guid);
     }
@@ -165,7 +165,7 @@ public class DataSetLineageService implements LineageService {
     @Override
     @GraphTransaction
     public String getSchema(String datasetName) throws AtlasException {
-        ParamChecker.notEmpty(datasetName, "table name");
+        datasetName = ParamChecker.notEmpty(datasetName, "table name");
         LOG.info("Fetching schema for tableName={}", datasetName);
         ReferenceableInstance datasetInstance = validateDatasetNameExists(datasetName);
 
@@ -182,7 +182,7 @@ public class DataSetLineageService implements LineageService {
     @Override
     @GraphTransaction
     public String getSchemaForEntity(String guid) throws AtlasException {
-        ParamChecker.notEmpty(guid, "Entity id");
+        guid = ParamChecker.notEmpty(guid, "Entity id");
         LOG.info("Fetching schema for entity guid={}", guid);
         String typeName = validateDatasetExists(guid);
         return getSchemaForId(typeName, guid);

repository/src/main/java/org/apache/atlas/discovery/graph/GraphBackedDiscoveryService.java

@@ -167,6 +167,11 @@ public class GraphBackedDiscoveryService implements DiscoveryService {
         LOG.info("Executing gremlin query={}", gremlinQuery);
         ScriptEngineManager manager = new ScriptEngineManager();
         ScriptEngine engine = manager.getEngineByName("gremlin-groovy");
+
+        if(engine == null) {
+            throw new DiscoveryException("gremlin-groovy: engine not found");
+        }
+
         Bindings bindings = engine.createBindings();
         bindings.put("g", titanGraph);
 

repository/src/main/java/org/apache/atlas/repository/graph/DeleteHandler.java

@@ -334,28 +334,29 @@ public abstract class DeleteHandler {
                     String keyPropertyName = GraphHelper.getQualifiedNameForMapKey(propertyName, key);
                     String mapEdgeId = GraphHelper.getProperty(outVertex, keyPropertyName);
                     Edge mapEdge = graphHelper.getEdgeByEdgeId(outVertex, keyPropertyName, mapEdgeId);
-                    Vertex mapVertex = mapEdge.getVertex(Direction.IN);
-                    if (mapVertex.getId().toString().equals(inVertex.getId().toString())) {
-                        //TODO keys.size includes deleted items as well. should exclude
-                        if (attributeInfo.multiplicity.nullAllowed() || keys.size() > attributeInfo.multiplicity.lower) {
-                            edge = mapEdge;
-                        }
-                        else {
-                            // Deleting this entry would violate the attribute's lower bound.
-                            throw new NullRequiredAttributeException(
-                                "Cannot remove map entry " + keyPropertyName + " from required attribute " +
-                                    GraphHelper.getQualifiedFieldName(type, attributeName) + " on " + string(outVertex) + " " + string(mapEdge));
-                        }
-
-                        if (shouldUpdateReverseAttribute) {
-                            //remove this key
-                            LOG.debug("Removing edge {}, key {} from the map attribute {}", string(mapEdge), key,
-                                    attributeName);
-                            keys.remove(key);
-                            GraphHelper.setProperty(outVertex, propertyName, keys);
-                            GraphHelper.setProperty(outVertex, keyPropertyName, null);
+                    if(mapEdge != null) {
+                        Vertex mapVertex = mapEdge.getVertex(Direction.IN);
+                        if (mapVertex.getId().toString().equals(inVertex.getId().toString())) {
+                            //TODO keys.size includes deleted items as well. should exclude
+                            if (attributeInfo.multiplicity.nullAllowed() || keys.size() > attributeInfo.multiplicity.lower) {
+                                edge = mapEdge;
+                            } else {
+                                // Deleting this entry would violate the attribute's lower bound.
+                                throw new NullRequiredAttributeException(
+                                        "Cannot remove map entry " + keyPropertyName + " from required attribute " +
+                                                GraphHelper.getQualifiedFieldName(type, attributeName) + " on " + string(outVertex) + " " + string(mapEdge));
+                            }
+
+                            if (shouldUpdateReverseAttribute) {
+                                //remove this key
+                                LOG.debug("Removing edge {}, key {} from the map attribute {}", string(mapEdge), key,
+                                        attributeName);
+                                keys.remove(key);
+                                GraphHelper.setProperty(outVertex, propertyName, keys);
+                                GraphHelper.setProperty(outVertex, keyPropertyName, null);
+                            }
+                            break;
                         }
-                        break;
                     }
                 }
             }

repository/src/main/java/org/apache/atlas/repository/graph/GraphBackedMetadataRepository.java

@@ -268,11 +268,13 @@ public class GraphBackedMetadataRepository implements MetadataRepository {
             final String entityTypeName = GraphHelper.getTypeName(instanceVertex);
             String relationshipLabel = GraphHelper.getTraitLabel(entityTypeName, traitNameToBeDeleted);
             Edge edge = GraphHelper.getEdgeForLabel(instanceVertex, relationshipLabel);
-            deleteHandler.deleteEdgeReference(edge, DataTypes.TypeCategory.TRAIT, false, true);
+            if(edge != null) {
+                deleteHandler.deleteEdgeReference(edge, DataTypes.TypeCategory.TRAIT, false, true);
 
-            // update the traits in entity once trait removal is successful
-            traitNames.remove(traitNameToBeDeleted);
-            updateTraits(instanceVertex, traitNames);
+                // update the traits in entity once trait removal is successful
+                traitNames.remove(traitNameToBeDeleted);
+                updateTraits(instanceVertex, traitNames);
+            }
         } catch (Exception e) {
             throw new RepositoryException(e);
         }

repository/src/main/java/org/apache/atlas/repository/graph/GraphHelper.java

@@ -429,20 +429,28 @@ public final class GraphHelper {
     }
 
     public static String string(Vertex vertex) {
-        if (LOG.isDebugEnabled()) {
-            return String.format("vertex[id=%s type=%s guid=%s]", vertex.getId().toString(), getTypeName(vertex),
-                    getIdFromVertex(vertex));
+        if(vertex == null) {
+            return "vertex[null]";
         } else {
-            return String.format("vertex[id=%s]", vertex.getId().toString());
+            if (LOG.isDebugEnabled()) {
+                return String.format("vertex[id=%s type=%s guid=%s]", vertex.getId().toString(), getTypeName(vertex),
+                        getIdFromVertex(vertex));
+            } else {
+                return String.format("vertex[id=%s]", vertex.getId().toString());
+            }
         }
     }
 
     public static String string(Edge edge) {
-        if (LOG.isDebugEnabled()) {
-            return String.format("edge[id=%s label=%s from %s -> to %s]", edge.getId().toString(), edge.getLabel(),
-                    string(edge.getVertex(Direction.OUT)), string(edge.getVertex(Direction.IN)));
+        if(edge == null) {
+            return "edge[null]";
         } else {
-            return String.format("edge[id=%s]", edge.getId().toString());
+            if (LOG.isDebugEnabled()) {
+                return String.format("edge[id=%s label=%s from %s -> to %s]", edge.getId().toString(), edge.getLabel(),
+                        string(edge.getVertex(Direction.OUT)), string(edge.getVertex(Direction.IN)));
+            } else {
+                return String.format("edge[id=%s]", edge.getId().toString());
+            }
         }
     }
 

repository/src/main/java/org/apache/atlas/repository/graph/TypedInstanceToGraphMapper.java

@@ -370,10 +370,12 @@ public final class TypedInstanceToGraphMapper {
                 if (!cloneElements.isEmpty()) {
                     for (String edgeIdForDelete : cloneElements) {
                         Edge edge = graphHelper.getEdgeByEdgeId(instanceVertex, edgeLabel, edgeIdForDelete);
-                        boolean deleted = deleteHandler.deleteEdgeReference(edge, entryType.getTypeCategory(),
-                                attributeInfo.isComposite, true);
-                        if (!deleted) {
-                            additionalElements.add(edgeIdForDelete);
+                        if(edge != null) {
+                            boolean deleted = deleteHandler.deleteEdgeReference(edge, entryType.getTypeCategory(),
+                                    attributeInfo.isComposite, true);
+                            if (!deleted) {
+                                additionalElements.add(edgeIdForDelete);
+                            }
                         }
                     }
                 }
@@ -454,11 +456,13 @@ public final class TypedInstanceToGraphMapper {
                 if (!newMap.values().contains(currentEdge)) {
                     String edgeLabel = GraphHelper.getQualifiedNameForMapKey(propertyName, currentKey);
                     Edge edge = graphHelper.getEdgeByEdgeId(instanceVertex, edgeLabel, currentMap.get(currentKey));
-                    boolean deleted =
-                            deleteHandler.deleteEdgeReference(edge, elementType.getTypeCategory(), attributeInfo.isComposite, true);
-                    if (!deleted) {
-                        additionalMap.put(currentKey, currentEdge);
-                        shouldDeleteKey = false;
+                    if(edge != null) {
+                        boolean deleted =
+                                deleteHandler.deleteEdgeReference(edge, elementType.getTypeCategory(), attributeInfo.isComposite, true);
+                        if (!deleted) {
+                            additionalMap.put(currentKey, currentEdge);
+                            shouldDeleteKey = false;
+                        }
                     }
                 }
             }
@@ -702,7 +706,9 @@ public final class TypedInstanceToGraphMapper {
         } else if (attributeInfo.dataType() == DataTypes.DATE_TYPE) {
             final Date dateVal = typedInstance.getDate(attributeInfo.name);
             //Convert Property value to Long  while persisting
-            propertyValue = dateVal.getTime();
+            if(dateVal != null) {
+                propertyValue = dateVal.getTime();
+            }
         } else if (attributeInfo.dataType().getTypeCategory() == DataTypes.TypeCategory.ENUM) {
             if (attrValue != null) {
                 propertyValue = ((EnumValue)attrValue).value;

repository/src/main/java/org/apache/atlas/repository/typestore/GraphBackedTypeStore.java

@@ -168,16 +168,20 @@ public class GraphBackedTypeStore implements ITypeStore {
         switch (attrDataType.getTypeCategory()) {
         case ARRAY:
             String attrType = TypeUtils.parseAsArrayType(attrDataType.getName());
-            IDataType elementType = typeSystem.getDataType(IDataType.class, attrType);
-            attrDataTypes.add(elementType);
+            if(attrType != null) {
+                IDataType elementType = typeSystem.getDataType(IDataType.class, attrType);
+                attrDataTypes.add(elementType);
+            }
             break;
 
         case MAP:
             String[] attrTypes = TypeUtils.parseAsMapType(attrDataType.getName());
-            IDataType keyType = typeSystem.getDataType(IDataType.class, attrTypes[0]);
-            IDataType valueType = typeSystem.getDataType(IDataType.class, attrTypes[1]);
-            attrDataTypes.add(keyType);
-            attrDataTypes.add(valueType);
+            if(attrTypes != null && attrTypes.length > 1) {
+                IDataType keyType = typeSystem.getDataType(IDataType.class, attrTypes[0]);
+                IDataType valueType = typeSystem.getDataType(IDataType.class, attrTypes[1]);
+                attrDataTypes.add(keyType);
+                attrDataTypes.add(valueType);
+            }
             break;
 
         case ENUM:

titan/src/main/java/com/thinkaurelius/titan/diskstorage/hbase/HBaseKeyColumnValueStore.java

@@ -330,18 +330,19 @@ public class HBaseKeyColumnValueStore implements KeyColumnValueStore {
             ensureOpen();
 
             return new RecordIterator<Entry>() {
-                private final Iterator<Map.Entry<byte[], NavigableMap<Long, byte[]>>> kv = currentRow.getMap().get(columnFamilyBytes).entrySet().iterator();
+                private final NavigableMap<byte[], NavigableMap<byte[], NavigableMap<Long, byte[]>>> currentMap = currentRow.getMap();
+                private final Iterator<Map.Entry<byte[], NavigableMap<Long, byte[]>>> kv = currentMap == null ? null : currentMap.get(columnFamilyBytes).entrySet().iterator();
 
                 @Override
                 public boolean hasNext() {
                     ensureOpen();
-                    return kv.hasNext();
+                    return kv == null ? false : kv.hasNext();
                 }
 
                 @Override
                 public Entry next() {
                     ensureOpen();
-                    return StaticArrayEntry.ofBytes(kv.next(), entryGetter);
+                    return kv == null ? null : StaticArrayEntry.ofBytes(kv.next(), entryGetter);
                 }
 
                 @Override

typesystem/src/main/java/org/apache/atlas/typesystem/persistence/Id.java

@@ -45,9 +45,9 @@ public class Id implements ITypedReferenceableInstance {
     public EntityState state;
 
     public Id(String id, int version, String typeName, String state) {
-        ParamChecker.notEmpty(id, "id");
-        ParamChecker.notEmpty(typeName, "typeName");
-        ParamChecker.notEmptyIfNotNull(state, "state");
+        id       = ParamChecker.notEmpty(id, "id");
+        typeName = ParamChecker.notEmpty(typeName, "typeName");
+        state    = ParamChecker.notEmptyIfNotNull(state, "state");
         this.id = id;
         this.typeName = typeName;
         this.version = version;

typesystem/src/main/java/org/apache/atlas/typesystem/types/AbstractDataType.java

@@ -47,12 +47,18 @@ abstract class AbstractDataType<T> implements IDataType<T> {
 
     @Override
     public void output(T val, Appendable buf, String prefix, Set<T> inProcess) throws AtlasException {
-        if (val instanceof Map) {
+        final String strValue;
+
+        if (val == null) {
+            strValue = "<null>";
+        } else if (val instanceof Map) {
             ImmutableSortedMap immutableSortedMap = ImmutableSortedMap.copyOf((Map) val);
-            TypeUtils.outputVal(val == null ? "<null>" : immutableSortedMap.toString(), buf, prefix);
+            strValue = immutableSortedMap.toString();
         } else {
-            TypeUtils.outputVal(val == null ? "<null>" : val.toString(), buf, prefix);
+            strValue = val.toString();
         }
+
+        TypeUtils.outputVal(strValue, buf, prefix);
     }
 
     @Override

typesystem/src/main/java/org/apache/atlas/typesystem/types/HierarchicalType.java

@@ -517,17 +517,20 @@ public abstract class HierarchicalType<ST extends HierarchicalType, T> extends A
         @Override
         public Path next() {
             Path p = pathQueue.poll();
-            ST t = null;
-            try {
-                t = (ST) typeSystem.getDataType(superTypeClass, p.typeName);
-            } catch (AtlasException me) {
-                throw new RuntimeException(me);
-            }
-            if (t.superTypes != null) {
-                ImmutableSet<String> sTs = t.superTypes;
-                for (String sT : sTs) {
-                    String nm = sT + "." + p.pathName;
-                    pathQueue.add(pathNameToPathMap.get(nm));
+
+            if(p != null) {
+                ST t = null;
+                try {
+                    t = (ST) typeSystem.getDataType(superTypeClass, p.typeName);
+                } catch (AtlasException me) {
+                    throw new RuntimeException(me);
+                }
+                if (t.superTypes != null) {
+                    ImmutableSet<String> sTs = t.superTypes;
+                    for (String sT : sTs) {
+                        String nm = sT + "." + p.pathName;
+                        pathQueue.add(pathNameToPathMap.get(nm));
+                    }
                 }
             }
             return p;

typesystem/src/main/java/org/apache/atlas/typesystem/types/ObjectGraphTraversal.java

@@ -172,7 +172,9 @@ public class ObjectGraphTraversal implements Iterator<ObjectGraphTraversal.Insta
     public InstanceTuple next() {
         try {
             InstanceTuple t = queue.poll();
-            processReferenceableInstance(t.instance);
+            if(t != null) {
+                processReferenceableInstance(t.instance);
+            }
             return t;
         } catch (AtlasException me) {
             throw new RuntimeException(me);

typesystem/src/main/java/org/apache/atlas/typesystem/types/ObjectGraphWalker.java

@@ -76,7 +76,9 @@ public class ObjectGraphWalker {
     public void walk() throws AtlasException {
         while (!queue.isEmpty()) {
             IReferenceableInstance r = queue.poll();
-            processReferenceableInstance(r);
+            if(r != null) {
+                processReferenceableInstance(r);
+            }
         }
     }
 

webapp/src/main/java/org/apache/atlas/Atlas.java

@@ -147,9 +147,12 @@ public final class Atlas {
     }
 
     static int getApplicationPort(CommandLine cmd, String enableTLSFlag, Configuration configuration) {
+        String optionValue = cmd.hasOption(APP_PORT) ? cmd.getOptionValue(APP_PORT) : null;
+
         final int appPort;
-        if (cmd.hasOption(APP_PORT)) {
-            appPort = Integer.valueOf(cmd.getOptionValue(APP_PORT));
+
+        if (StringUtils.isNotEmpty(optionValue)) {
+            appPort = Integer.valueOf(optionValue);
         } else {
             // default : atlas.enableTLS is true
             appPort = getPortValue(configuration, enableTLSFlag);

webapp/src/main/java/org/apache/atlas/examples/QuickStart.java

@@ -466,7 +466,7 @@ public class QuickStart {
             if (results != null) {
                 System.out.println("query [" + dslQuery + "] returned [" + results.length() + "] rows");
             } else {
-                System.out.println("query [" + dslQuery + "] failed, results:" + results.toString());
+                System.out.println("query [" + dslQuery + "] failed, results:" + results);
             }
         }
     }

webapp/src/main/java/org/apache/atlas/util/CredentialProviderUtility.java

@@ -74,26 +74,28 @@ public class CredentialProviderUtility {
         // prompt for the provider name
         CredentialProvider provider = getCredentialProvider(textDevice);
 
-        char[] cred;
-        for (String key : KEYS) {
-            cred = getPassword(textDevice, key);
-            // create a credential entry and store it
-            boolean overwrite = true;
-            if (provider.getCredentialEntry(key) != null) {
-                String choice = textDevice.readLine("Entry for %s already exists.  Overwrite? (y/n) [y]:", key);
-                overwrite = StringUtils.isEmpty(choice) || choice.equalsIgnoreCase("y");
-                if (overwrite) {
-                    provider.deleteCredentialEntry(key);
-                    provider.flush();
+        if(provider != null) {
+            char[] cred;
+            for (String key : KEYS) {
+                cred = getPassword(textDevice, key);
+                // create a credential entry and store it
+                boolean overwrite = true;
+                if (provider.getCredentialEntry(key) != null) {
+                    String choice = textDevice.readLine("Entry for %s already exists.  Overwrite? (y/n) [y]:", key);
+                    overwrite = StringUtils.isEmpty(choice) || choice.equalsIgnoreCase("y");
+                    if (overwrite) {
+                        provider.deleteCredentialEntry(key);
+                        provider.flush();
+                        provider.createCredentialEntry(key, cred);
+                        provider.flush();
+                        textDevice.printf("Entry for %s was overwritten with the new value.\n", key);
+                    } else {
+                        textDevice.printf("Entry for %s was not overwritten.\n", key);
+                    }
+                } else {
                     provider.createCredentialEntry(key, cred);
                     provider.flush();
-                    textDevice.printf("Entry for %s was overwritten with the new value.\n", key);
-                } else {
-                    textDevice.printf("Entry for %s was not overwritten.\n", key);
                 }
-            } else {
-                provider.createCredentialEntry(key, cred);
-                provider.flush();
             }
         }
     }
@@ -141,16 +143,21 @@ public class CredentialProviderUtility {
      */
     private static CredentialProvider getCredentialProvider(TextDevice textDevice) throws IOException {
         String providerPath = textDevice.readLine("Please enter the full path to the credential provider:");
-        File file = new File(providerPath);
-        if (file.exists()) {
-            textDevice
-                    .printf("%s already exists.  You will need to specify whether existing entries should be "
-                            + "overwritten "
-                            + "(default is 'yes')\n", providerPath);
+
+        if (providerPath != null) {
+            File file = new File(providerPath);
+            if (file.exists()) {
+                textDevice
+                        .printf("%s already exists.  You will need to specify whether existing entries should be "
+                                + "overwritten "
+                                + "(default is 'yes')\n", providerPath);
+            }
+            String providerURI = JavaKeyStoreProvider.SCHEME_NAME + "://file/" + providerPath;
+            Configuration conf = new Configuration(false);
+            conf.set(CredentialProviderFactory.CREDENTIAL_PROVIDER_PATH, providerURI);
+            return CredentialProviderFactory.getProviders(conf).get(0);
         }
-        String providerURI = JavaKeyStoreProvider.SCHEME_NAME + "://file/" + providerPath;
-        Configuration conf = new Configuration(false);
-        conf.set(CredentialProviderFactory.CREDENTIAL_PROVIDER_PATH, providerURI);
-        return CredentialProviderFactory.getProviders(conf).get(0);
+
+        return null;
     }
 }

webapp/src/main/java/org/apache/atlas/web/dao/UserDao.java

@@ -19,6 +19,7 @@ package org.apache.atlas.web.dao;
 
 import com.google.common.annotations.VisibleForTesting;
 import java.io.FileInputStream;
+import java.io.InputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Properties;
@@ -54,6 +55,8 @@ public class UserDao {
 
     void loadFileLoginsDetails() {
         String PROPERTY_FILE_PATH = null;
+        InputStream inStr = null;
+
         try {
 
             Configuration configuration = ApplicationProperties.get();
@@ -61,7 +64,8 @@ public class UserDao {
                     .getString("atlas.authentication.method.file.filename");
             if (PROPERTY_FILE_PATH != null && !"".equals(PROPERTY_FILE_PATH)) {
                 userLogins = new Properties();
-                userLogins.load(new FileInputStream(PROPERTY_FILE_PATH));
+                inStr = new FileInputStream(PROPERTY_FILE_PATH);
+                userLogins.load(inStr);
             }else {
                 LOG.error("Error while reading user.properties file, filepath="
                         + PROPERTY_FILE_PATH);
@@ -70,6 +74,14 @@ public class UserDao {
         } catch (IOException | AtlasException e) {
             LOG.error("Error while reading user.properties file, filepath="
                     + PROPERTY_FILE_PATH, e);
+        } finally {
+            if(inStr != null) {
+                try {
+                    inStr.close();
+                } catch(Exception excp) {
+                    // ignore
+                }
+            }
         }
     }
 

webapp/src/main/java/org/apache/atlas/web/resources/EntityResource.java

@@ -339,7 +339,7 @@ public class EntityResource {
     private Response updateEntityPartialByGuid(String guid, HttpServletRequest request) {
         String entityJson = null;
         try {
-            ParamChecker.notEmpty(guid, "Guid property cannot be null");
+            guid = ParamChecker.notEmpty(guid, "Guid property cannot be null");
             entityJson = Servlets.getRequestPayload(request);
             LOG.info("partially updating entity for guid {} : {} ", guid, entityJson);
 
@@ -468,7 +468,7 @@ public class EntityResource {
             }
 
             LOG.debug("Fetching entity definition for guid={} ", guid);
-            ParamChecker.notEmpty(guid, "guid cannot be null");
+            guid = ParamChecker.notEmpty(guid, "guid cannot be null");
             final String entityDefinition = metadataService.getEntityDefinition(guid);
 
             JSONObject response = new JSONObject();
@@ -564,9 +564,9 @@ public class EntityResource {
     public Response getEntityDefinitionByAttribute(String entityType, String attribute, String value) {
         try {
             LOG.debug("Fetching entity definition for type={}, qualified name={}", entityType, value);
-            ParamChecker.notEmpty(entityType, "Entity type cannot be null");
-            ParamChecker.notEmpty(attribute, "attribute name cannot be null");
-            ParamChecker.notEmpty(value, "attribute value cannot be null");
+            entityType = ParamChecker.notEmpty(entityType, "Entity type cannot be null");
+            attribute  = ParamChecker.notEmpty(attribute, "attribute name cannot be null");
+            value      = ParamChecker.notEmpty(value, "attribute value cannot be null");
 
             final String entityDefinition = metadataService.getEntityDefinition(entityType, attribute, value);
 

webapp/src/main/java/org/apache/atlas/web/resources/MetadataDiscoveryResource.java

@@ -91,7 +91,7 @@ public class MetadataDiscoveryResource {
                            @DefaultValue(LIMIT_OFFSET_DEFAULT) @QueryParam("offset") int offset) {
         AtlasPerfTracer perf = null;
         if (AtlasPerfTracer.isPerfTraceEnabled(PERF_LOG)) {
-            perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.search(" + query + ")");
+            perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.search(" + query + ", " + limit + ", " + offset + ")");
         }
         Response response = searchUsingQueryDSL(query, limit, offset);
         if (response.getStatus() != Response.Status.OK.getStatusCode()) {
@@ -123,10 +123,10 @@ public class MetadataDiscoveryResource {
         AtlasPerfTracer perf = null;
         try {
             if (AtlasPerfTracer.isPerfTraceEnabled(PERF_LOG)) {
-                perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.searchUsingQueryDSL(" + dslQuery + ")");
+                perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.searchUsingQueryDSL(" + dslQuery + ", " + limit + ", " + offset + ")");
             }
 
-            ParamChecker.notEmpty(dslQuery, "dslQuery cannot be null");
+            dslQuery = ParamChecker.notEmpty(dslQuery, "dslQuery cannot be null");
             QueryParams queryParams = validateQueryParams(limit, offset);
             final String jsonResultStr = discoveryService.searchByDSL(dslQuery, queryParams);
 
@@ -184,7 +184,7 @@ public class MetadataDiscoveryResource {
                 perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.searchUsingGremlinQuery(" + gremlinQuery + ")");
             }
 
-            ParamChecker.notEmpty(gremlinQuery, "gremlinQuery cannot be null or empty");
+            gremlinQuery = ParamChecker.notEmpty(gremlinQuery, "gremlinQuery cannot be null or empty");
             final List<Map<String, String>> results = discoveryService.searchByGremlin(gremlinQuery);
 
             JSONObject response = new JSONObject();
@@ -230,10 +230,10 @@ public class MetadataDiscoveryResource {
         AtlasPerfTracer perf = null;
         try {
             if (AtlasPerfTracer.isPerfTraceEnabled(PERF_LOG)) {
-                perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.searchUsingFullText(" + query + ")");
+                perf = AtlasPerfTracer.getPerfTracer(PERF_LOG, "MetadataDiscoveryResource.searchUsingFullText(" + query + ", " + limit + ", " + offset + ")");
             }
 
-            ParamChecker.notEmpty(query, "query cannot be null or empty");
+            query = ParamChecker.notEmpty(query, "query cannot be null or empty");
             QueryParams queryParams = validateQueryParams(limit, offset);
             final String jsonResultStr = discoveryService.searchByFullText(query, queryParams);
             JSONArray rowsJsonArr = new JSONArray(jsonResultStr);

webapp/src/main/java/org/apache/atlas/web/security/AtlasAuthenticationProvider.java

@@ -69,35 +69,32 @@ public class AtlasAuthenticationProvider extends
 
         if (ldapType.equalsIgnoreCase("LDAP")) {
             try {
-                authentication = ldapAuthenticationProvider
-                        .authenticate(authentication);
+                authentication = ldapAuthenticationProvider.authenticate(authentication);
             } catch (Exception ex) {
                 LOG.error("Error while LDAP authentication", ex);
             }
         } else if (ldapType.equalsIgnoreCase("AD")) {
             try {
-                authentication = adAuthenticationProvider
-                        .authenticate(authentication);
+                authentication = adAuthenticationProvider.authenticate(authentication);
             } catch (Exception ex) {
                 LOG.error("Error while AD authentication", ex);
             }
         }
 
-        if (authentication != null && authentication.isAuthenticated()) {
-            return authentication;
-        } else {
-            // If the LDAP/AD authentication fails try the local filebased login method
-            if (fileAuthenticationMethodEnabled) {
-                authentication = fileAuthenticationProvider
-                        .authenticate(authentication);
-            }
-            if (authentication != null && authentication.isAuthenticated()) {
+        if (authentication != null) {
+            if (authentication.isAuthenticated()) {
                 return authentication;
-            } else {
-                LOG.error("Authentication failed.");
-                throw new AtlasAuthenticationException("Authentication failed.");
+            } else if (fileAuthenticationMethodEnabled) {  // If the LDAP/AD authentication fails try the local filebased login method
+                authentication = fileAuthenticationProvider.authenticate(authentication);
+
+                if (authentication != null && authentication.isAuthenticated()) {
+                    return authentication;
+                }
             }
         }
+
+        LOG.error("Authentication failed.");
+        throw new AtlasAuthenticationException("Authentication failed.");
     }
 
 }