Javadocs, refactors, anonUserName NullPointer fix

Author: patrick-austin

src/main/java/org/icatproject/topcat/IcatClient.java

@@ -27,6 +27,24 @@ public class DatafilesResponse {
 		public final List<Long> ids = new ArrayList<>();
 		public final Set<String> missing = new HashSet<>();
 		public long totalSize = 0L;
+
+		/**
+		 * Submit a query for Datafiles, then appends the ids, increments the size, and
+		 * records any missing file locations.
+		 * 
+		 * @param query Query to submit
+		 * @throws TopcatException If the query returns not authorized, or not found.
+		 */
+		public void submitDatafilesQuery(String query)
+				throws TopcatException {
+			JsonArray jsonArray = submitQuery(query);
+			for (JsonObject jsonObject : jsonArray.getValuesAs(JsonObject.class)) {
+				JsonObject datafile = jsonObject.getJsonObject("Datafile");
+				ids.add(datafile.getJsonNumber("id").longValueExact());
+				missing.remove(datafile.getString("location"));
+				totalSize += datafile.getJsonNumber("fileSize").longValueExact();
+			}
+		}
 	}
 
 	private Logger logger = LoggerFactory.getLogger(IcatClient.class);
@@ -185,13 +203,7 @@ public DatafilesResponse getDatafiles(List<String> files) throws TopcatException
 			String quotedFile = "'" + file + "'";
 			int encodedFileLength = URLEncoder.encode(quotedFile, "UTF8").length();
 			if (chunkSize + 3 + encodedFileLength > chunkLimit) {
-				JsonArray jsonArray = submitQuery(queryPrefix + chunkedFiles + querySuffix);
-				for (JsonObject jsonObject : jsonArray.getValuesAs(JsonObject.class)) {
-					JsonObject datafile = jsonObject.getJsonObject("Datafile");
-					response.ids.add(datafile.getJsonNumber("id").longValueExact());
-					response.missing.remove(datafile.getString("location"));
-					response.totalSize += datafile.getJsonNumber("fileSize").longValueExact();
-				}
+				response.submitDatafilesQuery(queryPrefix + chunkedFiles + querySuffix);
 
 				chunkedFiles = quotedFile;
 				chunkSize = encodedFileLength;
@@ -202,13 +214,7 @@ public DatafilesResponse getDatafiles(List<String> files) throws TopcatException
 				response.missing.add(file);
 			}
 		}
-		JsonArray jsonArray = submitQuery(queryPrefix + chunkedFiles + querySuffix);
-		for (JsonObject jsonObject : jsonArray.getValuesAs(JsonObject.class)) {
-			JsonObject datafile = jsonObject.getJsonObject("Datafile");
-			response.ids.add(datafile.getJsonNumber("id").longValueExact());
-			response.missing.remove(datafile.getString("location"));
-			response.totalSize += datafile.getJsonNumber("fileSize").longValueExact();
-		}
+		response.submitDatafilesQuery(queryPrefix + chunkedFiles + querySuffix);
 
 		return response;
 	}
@@ -238,13 +244,9 @@ public long getDatasetFileCount(long datasetId) throws TopcatException {
 	 * @throws TopcatException
 	 */
 	public long getDatasetFileSize(long datasetId) throws TopcatException {
-			String query = "SELECT datafile.fileSize FROM Datafile datafile WHERE datafile.dataset.id = " + datasetId;
+			String query = "SELECT SUM(datafile.fileSize) FROM Datafile datafile WHERE datafile.dataset.id = " + datasetId;
 		JsonArray jsonArray = submitQuery(query);
-		long size = 0L;
-		for (JsonNumber number : jsonArray.getValuesAs(JsonNumber.class)) {
-			size += number.longValueExact();
-		}
-		return size;
+		return jsonArray.getJsonNumber(0).longValueExact();
 	}
 
 	/**
@@ -276,6 +278,11 @@ private JsonArray submitQuery(String query) throws TopcatException {
 	/**
 	 * Gets a single Entity of the specified type, without any other conditions.
 	 * 
+	 * NOTE: This function is written and intended for getting Investigation,
+	 * Dataset or Datafile entities as part of the tests. It does not handle casing of
+	 * entities containing multiple words, or querying for a specific instance of an
+	 * entity.
+	 * 
 	 * @param entityType Type of ICAT Entity to get
 	 * @return A single ICAT Entity of the specified type as a JsonObject
 	 * @throws TopcatException
@@ -429,7 +436,8 @@ public int getQueuePriority(String userName) throws TopcatException {
 			}
 		}
 
-		if (!userName.startsWith(Properties.getInstance().getProperty("anonUserName"))) {
+		String anonUserName = Properties.getInstance().getProperty("anonUserName");
+		if (anonUserName == null || !userName.startsWith(anonUserName)) {
 			// The anonymous cart username will end with the user's sessionId so cannot do .equals
 			return priorityMap.getAuthenticatedPriority();
 		} else {

src/main/java/org/icatproject/topcat/PriorityMap.java

@@ -35,6 +35,10 @@ public PriorityMap() {
         Properties properties = Properties.getInstance();
 
         anonUserName = properties.getProperty("anonUserName", "");
+        if (anonUserName.equals("")) {
+            logger.warn("anonUserName not defined, cannot distinguish anonymous and authenticated users so "
+                    + "authenticated priority will be used as default level");
+        }
         anonDownloadEnabled = Boolean.parseBoolean(properties.getProperty("anonDownloadEnabled", "true"));
         String defaultString;
         if (anonDownloadEnabled) {

src/main/java/org/icatproject/topcat/web/rest/UserResource.java

@@ -983,7 +983,8 @@ public Response queueAllowed(@QueryParam("sessionId") String sessionId,
 	 *                     Download. Defaults to facilityName_visitId.
 	 * @param email        Optional email to notify upon completion
 	 * @param files        ICAT Datafile.locations to download
-	 * @return Array of Download ids
+	 * @return The resultant downloadId and an array of any locations which could not
+	 * 		   be found
 	 * @throws TopcatException
 	 * @throws UnsupportedEncodingException 
 	 */

src/test/java/org/icatproject/topcat/IcatClientTest.java

@@ -12,6 +12,8 @@
 import org.icatproject.topcat.httpclient.HttpClient;
 import org.icatproject.topcat.httpclient.Response;
 import org.icatproject.topcat.domain.*;
+import org.icatproject.topcat.exceptions.TopcatException;
+
 import java.net.URLEncoder;
 
 import org.icatproject.topcat.repository.CacheRepository;
@@ -238,6 +240,20 @@ public void testCheckUserFound() throws Exception {
 		}
 	}
 
+	@Test
+	public void testGetDatasetFileCount() throws TopcatException {
+		IcatClient icatClient = new IcatClient("https://localhost:8181", sessionId);
+		long datasetId = icatClient.getEntity("Dataset").getJsonNumber("id").longValueExact();
+		assertNotEquals(0, icatClient.getDatasetFileCount(datasetId));
+	}
+
+	@Test
+	public void testGetDatasetFileSize() throws TopcatException {
+		IcatClient icatClient = new IcatClient("https://localhost:8181", sessionId);
+		long datasetId = icatClient.getEntity("Dataset").getJsonNumber("id").longValueExact();
+		assertNotEquals(0, icatClient.getDatasetFileSize(datasetId));
+	}
+
 	/*
 	 * @Test public void testGetSize() throws Exception { IcatClient icatClient =
 	 * new IcatClient("https://localhost:8181", sessionId);