Remove boolean extract parameters from DataCollection endpoint

Author: patrick-austin

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

@@ -148,13 +148,9 @@ private static DownloadItem createDownloadItem(Download download, long entityId,
 	 * Investigations will be split into constituent Datasets.
 	 * 
 	 * @param dataCollectionId      ICAT DataCollection.id
-	 * @param extractInvestigations Whether to use the DataCollectionInvestigations
-	 * @param extractDatasets       Whether to use the DataCollectionDatasets
-	 * @param extractDatafiles      Whether to use the DataCollectionDatafiles
 	 * @throws TopcatException if querying ICAT fails
 	 */
-    public void extractDataCollection(Long dataCollectionId, Boolean extractInvestigations, Boolean extractDatasets,
-            Boolean extractDatafiles) throws TopcatException {
+    public void extractDataCollection(Long dataCollectionId) throws TopcatException {
 
 		logger.info("extractDataCollection called for {}", dataCollectionId);
 		if (dataCollectionId == null || dataCollectionId < 1) {
@@ -167,19 +163,10 @@ public void extractDataCollection(Long dataCollectionId, Boolean extractInvestig
 
 		JsonArrayBuilder datasetsBuilder = Json.createArrayBuilder();
 		JsonArray datafiles = JsonArray.EMPTY_JSON_ARRAY;
-		if (extractInvestigations) {
-			for (JsonValue dataset : icatClient.getDataCollectionInvestigationDatasets(dataCollectionId)) {
-				datasetsBuilder.add(dataset);
-			}
-		}
-		if (extractDatasets) {
-			for (JsonValue dataset : icatClient.getDataCollectionDatasets(dataCollectionId)) {
-				datasetsBuilder.add(dataset);
-			}
-		}
-		if (extractDatafiles) {
-			datafiles = icatClient.getDataCollectionDatafiles(dataCollectionId);
+		for (JsonValue dataset : icatClient.getDataCollectionDatasets(dataCollectionId)) {
+			datasetsBuilder.add(dataset);
 		}
+		datafiles = icatClient.getDataCollectionDatafiles(dataCollectionId);
 		JsonArray datasets = datasetsBuilder.build();
 
 		if (datasets.size() == 0 && datafiles.size() == 0) {

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

@@ -234,24 +234,6 @@ public DatafilesResponse getDatafiles(List<String> files) throws TopcatException
 		return response;
 	}
 
-	/**
-	 * Get all Datasets whose parent Investigation is in the specified DataCollection.
-	 * 
-	 * @param dataCollectionId ICAT DataCollection.id
-	 * @return JsonArray of Dataset fields, where each entry is a JsonArray of
-	 *         [dataset.id, dataset.fileCount, dataset.fileSize].
-	 * @throws TopcatException
-	 */
-	public JsonArray getDataCollectionInvestigationDatasets(long dataCollectionId) throws TopcatException {
-		System.out.println(dataCollectionId);
-		String query = "SELECT DISTINCT dataset.id, dataset.fileCount, dataset.fileSize";
-		query += " FROM DataCollectionInvestigation dataCollectionInvestigation";
-		query += " JOIN Investigation investigation JOIN Dataset dataset";
-		query += " WHERE dataCollectionInvestigation.dataCollection.id = " + dataCollectionId;
-		query += " ORDER BY dataset.id";
-		return submitQuery(query);
-	}
-
 	/**
 	 * Get all Datasets in the specified DataCollection.
 	 * 

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

@@ -908,16 +908,16 @@ public Response queueVisitId(@FormParam("facilityName") String facilityName,
 	}
 
 	/**
-	 * Queue an entire visit for download, split by Dataset into part Downloads if
-	 * needed.
+	 * Queues all Datasets and Datafiles in a DataCollection for download, split into
+	 * part Downloads if needed. Investigations are not extracted.
 	 * 
-	 * @param facilityName ICAT Facility.name
-	 * @param sessionId    ICAT sessionId
-	 * @param transport    Transport mechanism to use
-	 * @param fileName     Optional name to use as the root for each individual part
-	 *                     Download. Defaults to facilityName_visitId.
-	 * @param email        Optional email to notify upon completion
-	 * @param visitId      ICAT Investigation.visitId to submit
+	 * @param facilityName     ICAT Facility.name
+	 * @param sessionId        ICAT sessionId
+	 * @param transport        Transport mechanism to use
+	 * @param fileName         Optional name to use as the root for each individual part
+	 *                         Download. Defaults to facilityName_visitId.
+	 * @param email            Optional email to notify upon completion
+	 * @param dataCollectionId ICAT DataCollection.id to submit
 	 * @return Array of Download ids
 	 * @throws TopcatException
 	 */
@@ -926,13 +926,10 @@ public Response queueVisitId(@FormParam("facilityName") String facilityName,
 	public Response queueDataCollection(@FormParam("facilityName") String facilityName,
 			@FormParam("sessionId") String sessionId, @FormParam("transport") String transport,
 			@FormParam("fileName") String fileName, @FormParam("email") String email,
-			@FormParam("dataCollectionId") Long dataCollectionId,
-			@FormParam("extractInvestigations") Boolean extractInvestigations,
-			@FormParam("extractDatasets") Boolean extractDatasets,
-			@FormParam("extractDatafiles") Boolean extractDatafiles) throws TopcatException {
+			@FormParam("dataCollectionId") Long dataCollectionId) throws TopcatException {
 
 		DownloadBuilder downloadBuilder = new DownloadBuilder(sessionId, email, fileName, transport, facilityName);
-		downloadBuilder.extractDataCollection(dataCollectionId, extractInvestigations, extractDatasets, extractDatafiles);
+		downloadBuilder.extractDataCollection(dataCollectionId);
 
 		String transportUrl = getDownloadUrl(downloadBuilder.facilityName, downloadBuilder.transport);
 		IdsClient idsClient = new IdsClient(transportUrl);

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

@@ -440,62 +440,51 @@ public void testQueueFilesNotFound() throws Exception {
 	public void testQueueDataCollection() throws Exception {
 		System.out.println("DEBUG testQueueDataCollection");
 		List<Long> downloadIds = new ArrayList<>();
-		long finalId = 0L;
+		Long downloadIdDataset = null;
+		Long downloadIdDatafile = null;
 		try {
 			String transport = "http";
 			String email = "";
 			IcatClient icatClient = new IcatClient("https://localhost:8181", sessionId);
 			JsonObject dataCollection = icatClient.getEntity("DataCollection");
 			long entityId = dataCollection.getInt("id");
-			Response response = userResource.queueDataCollection(null, sessionId, transport, null, email, entityId, true, true, true);
+			Response response = userResource.queueDataCollection(null, sessionId, transport, null, email, entityId);
 			assertEquals(200, response.getStatus());
 
 			JsonArray downloadIdsArray = Utils.parseJsonArray(response.getEntity().toString());
-			assertEquals(302, downloadIdsArray.size());
-			long part = 1;
-			for (JsonNumber downloadIdJson : downloadIdsArray.getValuesAs(JsonNumber.class)) {
-				long downloadId = downloadIdJson.longValueExact();
-				downloadIds.add(downloadId);
-			}
-			finalId = downloadIds.remove(downloadIds.size() - 1);
-			for (long downloadId : downloadIds) {
-				Download download = downloadRepository.getDownload(downloadId);
-				assertNull(download.getPreparedId());
-				assertEquals(DownloadStatus.QUEUED, download.getStatus());
-				assertEquals(0, download.getInvestigationIds().size());
-				assertEquals(1, download.getDatasetIds().size());
-				assertEquals(0, download.getDatafileIds().size());
-				if (part < 10) {
-					assertEquals("LILS_DataCollection" + entityId + "_part_00" + part + "_of_302", download.getFileName());
-				} else if (part < 100) {
-					assertEquals("LILS_DataCollection" + entityId + "_part_0" + part + "_of_302", download.getFileName());
-				} else {
-					assertEquals("LILS_DataCollection" + entityId + "_part_" + part + "_of_302", download.getFileName());
-				}
-				assertEquals(transport, download.getTransport());
-				assertEquals("simple/root", download.getUserName());
-				assertEquals("simple/root", download.getFullName());
-				assertEquals("", download.getEmail());
-				assertNotEquals(0L, download.getSize());
-				part += 1;
-			}
-			Download download = downloadRepository.getDownload(finalId);
+			assertEquals(2, downloadIdsArray.size());
+			List<JsonNumber> downloadIdJsonNumbers = downloadIdsArray.getValuesAs(JsonNumber.class);
+			downloadIdDataset = downloadIdJsonNumbers.get(0).longValueExact();
+			downloadIdDatafile = downloadIdJsonNumbers.get(1).longValueExact();
+
+			Download download = downloadRepository.getDownload(downloadIdDataset);
+			assertNull(download.getPreparedId());
+			assertEquals(DownloadStatus.QUEUED, download.getStatus());
+			assertEquals(0, download.getInvestigationIds().size());
+			assertEquals(1, download.getDatasetIds().size());
+			assertEquals(0, download.getDatafileIds().size());
+			assertEquals("LILS_DataCollection" + entityId + "_part_1_of_2", download.getFileName());
+			assertEquals(transport, download.getTransport());
+			assertEquals("simple/root", download.getUserName());
+			assertEquals("simple/root", download.getFullName());
+			assertEquals("", download.getEmail());
+			assertNotEquals(0L, download.getSize());
+
+			download = downloadRepository.getDownload(downloadIdDatafile);
 			assertNull(download.getPreparedId());
 			assertEquals(DownloadStatus.QUEUED, download.getStatus());
 			assertEquals(0, download.getInvestigationIds().size());
 			assertEquals(0, download.getDatasetIds().size());
 			assertEquals(1, download.getDatafileIds().size());
-			assertEquals("LILS_DataCollection" + entityId + "_part_" + part + "_of_302", download.getFileName());
+			assertEquals("LILS_DataCollection" + entityId + "_part_2_of_2", download.getFileName());
 			assertEquals(transport, download.getTransport());
 			assertEquals("simple/root", download.getUserName());
 			assertEquals("simple/root", download.getFullName());
 			assertEquals("", download.getEmail());
 			assertNotEquals(0L, download.getSize());
 		} finally {
-			for (long downloadId : downloadIds) {
-				downloadRepository.removeDownload(downloadId);
-			}
-			downloadRepository.removeDownload(finalId);
+			downloadRepository.removeDownload(downloadIdDataset);
+			downloadRepository.removeDownload(downloadIdDatafile);
 		}
 	}