#151 merge

README.md

@@ -13,6 +13,7 @@ Work for milestone https://github.com/DICE-UNC/jargon/milestones/4.0.3.1%20secon
 ## News
 
 
+
 https://github.com/DICE-UNC/jargon/issues?q=is%3Aopen+is%3Aissue+milestone%3A%22features+branch+4.0.3%22
 
 Please go to [[https://github.com/DICE-UNC/jargon]] for the latest news and info.
@@ -48,7 +49,14 @@ Updated semantics of move collection to avoid 'collection already exists errors'
 
 ###  Rename operation in DTO #147 
 
-Added a rename() operation to DataTransferOperations to clarify difference between a rename and a move
+###  across federation browsing under strict acls doesn't interpolate home/ and find subdirs viewable #39 
+
+More gracefully handle path guessing heuristics cross-federation browsing when drilling down and stict ACLs is on.  
+
+###  CI integration with iRODS 4 #18 
+
+Changes in build automation and testing to integrate Jargon testing into iRODS Consortium Continuous integration
+
 
 ###  CollectionPager not navigating strict acl dirs with heuristics #148 
 

jargon-core/src/main/java/org/irods/jargon/core/pub/DataAOHelper.java

@@ -119,8 +119,6 @@ void buildSelects(final IRODSGenQueryBuilder builder)
 					.addSelectAsGenQueryValue(
 							RodsGenQueryEnum.COL_DATA_TYPE_NAME)
 					.addSelectAsGenQueryValue(RodsGenQueryEnum.COL_DATA_SIZE)
-					.addSelectAsGenQueryValue(
-							RodsGenQueryEnum.COL_D_RESC_GROUP_NAME)
 					.addSelectAsGenQueryValue(RodsGenQueryEnum.COL_D_RESC_NAME)
 					.addSelectAsGenQueryValue(RodsGenQueryEnum.COL_D_DATA_PATH)
 					.addSelectAsGenQueryValue(RodsGenQueryEnum.COL_D_OWNER_NAME)
@@ -167,21 +165,20 @@ public static DataObject buildDomainFromResultSetRow(
 				.getIntOrZeroFromIRODSValue(row.getColumn(5)));
 		dataObject.setDataTypeName(row.getColumn(6));
 		dataObject.setDataSize(Long.parseLong(row.getColumn(7)));
-		dataObject.setResourceGroupName(row.getColumn(8));
-		dataObject.setResourceName(row.getColumn(9));
-		dataObject.setDataPath(row.getColumn(10));
-		dataObject.setDataOwnerName(row.getColumn(11));
-		dataObject.setDataOwnerZone(row.getColumn(12));
-		dataObject.setReplicationStatus(row.getColumn(13));
-		dataObject.setDataStatus(row.getColumn(14));
-		dataObject.setChecksum(row.getColumn(15));
-		dataObject.setExpiry(row.getColumn(16));
-		dataObject.setDataMapId(Integer.parseInt(row.getColumn(17)));
-		dataObject.setComments(row.getColumn(18));
+		dataObject.setResourceName(row.getColumn(8));
+		dataObject.setDataPath(row.getColumn(9));
+		dataObject.setDataOwnerName(row.getColumn(10));
+		dataObject.setDataOwnerZone(row.getColumn(11));
+		dataObject.setReplicationStatus(row.getColumn(12));
+		dataObject.setDataStatus(row.getColumn(13));
+		dataObject.setChecksum(row.getColumn(14));
+		dataObject.setExpiry(row.getColumn(15));
+		dataObject.setDataMapId(Integer.parseInt(row.getColumn(16)));
+		dataObject.setComments(row.getColumn(17));
 		dataObject.setCreatedAt(IRODSDataConversionUtil
-				.getDateFromIRODSValue(row.getColumn(19)));
+				.getDateFromIRODSValue(row.getColumn(18)));
 		dataObject.setUpdatedAt(IRODSDataConversionUtil
-				.getDateFromIRODSValue(row.getColumn(20)));
+				.getDateFromIRODSValue(row.getColumn(19)));
 
 		// add info to track position in records for possible requery
 		dataObject.setLastResult(row.isLastResult());

jargon-core/src/main/java/org/irods/jargon/core/pub/DataObjectAOImpl.java

@@ -627,14 +627,12 @@ private void putCommonProcessing(final File localFile,
 						targetFile, getIRODSProtocol(), transferControlBlock,
 						transferStatusCallbackListener);
 			} catch (FileNotFoundException e) {
-				log.error(
-						"File not found for local file I was trying to put:{}",
-						localFile.getAbsolutePath());
-				throw new DataNotFoundException(
-						"localFile not found to put to irods", e);
+				log.error("iRODS file missing in put operation:{}",
+						targetFile.getAbsolutePath());
+				throw new DataNotFoundException("irodsFile not found", e);
 			} catch (java.io.FileNotFoundException e) {
 				throw new DataNotFoundException(
-						"irods destination not found in put to irods", e);
+						"local file not found in put to irods", e);
 			}
 		} else {
 

jargon-core/src/main/java/org/irods/jargon/core/pub/DataTransferOperationsImpl.java

@@ -1773,7 +1773,7 @@ private void processCopyWhenSourceIsDir(
 				operativeTransferControlBlock);
 
 		/*
-		 * Don't copy to self
+		 * Don't copy to self or parent
 		 */
 		if (targetFile.getAbsolutePath().equals(sourceFile.getParent())) {
 			log.error("source file is being copied to own parent:{}",
@@ -1782,6 +1782,13 @@ private void processCopyWhenSourceIsDir(
 					"attempt to copy source file to its parent");
 		}
 
+		if (targetFile.getAbsolutePath().equals(sourceFile.getAbsolutePath())) {
+			log.error("source file is being copied to self:{}",
+					sourceFile.getAbsolutePath());
+			throw new DuplicateDataException(
+					"attempt to copy source file to itself");
+		}
+
 		// if the target is a file throw an exception
 		if (targetFile.exists() && targetFile.isFile()) {
 			targetFile = (IRODSFile) targetFile.getParentFile();

jargon-core/src/main/java/org/irods/jargon/testutils/TestingPropertiesHelper.java

@@ -799,6 +799,44 @@ public String buildIRODSCollectionAbsolutePathFromFederatedZoneReadTestPropertie
 		return pathBuilder.toString();
 	}
 
+	/**
+	 * Handy method to give, from the root IRODS collection, a full path to a
+	 * given user home collection in the federated zone. So if user1 in zone1
+	 * wants to see his home collection in federated zone zone2, the path
+	 * returned would be /zone2/home/user1#zone1 plus the extra path info
+	 * 
+	 * @param testingProperties
+	 *            <code>Properties</code> that define test behavior
+	 * @param collectionPathBelowScratch
+	 *            <code>String</code> with no leading '/' that defines the
+	 *            desired path underneath the IRODS scratch directory
+	 * @return <code>String</code> with trailing '/' that gives the absolute
+	 *         path for an IRODS collection
+	 * @throws TestingUtilsException
+	 * @throws URISyntaxException
+	 */
+	public String buildIRODSCollectionAbsolutePathFromFederatedZoneHomeDirTestProperties(
+			final Properties testingProperties,
+			final String collectionPathBelowScratch)
+			throws TestingUtilsException {
+
+		if (testingProperties.get(IRODS_SCRATCH_DIR_KEY) == null) {
+			throw new TestingUtilsException(
+					"scratch path not provided in testing.properties");
+		}
+
+		StringBuilder pathBuilder = new StringBuilder();
+		pathBuilder.append('/');
+		pathBuilder.append(testingProperties.get(IRODS_FEDERATED_ZONE_KEY));
+		pathBuilder.append("/home/");
+		pathBuilder.append(testingProperties.get(IRODS_USER_KEY));
+		pathBuilder.append("#");
+		pathBuilder.append(testingProperties.get(IRODS_ZONE_KEY));
+		pathBuilder.append('/');
+		pathBuilder.append(collectionPathBelowScratch);
+		return pathBuilder.toString();
+	}
+
 	/**
 	 * Handy method to give, from the root IRODS collection, a full path to a
 	 * given collection in the IRODS test scratch area on IRODS

jargon-core/src/test/java/org/irods/jargon/core/pub/DataTransferOperationsImplTest.java

@@ -3552,7 +3552,7 @@ public void testCopyCollectionToTarget() throws Exception {
 	}
 
 	/**
-	 * Normal test of consilidated 'copy()' method, this time with a collection,
+	 * Normal test of consolidated 'copy()' method, this time with a collection,
 	 * using the string path sigs
 	 * 
 	 * @throws Exception
@@ -3611,6 +3611,66 @@ public void testCopyCollectionToTargetCollection() throws Exception {
 
 	}
 
+	/**
+	 * Bug https://github.com/DICE-UNC/jargon/issues/151
+	 * 
+	 * @throws Exception
+	 */
+	@Test(expected = DuplicateDataException.class)
+	public void testCopyCollectionToTargetCollectionSelfBug151()
+			throws Exception {
+
+		// generate a local scratch file
+		String testOrigDirectory = "testCopyCollectionToTargetCollectionSelfBug151";
+		String testTargetDirectory = "testCopyCollectionToTargetCollectionSelfBug151";
+
+		String localCollectionAbsolutePath = scratchFileUtils
+				.createAndReturnAbsoluteScratchPath(IRODS_TEST_SUBDIR_PATH
+						+ '/' + testOrigDirectory);
+
+		String irodsCollectionRootAbsolutePath = testingPropertiesHelper
+				.buildIRODSCollectionAbsolutePathFromTestProperties(
+						testingProperties, IRODS_TEST_SUBDIR_PATH);
+
+		String irodsOriginalAbsolutePath = testingPropertiesHelper
+				.buildIRODSCollectionAbsolutePathFromTestProperties(
+						testingProperties, IRODS_TEST_SUBDIR_PATH + "/"
+								+ testOrigDirectory);
+
+		String irodsTargetAbsolutePath = testingPropertiesHelper
+				.buildIRODSCollectionAbsolutePathFromTestProperties(
+						testingProperties, IRODS_TEST_SUBDIR_PATH + "/"
+								+ testTargetDirectory);
+
+		FileGenerator
+				.generateManyFilesAndCollectionsInParentCollectionByAbsolutePath(
+						localCollectionAbsolutePath, "prefixForColl", 2, 3, 2,
+						"testFile", ".txt", 2, 2, 1, 2);
+
+		IRODSAccount irodsAccount = testingPropertiesHelper
+				.buildIRODSAccountFromTestProperties(testingProperties);
+
+		DataTransferOperations dataTransferOperations = irodsFileSystem
+				.getIRODSAccessObjectFactory().getDataTransferOperations(
+						irodsAccount);
+
+		dataTransferOperations.putOperation(localCollectionAbsolutePath,
+				irodsCollectionRootAbsolutePath, "", null, null);
+
+		dataTransferOperations.copy(irodsOriginalAbsolutePath, "",
+				irodsTargetAbsolutePath, null, null);
+
+		File localFile = new File(localCollectionAbsolutePath);
+		IRODSFile targetFile = irodsFileSystem
+				.getIRODSFileFactory(irodsAccount).instanceIRODSFile(
+						irodsTargetAbsolutePath, testOrigDirectory);
+
+		// compare the local source to the copied-to target
+		assertionHelper.assertTwoFilesAreEqualByRecursiveTreeComparison(
+				localFile, (File) targetFile);
+
+	}
+
 	@Test
 	public void testCopyCollectionToTargetCollectionWithResource()
 			throws Exception {

jargon-core/src/test/java/org/irods/jargon/core/pub/FederatedCollectionAndDataObjectListAndSearchAOImplTest.java

@@ -10,6 +10,7 @@
 import org.irods.jargon.core.exception.FileNotFoundException;
 import org.irods.jargon.core.protovalues.FilePermissionEnum;
 import org.irods.jargon.core.pub.domain.Collection;
+import org.irods.jargon.core.pub.domain.ObjStat;
 import org.irods.jargon.core.pub.domain.UserFilePermission;
 import org.irods.jargon.core.pub.io.IRODSFile;
 import org.irods.jargon.core.pub.io.IRODSFileFactory;
@@ -127,6 +128,62 @@ public void testListCollectionWithOneDataObject() throws Exception {
 
 	}
 
+	@Test
+	public void testRetrieveObjStatInFederatedZone() throws Exception {
+
+		if (!testingPropertiesHelper.isTestFederatedZone(testingProperties)) {
+			return;
+		}
+
+		String fileName = "testRetrieveObjStatInFederatedZone.txt";
+		String testSubdir = "testRetrieveObjStatInFederatedZone";
+
+		IRODSAccount irodsAccount = testingPropertiesHelper
+				.buildIRODSAccountForFederatedZoneFromTestProperties(testingProperties);
+
+		String targetIrodsPath = testingPropertiesHelper
+				.buildIRODSCollectionAbsolutePathFromFederatedZoneReadTestProperties(
+						testingProperties, IRODS_TEST_SUBDIR_PATH + "/"
+								+ testSubdir);
+
+		String absPath = scratchFileUtils
+				.createAndReturnAbsoluteScratchPath(IRODS_TEST_SUBDIR_PATH);
+		String localFilePath = FileGenerator
+				.generateFileOfFixedLengthGivenName(absPath, fileName, 3);
+		File localFile = new File(localFilePath);
+
+		IRODSFileFactory irodsFileFactory = irodsFileSystem
+				.getIRODSFileFactory(irodsAccount);
+		IRODSFile destFile = irodsFileFactory
+				.instanceIRODSFile(targetIrodsPath);
+
+		// delete to clean up
+		destFile.deleteWithForceOption();
+		destFile.mkdirs();
+
+		DataTransferOperations dataTransferOperationsAO = irodsFileSystem
+				.getIRODSAccessObjectFactory().getDataTransferOperations(
+						irodsAccount);
+
+		dataTransferOperationsAO.putOperation(localFile, destFile, null, null);
+
+		/*
+		 * setup done, now connect from the first zone and try to list the coll
+		 * with the data object
+		 */
+
+		IRODSAccount fedAccount = testingPropertiesHelper
+				.buildIRODSAccountFromTestProperties(testingProperties);
+
+		CollectionAndDataObjectListAndSearchAO collectionListAndSearchAO = irodsFileSystem
+				.getIRODSAccessObjectFactory()
+				.getCollectionAndDataObjectListAndSearchAO(fedAccount);
+		ObjStat objStat = collectionListAndSearchAO
+				.retrieveObjectStatForPath(targetIrodsPath + "/" + fileName);
+		Assert.assertNotNull("null objstat", objStat);
+
+	}
+
 	@Test
 	public void testListDataObjectsUnderPathInAnotherZone() throws Exception {