1.12 Merge Add tests for H5Ocopy of new object refs (#1339)

* Add tests for H5Ocopy of new object refs

* Correct class name

* Skip test because of issue with debug assertions

* Update reference file

* Fix object examples for new refs and spelling fixs

* Fix ref try-catch blocks

1 files changed, 398 insertions, 0 deletions

diff --git a/java/test/TestH5OcopyOld.java b/java/test/TestH5OcopyOld.java
new file mode 100644
index 0000000..b360cd0
--- /dev/null
+++ b/java/test/TestH5OcopyOld.java
@@ -0,0 +1,398 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import hdf.hdf5lib.H5;
+import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.exceptions.HDF5Exception;
+import hdf.hdf5lib.exceptions.HDF5LibraryException;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TestName;
+
+public class TestH5OcopyOld {
+    @Rule public TestName testname = new TestName();
+    private static final String FILENAME = "testRefsattribute.h5";
+    private static final int DIM_X = 4;
+    private static final int DIM_Y = 6;
+    long H5fid = HDF5Constants.H5I_INVALID_HID;
+    long H5dsid = HDF5Constants.H5I_INVALID_HID;
+    long H5did1 = HDF5Constants.H5I_INVALID_HID;
+    long H5did2 = HDF5Constants.H5I_INVALID_HID;
+    long H5gcpl = HDF5Constants.H5I_INVALID_HID;
+    long H5gid = HDF5Constants.H5I_INVALID_HID;
+    long H5dsid2 = HDF5Constants.H5I_INVALID_HID;
+    long[] dims = { 2 };
+
+    private final void _deleteFile(String filename) {
+        File file = new File(filename);
+
+        if (file.exists()) {
+            try {
+                file.delete();
+            }
+            catch (Exception e) {
+                e.printStackTrace();
+            }
+        }
+    }
+
+    private final long _createDataset(long fid, long dsid, String name, long dapl) {
+        long did = HDF5Constants.H5I_INVALID_HID;
+        try {
+            did = H5.H5Dcreate(fid, name,
+                        HDF5Constants.H5T_STD_I32BE, dsid,
+                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("H5.H5Dcreate: " + err);
+        }
+        assertTrue("TestH5O._createDataset: ",did >= 0);
+
+        return did;
+    }
+
+    private final long _createGroup(long fid, String name) {
+        long gid = HDF5Constants.H5I_INVALID_HID;
+        try {
+            H5gcpl = HDF5Constants.H5P_DEFAULT;
+            gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT,
+                    H5gcpl, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("H5.H5Gcreate: " + err);
+        }
+        assertTrue("TestH5O._createGroup: ",gid >= 0);
+
+        return gid;
+    }
+
+    @Before
+    public void createH5file()
+            throws NullPointerException, HDF5Exception {
+        assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
+        System.out.print(testname.getMethodName());
+        try {
+            H5fid = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC,
+                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            H5dsid2 =  H5.H5Screate(HDF5Constants.H5S_SCALAR);
+            H5did1 = _createDataset(H5fid, H5dsid2, "DS2", HDF5Constants.H5P_DEFAULT);
+            H5dsid = H5.H5Screate_simple(1, dims, null);
+            H5gid = _createGroup(H5fid, "/G1");
+            H5did2 = _createDataset(H5gid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("TestH5O.createH5file: " + err);
+        }
+        assertTrue("TestH5O.createH5file: H5.H5Fcreate: ",H5fid >= 0);
+        assertTrue("TestH5O.createH5file: H5.H5Screate_simple: ",H5dsid >= 0);
+        assertTrue("TestH5O.createH5file: H5.H5Gcreate: ",H5gid >= 0);
+
+        H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+    }
+
+    @After
+    public void deleteH5file() throws HDF5LibraryException {
+        if (H5gid > 0)
+            try {H5.H5Gclose(H5gid);} catch (Exception ex) {}
+        if (H5did2 > 0)
+            try {H5.H5Dclose(H5did2);} catch (Exception ex) {}
+        if (H5dsid > 0)
+            try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
+        if (H5dsid2 > 0)
+            try {H5.H5Sclose(H5dsid2);} catch (Exception ex) {}
+        if (H5did1 > 0)
+            try {H5.H5Dclose(H5did1);} catch (Exception ex) {}
+        if (H5fid > 0)
+            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
+
+        _deleteFile(FILENAME);
+        System.out.println();
+    }
+
+    @Test
+    public void testH5OcopyRefsAttr() {
+        long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
+        byte rbuf0[]=null , rbuf1[] = null;
+        byte[] dset_data = new byte[16];
+        long attribute_id = HDF5Constants.H5I_INVALID_HID;
+
+
+        try {
+            rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
+            rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
+            //System.arraycopy(rbuf0, 0, dset_data, 0, 8);
+            System.arraycopy(rbuf1, 0, dset_data, 8, 8);
+        }
+        catch (Exception ex) {
+            fail("testH5OcopyRefsAttr: H5Rcreate failed");
+        }
+
+        try {
+            attribute_id = H5.H5Acreate(H5did2, "A1", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            assertTrue("testH5OcopyRefsAttr.H5Acreate: ", attribute_id >= 0);
+            H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
+
+            H5.H5Aclose(attribute_id);
+        }
+        catch (Exception ex) {
+            fail("testH5OcopyRefsAttr: H5Awrite failed");
+        }
+        finally {
+            try {H5.H5Aclose(attribute_id);} catch (Exception exx) {}
+        }
+
+        try {
+            ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
+            assertTrue("testH5OcopyRefsAttr.H5Pcreate: ", ocp_plist_id >= 0);
+            H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
+            H5.H5Ocopy(H5fid, ".", H5fid, "CPYREF", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception ex) {
+             fail("testH5OcopyRefsAttr: H5Ocopy failed");
+        }
+        finally {
+            try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
+        }
+    }
+
+    @Test
+    public void testH5OcopyRefsDatasettodiffFile() {
+        byte rbuf1[] = null;
+        byte[] dset_data = new byte[16];
+        long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long H5fid2 = HDF5Constants.H5I_INVALID_HID;
+
+        try {
+            rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
+            System.arraycopy(rbuf1, 0, dset_data, 8, 8);
+
+            dataset_id = H5.H5Dcreate(H5fid, "DSREF",
+                    HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
+                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            assertTrue("testH5OcopyRefsDatasettodiffFile.H5Dcreate: ", dataset_id >= 0);
+            H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ,
+                    HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+                    HDF5Constants.H5P_DEFAULT, dset_data);
+            H5.H5Dclose(dataset_id);
+        }
+        catch (Exception ex) {
+            fail("testH5OcopyRefsDatasettodiffFile: create dataset failed");
+        }
+        finally {
+            try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
+        }
+
+        try {
+            //create new file
+            H5fid2 = H5.H5Fcreate("copy.h5", HDF5Constants.H5F_ACC_TRUNC,
+                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            assertTrue("testH5OcopyRefsDatasettodiffFile.H5Fcreate: ", H5fid2 >= 0);
+            H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL);
+        }
+        catch (Exception ex) {
+            try {H5.H5Fclose(H5fid2);} catch (Exception exx) {}
+            fail("testH5OcopyRefsDatasettodiffFile: H5Fcreate failed");
+        }
+
+        try {
+            //create object copy property list id and set the flags.
+            ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
+            assertTrue("testH5OcopyRefsDatasettodiffFile.H5Pcreate: ", ocp_plist_id >= 0);
+            H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
+
+            //Perform copy function.
+            H5.H5Ocopy(H5fid, ".", H5fid2, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception ex){
+            ex.printStackTrace();
+            fail("testH5OcopyRefsDatasettodiffFile: H5Ocopy failed");
+        }
+        finally {
+            try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
+            try {H5.H5Fclose(H5fid2);} catch (Exception ex) {}
+        }
+        _deleteFile("copy.h5");
+    }
+
+    @Test
+    public void testH5OcopyRefsDatasettosameFile() {
+        byte rbuf0[]=null , rbuf1[] = null;
+        byte[] dset_data = new byte[16];
+        long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long did = HDF5Constants.H5I_INVALID_HID;
+        int obj_type = -1;
+        byte[] read_data = new byte[16];
+
+        try {
+            rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
+            rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
+            System.arraycopy(rbuf0, 0, dset_data, 0, 8);
+            System.arraycopy(rbuf1, 0, dset_data, 8, 8);
+
+            //Create a dataset and write object references to it.
+            dataset_id = H5.H5Dcreate(H5fid, "DSREF",
+                    HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
+                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            assertTrue("testH5OcopyRefsDatasettosameFile.H5Dcreate: ", dataset_id >= 0);
+            H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ,
+                    HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
+                    HDF5Constants.H5P_DEFAULT, dset_data);
+            //Close the dataset.
+            H5.H5Dclose(dataset_id);
+        }
+        catch (Exception ex) {
+            try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
+            fail("testH5OcopyRefsDatasettosameFile: create dataset failed");
+        }
+
+        try {
+            ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
+            assertTrue("testH5OcopyRefsDatasettosameFile.H5Pcreate: ", ocp_plist_id >= 0);
+            H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
+        }
+        catch (Exception ex) {
+            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
+            fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed");
+        }
+
+        //Perform copy function.
+        try {
+            H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
+        }
+        catch(Exception ex) {
+            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
+            fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
+        }
+
+        //Open the dataset that has been copied
+        try {
+            did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT);
+            assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0);
+        }
+        catch (Exception e) {
+            try {H5.H5Dclose(did);} catch (Exception exx) {}
+            e.printStackTrace();
+            fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed");
+        }
+
+        try {
+            //Read the dataset object references in the read_data buffer.
+            H5.H5Dread(did, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data);
+            System.arraycopy(read_data, 0, rbuf0, 0, 8);
+            System.arraycopy(read_data, 8, rbuf1, 0, 8);
+
+            //Get the type of object the reference points to.
+            obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf1);
+            assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
+
+            obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf0);
+            assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP);
+        }
+        catch (Exception ex) {
+            ex.printStackTrace();
+        }
+        finally {
+            try {H5.H5Dclose(did);} catch (Exception ex) {}
+            try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
+        }
+     }
+    
+    @Test
+    public void testH5OcopyNullRef() throws Throwable {
+        final long _pid_ = HDF5Constants.H5P_DEFAULT;
+        long sid = HDF5Constants.H5I_INVALID_HID;
+        long did = HDF5Constants.H5I_INVALID_HID;
+        long aid = HDF5Constants.H5I_INVALID_HID;
+
+        try {
+            sid = H5.H5Screate_simple(1, new long[] {1}, null);
+            assertTrue("testH5OcopyNullRef.H5Screate_simple: ", sid >= 0);
+            did = H5.H5Dcreate(H5fid, "Dataset_with_null_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_, _pid_, _pid_);
+            assertTrue("testH5OcopyNullRef.H5Dcreate: ", did > 0);
+            aid = H5.H5Acreate(did, "Null_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
+            assertTrue("testH5OcopyNullRef.H5Acreate: ", aid > 0);
+        }
+        catch (Exception ex) {
+            ex.printStackTrace();
+        }
+        finally {
+            try {H5.H5Dclose(did);} catch (Exception exx) {}
+            try {H5.H5Aclose(aid);} catch (Exception exx) {}
+            try {H5.H5Sclose(sid);} catch (Exception exx) {}
+        }
+
+        long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
+        assertTrue("testH5OcopyNullRef.H5Pcreate: ", ocp_plist_id >= 0);
+        H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
+        try {
+            H5.H5Ocopy(H5fid, "/Dataset_with_null_Ref", H5fid, "/Dataset_with_null_Ref_cp", ocp_plist_id, _pid_);
+        }
+        finally {
+            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
+        }
+    }
+
+//    @Ignore because of JIRA HDF5-9547
+//    @Test(expected = HDF5LibraryException.class)
+//    public void testH5OcopyInvalidRef() throws Throwable {
+//        final long _pid_ = HDF5Constants.H5P_DEFAULT;
+//        long sid = HDF5Constants.H5I_INVALID_HID;
+//        long did = HDF5Constants.H5I_INVALID_HID;
+//        long aid = HDF5Constants.H5I_INVALID_HID;
+//
+//        try {
+//            sid = H5.H5Screate_simple(1, new long[] {1}, null);
+//            assertTrue("testH5OcopyInvalidRef.H5Screate_simple: ", sid >= 0);
+//            did = H5.H5Dcreate(H5fid, "Dataset_with_invalid_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_, _pid_, _pid_);
+//            assertTrue("testH5OcopyInvalidRef.H5Dcreate: ", did > 0);
+//            aid = H5.H5Acreate(did, "Invalid_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
+//            assertTrue("testH5OcopyInvalidRef.H5Acreate: ", aid > 0);
+//            H5.H5Awrite(aid, HDF5Constants.H5T_STD_REF_OBJ, new long[]{-1});
+//        }
+//        catch (Exception ex) {
+//            ex.printStackTrace();
+//        }
+//        finally {
+//            try {H5.H5Dclose(did);} catch (Exception exx) {}
+//            try {H5.H5Aclose(aid);} catch (Exception exx) {}
+//            try {H5.H5Sclose(sid);} catch (Exception exx) {}
+//        }
+//
+//        long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
+//        assertTrue("testH5OcopyInvalidRef.H5Pcreate: ", ocp_plist_id >= 0);
+//        H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
+//        try {
+//            H5.H5Ocopy(H5fid, "/Dataset_with_invalid_Ref", H5fid, "/Dataset_with_invalid_Ref_cp", ocp_plist_id, _pid_);
+//        }
+//        finally {
+//            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
+//        }
+//    }
+
+}