path: root/java/test/TestH5Ocopy.java

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * 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 files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdfgroup.org/HDF5/doc/Copyright.html.  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 TestH5Ocopy {
    @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 = -1;
    long H5dsid = -1;
    long H5did1 = -1;
    long H5did2 = -1;
    long H5gcpl = -1;
    long H5gid = -1;
    long H5dsid2 = -1;
    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 = -1;
        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 = -1;
        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 = -1;
        byte rbuf0[]=null , rbuf1[] = null;
        byte[] dset_data = new byte[16];
        long attribute_id = -1;


        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 = -1;
        long dataset_id = -1;
        long H5fid2 = -1;

        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) {}
        }
    }

    @Test
    public void testH5OcopyRefsDatasettosameFile() {
        byte rbuf0[]=null , rbuf1[] = null;
        byte[] dset_data = new byte[16];
        long ocp_plist_id = -1;
        long dataset_id = -1;
        long did = -1;
        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) {}
        }
     }

//    @Ignore because of JIRA HDF5-9547
//    @Test(expected = HDF5LibraryException.class)
//    public void testH5OcopyInvalidRef() throws Throwable {
//        final long _pid_ = HDF5Constants.H5P_DEFAULT;
//        long sid = -1;
//        long did = -1;
//        long aid = -1;
//
//        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) {}
//        }
//    }

}